Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~marine/2CV0.out Дата изменения: Sat Sep 26 19:33:28 2009 Дата индексирования: Mon Oct 1 21:52:57 2012 Кодировка:

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This structure has broken O3'[i] to P[i+1] linkages
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3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
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1. The list of the parameters given below correspond to the 5' to 3' direction
of strand I and 3' to 5' direction of strand II.

2. All angular parameters, except for the phase angle of sugar pseudo-
rotation, are measured in degrees in the range of [-180, +180], and all
displacements are measured in Angstrom units.
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File name: 2CV0.pdb
Date and time: Sat Sep 26 19:33:27 2009

Number of base-pairs: 56
Number of atoms: 11125
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HEADER LIGASE/RNA 31-MAY-05 2CV0
TITLE GLUTAMYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS IN
TITLE 2 COMPLEX WITH TRNA(GLU) AND L-GLUTAMATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRNA;
COMPND 3 CHAIN: C, D;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: GLUTAMYL-TRNA SYNTHETASE;
COMPND 7 CHAIN: A, B;
COMPND 8 SYNONYM: GLUTAMATE--TRNA LIGASE, GLURS;
COMPND 9 EC: 6.1.1.17;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIPTION;
SOURCE 4 MOL_ID: 2;
SOURCE 5 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS;
SOURCE 6 ORGANISM_TAXID: 274;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PK7
KEYWDS LIGASE, RNA, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT
KEYWDS 2 ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN
KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, LIGASE/RNA
KEYWDS 4 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.SEKINE,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS
AUTHOR 2 INITIATIVE (RSGI)
REVDAT 3 24-FEB-09 2CV0 1 VERSN
REVDAT 2 28-AUG-07 2CV0 1 JRNL REMARK
REVDAT 1 05-SEP-06 2CV0 0
JRNL AUTH S.SEKINE,M.SHICHIRI,S.BERNIER,R.CHENEVERT,
JRNL AUTH 2 J.LAPOINTE,S.YOKOYAMA
JRNL TITL STRUCTURAL BASES OF TRANSFER RNA-DEPENDENT AMINO
JRNL TITL 2 ACID RECOGNITION AND ACTIVATION BY GLUTAMYL-TRNA
JRNL TITL 3 SYNTHETASE
JRNL REF STRUCTURE V. 14 1791 2006
JRNL REFN ISSN 0969-2126
JRNL PMID 17161369
JRNL DOI 10.1016/J.STR.2006.10.005
HELIX 1 1 HIS A 15 ASN A 32 1 18
HELIX 2 2 GLY A 51 GLY A 64 1 14
HELIX 3 3 ARG A 81 GLU A 84 5 4
HELIX 4 4 ARG A 85 ARG A 99 1 15
HELIX 5 5 THR A 108 GLY A 120 1 13
HELIX 6 6 GLY A 124 ILE A 129 5 6
HELIX 7 7 PRO A 130 ARG A 140 1 11
HELIX 8 8 GLN A 171 ILE A 173 5 3
HELIX 9 9 THR A 186 MET A 198 1 13
HELIX 10 10 GLU A 208 VAL A 211 5 4
HELIX 11 11 SER A 212 GLY A 224 1 13
HELIX 12 12 SER A 252 GLU A 259 1 8
HELIX 13 13 LEU A 262 LEU A 272 1 11
HELIX 14 14 THR A 285 PHE A 293 1 9
HELIX 15 15 THR A 294 VAL A 298 5 5
HELIX 16 16 ASP A 306 VAL A 321 1 16
HELIX 17 17 SER A 323 ALA A 338 1 16
HELIX 18 18 SER A 344 ARG A 356 1 13
HELIX 19 19 PRO A 357 PHE A 359 5 3
HELIX 20 20 LYS A 363 ALA A 369 1 7
HELIX 21 21 ARG A 370 PHE A 373 5 4
HELIX 22 22 SER A 380 GLN A 404 1 25
HELIX 23 23 THR A 408 LYS A 423 1 16
HELIX 24 24 LYS A 426 GLY A 440 1 15
HELIX 25 25 GLY A 446 ALA A 468 1 23
HELIX 26 26 HIS B 15 ASN B 32 1 18
HELIX 27 27 GLY B 51 GLY B 64 1 14
HELIX 28 28 ARG B 81 GLU B 84 5 4
HELIX 29 29 ARG B 85 ARG B 99 1 15
HELIX 30 30 THR B 108 GLY B 120 1 13
HELIX 31 31 GLY B 124 ILE B 129 5 6
HELIX 32 32 PRO B 130 ARG B 140 1 11
HELIX 33 33 GLN B 171 ILE B 173 5 3
HELIX 34 34 THR B 186 MET B 198 1 13
HELIX 35 35 GLU B 208 VAL B 211 5 4
HELIX 36 36 SER B 212 GLY B 224 1 13
HELIX 37 37 SER B 252 GLU B 259 1 8
HELIX 38 38 LEU B 262 MET B 273 1 12
HELIX 39 39 THR B 285 PHE B 293 1 9
HELIX 40 40 THR B 294 VAL B 298 5 5
HELIX 41 41 ASP B 306 VAL B 321 1 16
HELIX 42 42 SER B 323 ALA B 338 1 16
HELIX 43 43 SER B 344 ARG B 356 1 13
HELIX 44 44 PRO B 357 PHE B 359 5 3
HELIX 45 45 LYS B 363 ALA B 369 1 7
HELIX 46 46 ARG B 370 PHE B 373 5 4
HELIX 47 47 SER B 380 ALA B 403 1 24
HELIX 48 48 THR B 408 LYS B 423 1 16
HELIX 49 49 LYS B 426 GLY B 440 1 15
HELIX 50 50 GLY B 446 LEU B 454 1 9
HELIX 51 51 GLY B 455 ALA B 468 1 14
SHEET 1 A 2 VAL A 3 ILE A 6 0
SHEET 2 A 2 ARG A 35 VAL A 38 1 O ARG A 35 N THR A 4
SHEET 1 B 3 ALA A 102 ALA A 105 0
SHEET 2 B 3 VAL A 145 LEU A 148 -1 O ARG A 147 N TYR A 103
SHEET 3 B 3 VAL A 177 LEU A 179 -1 O LEU A 178 N ILE A 146
SHEET 1 C 2 THR A 155 ASP A 160 0
SHEET 2 C 2 GLY A 164 ASP A 169 -1 O VAL A 166 N VAL A 158
SHEET 1 D 2 ASP A 202 ALA A 206 0
SHEET 2 D 2 ARG A 229 MET A 233 1 O MET A 233 N ARG A 205
SHEET 1 E 2 VAL B 3 ILE B 6 0
SHEET 2 E 2 ARG B 35 VAL B 38 1 O ARG B 35 N THR B 4
SHEET 1 F 3 ALA B 102 ALA B 105 0
SHEET 2 F 3 VAL B 145 LEU B 148 -1 O ARG B 147 N TYR B 103
SHEET 3 F 3 VAL B 177 LEU B 179 -1 O LEU B 178 N ILE B 146
SHEET 1 G 2 THR B 155 ASP B 160 0
SHEET 2 G 2 GLY B 164 ASP B 169 -1 O VAL B 166 N VAL B 158
SHEET 1 H 2 ASP B 202 ALA B 206 0
SHEET 2 H 2 ARG B 229 MET B 233 1 O MET B 233 N ARG B 205
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

Strand I Strand II Helix
1 (0.011) C:.501_:[..G]G-----C[..C]:.572_:C (0.008) |
2 (0.008) C:.502_:[..G]G-*---U[..U]:.571_:C (0.007) |
3 (0.005) C:.503_:[..C]C-----G[..G]:.570_:C (0.004) |
4 (0.005) C:.504_:[..C]C-----G[..G]:.569_:C (0.008) |
5 (0.007) C:.505_:[..C]C-----G[..G]:.568_:C (0.009) |
6 (0.006) C:.506_:[..C]C-----G[..G]:.567_:C (0.004) |
7 (0.004) C:.507_:[..A]Ax----U[..U]:.566_:C (0.004) |
8 (0.008) C:.549_:[..G]G-----C[..C]:.565_:C (0.003) |
9 (0.006) C:.550_:[..G]G-----C[..C]:.564_:C (0.005) |
10 (0.005) C:.551_:[..G]G-----C[..C]:.563_:C (0.002) |
11 (0.003) C:.552_:[..G]G-----C[..C]:.562_:C (0.004) |
12 (0.008) C:.553_:[..G]G----xC[..C]:.561_:C (0.004) |
13 (0.007) C:.554_:[..U]U-**-xA[..A]:.558_:C (0.003) |
14 (0.009) C:.555_:[..U]Ux**+xG[..G]:.518_:C (0.014) x
15 (0.006) C:.538_:[..A]A-*---C[..C]:.532_:C (0.006) |
16 (0.007) C:.539_:[..G]G-----C[..C]:.531_:C (0.003) |
17 (0.009) C:.540_:[..G]G-----C[..C]:.530_:C (0.007) |
18 (0.003) C:.541_:[..C]C-----G[..G]:.529_:C (0.006) |
19 (0.008) C:.542_:[..C]C-----G[..G]:.528_:C (0.007) |
20 (0.007) C:.543_:[..G]G-----C[..C]:.527_:C (0.009) |
21 (0.011) C:.544_:[..A]Ax*---G[..G]:.526_:C (0.009) |
22 (0.012) C:.510_:[..G]G-----C[..C]:.525_:C (0.005) |
23 (0.005) C:.511_:[..U]U-----A[..A]:.524_:C (0.006) |
24 (0.005) C:.512_:[..C]C-----G[..G]:.523_:C (0.010) |
25 (0.007) C:.513_:[..U]U-*--xG[..G]:.522_:C (0.013) |
26 (0.009) C:.514_:[..A]A-**-xU[..U]:.508_:C (0.005) |
27 (0.024) C:.515_:[..G]Gx**+xC[..C]:.548_:C (0.013) x
28 (0.012) C:.519_:[..G]Gx---xC[..C]:.556_:C (0.003) +
29 (0.011) D:.501_:[..G]G-----C[..C]:.572_:D (0.010) |
30 (0.008) D:.502_:[..G]G-*---U[..U]:.571_:D (0.007) |
31 (0.010) D:.503_:[..C]C-----G[..G]:.570_:D (0.007) |
32 (0.006) D:.504_:[..C]C-----G[..G]:.569_:D (0.009) |
33 (0.011) D:.505_:[..C]C-----G[..G]:.568_:D (0.008) |
34 (0.004) D:.506_:[..C]C-----G[..G]:.567_:D (0.004) |
35 (0.005) D:.507_:[..A]Ax----U[..U]:.566_:D (0.002) |
36 (0.006) D:.549_:[..G]G-----C[..C]:.565_:D (0.006) |
37 (0.004) D:.550_:[..G]G-----C[..C]:.564_:D (0.004) |
38 (0.003) D:.551_:[..G]G-----C[..C]:.563_:D (0.003) |
39 (0.006) D:.552_:[..G]G-----C[..C]:.562_:D (0.002) |
40 (0.004) D:.553_:[..G]G----xC[..C]:.561_:D (0.007) |
41 (0.004) D:.554_:[..U]U-**-xA[..A]:.558_:D (0.005) |
42 (0.008) D:.555_:[..U]Ux**+xG[..G]:.518_:D (0.009) x
43 (0.010) D:.538_:[..A]A-*---C[..C]:.532_:D (0.007) |
44 (0.011) D:.539_:[..G]G-----C[..C]:.531_:D (0.010) |
45 (0.008) D:.540_:[..G]G-----C[..C]:.530_:D (0.004) |
46 (0.005) D:.541_:[..C]C-----G[..G]:.529_:D (0.009) |
47 (0.007) D:.542_:[..C]C-----G[..G]:.528_:D (0.011) |
48 (0.008) D:.543_:[..G]G-----C[..C]:.527_:D (0.005) |
49 (0.011) D:.544_:[..A]Ax*---G[..G]:.526_:D (0.010) |
50 (0.005) D:.510_:[..G]G-----C[..C]:.525_:D (0.009) |
51 (0.007) D:.511_:[..U]U-----A[..A]:.524_:D (0.007) |
52 (0.005) D:.512_:[..C]C-----G[..G]:.523_:D (0.010) |
53 (0.005) D:.513_:[..U]U-*--xG[..G]:.522_:D (0.012) |
54 (0.010) D:.514_:[..A]A-**-xU[..U]:.508_:D (0.009) |
55 (0.020) D:.515_:[..G]Gx**+xC[..C]:.548_:D (0.006) x
56 (0.008) D:.519_:[..G]G-----C[..C]:.556_:D (0.003) +

Note: This structure contains 16[8] non-Watson-Crick base-pairs.
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Detailed H-bond information: atom-name pair and length [ON]
1 G-----C [3] O6 - N4 2.62 N1 - N3 2.83 N2 - O2 2.94
2 G-*---U [2] O6 - N3 2.85 N1 - O2 2.91
3 C-----G [3] O2 - N2 2.96 N3 - N1 2.95 N4 - O6 2.88
4 C-----G [3] O2 - N2 2.94 N3 - N1 3.09 N4 - O6 3.10
5 C-----G [3] O2 - N2 2.98 N3 - N1 2.94 N4 - O6 2.87
6 C-----G [3] O2 - N2 2.73 N3 - N1 2.87 N4 - O6 2.97
7 A-----U [2] N6 - O4 2.94 N1 - N3 3.07
8 G-----C [3] O6 - N4 3.44 N1 - N3 3.23 N2 - O2 2.91
9 G-----C [3] O6 - N4 2.88 N1 - N3 2.91 N2 - O2 2.83
10 G-----C [3] O6 - N4 3.27 N1 - N3 3.07 N2 - O2 2.72
11 G-----C [3] O6 - N4 3.06 N1 - N3 2.92 N2 - O2 2.68
12 G-----C [3] O6 - N4 3.25 N1 - N3 3.22 N2 - O2 3.06
13 U-**--A [3] O2 - N6 3.17 N3 - N7 3.19 O4 * OP1 3.90
14 U-**+-G [2] O4'* O6 3.84 O2 - N2 2.70
15 A-*---C [1] N6 - O2 3.15
16 G-----C [3] O6 - N4 3.03 N1 - N3 2.90 N2 - O2 2.68
17 G-----C [3] O6 - N4 3.13 N1 - N3 2.88 N2 - O2 2.55
18 C-----G [3] O2 - N2 2.61 N3 - N1 2.73 N4 - O6 2.76
19 C-----G [3] O2 - N2 2.51 N3 - N1 2.69 N4 - O6 2.77
20 G-----C [3] O6 - N4 2.96 N1 - N3 2.89 N2 - O2 2.86
21 A-*---G [2] N6 - O6 3.10 N1 - N1 2.88
22 G-----C [3] O6 - N4 3.09 N1 - N3 3.05 N2 - O2 2.90
23 U-----A [2] N3 - N1 2.74 O4 - N6 3.07
24 C-----G [3] O2 - N2 2.74 N3 - N1 2.89 N4 - O6 2.94
25 U-*---G [2] O2 - N1 2.65 N3 - O6 2.96
26 A-**--U [3] OP2* O4 3.34 N7 - N3 2.76 N6 - O2 2.60
27 G-**+-C [2] N1 - O2 3.24 N2 - N3 2.95
28 G-----C [3] O6 - N4 2.82 N1 - N3 2.94 N2 - O2 3.25
29 G-----C [3] O6 - N4 2.69 N1 - N3 2.83 N2 - O2 2.96
30 G-*---U [2] O6 - N3 2.91 N1 - O2 2.94
31 C-----G [3] O2 - N2 2.95 N3 - N1 2.88 N4 - O6 2.77
32 C-----G [3] O2 - N2 2.84 N3 - N1 3.01 N4 - O6 3.03
33 C-----G [3] O2 - N2 2.90 N3 - N1 2.90 N4 - O6 2.79
34 C-----G [3] O2 - N2 2.75 N3 - N1 2.92 N4 - O6 3.03
35 A-----U [2] N6 - O4 2.84 N1 - N3 3.02
36 G-----C [3] O6 - N4 3.46 N1 - N3 3.26 N2 - O2 2.99
37 G-----C [3] O6 - N4 2.88 N1 - N3 2.90 N2 - O2 2.81
38 G-----C [3] O6 - N4 3.25 N1 - N3 3.07 N2 - O2 2.74
39 G-----C [3] O6 - N4 3.04 N1 - N3 2.93 N2 - O2 2.71
40 G-----C [3] O6 - N4 3.26 N1 - N3 3.21 N2 - O2 3.02
41 U-**--A [3] O2 - N6 3.15 N3 - N7 3.19 O4 * OP1 3.91
42 U-**+-G [1] O2 - N2 2.90
43 A-*---C [1] N6 - O2 3.00
44 G-----C [3] O6 - N4 2.94 N1 - N3 2.87 N2 - O2 2.70
45 G-----C [3] O6 - N4 3.16 N1 - N3 2.85 N2 - O2 2.47
46 C-----G [3] O2 - N2 2.57 N3 - N1 2.69 N4 - O6 2.74
47 C-----G [3] O2 - N2 2.45 N3 - N1 2.67 N4 - O6 2.81
48 G-----C [3] O6 - N4 3.02 N1 - N3 2.83 N2 - O2 2.69
49 A-*---G [2] N6 - O6 3.06 N1 - N1 2.85
50 G-----C [3] O6 - N4 3.07 N1 - N3 3.05 N2 - O2 2.90
51 U-----A [2] N3 - N1 2.74 O4 - N6 3.12
52 C-----G [3] O2 - N2 2.68 N3 - N1 2.88 N4 - O6 2.92
53 U-*---G [2] O2 - N1 2.60 N3 - O6 2.91
54 A-**--U [3] OP2* O4 3.36 N7 - N3 2.83 N6 - O2 2.77
55 G-**+-C [2] N1 - O2 3.19 N2 - N3 3.01
56 G-----C [3] O6 - N4 3.37 N1 - N3 3.38 N2 - O2 3.62
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Overlap area in Angstrom^2 between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the designed base-pair step.

Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and
inter-strand overlap is designated according to the following diagram:

i2 3' 5' j2
/|\ |
| |
Strand I | | II
| |
| |
| \|/
i1 5' 3' j1

step i1-i2 i1-j2 j1-i2 j1-j2 sum
1 GG/UC 1.18( 0.12) 0.00( 0.00) 0.00( 0.00) 0.91( 0.00) 2.09( 0.12)
2 GC/GU 7.14( 4.30) 0.00( 0.00) 0.00( 0.00) 6.63( 4.10) 13.76( 8.40)
3 CC/GG 0.16( 0.01) 0.00( 0.00) 0.30( 0.00) 2.78( 1.27) 3.24( 1.28)
4 CC/GG 0.00( 0.00) 0.00( 0.00) 0.16( 0.00) 3.82( 2.48) 3.98( 2.48)
5 CC/GG 0.18( 0.01) 0.00( 0.00) 0.31( 0.00) 2.91( 1.49) 3.40( 1.49)
6 CA/UG 0.05( 0.00) 0.00( 0.00) 2.00( 0.48) 0.56( 0.14) 2.62( 0.62)
7 AG/CU 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 2.91( 1.00) 2.91( 1.00)
8 GG/CC 2.16( 0.71) 0.00( 0.00) 0.24( 0.00) 0.62( 0.19) 3.02( 0.89)
9 GG/CC 4.21( 2.85) 0.00( 0.00) 0.01( 0.00) 0.52( 0.00) 4.74( 2.85)
10 GG/CC 3.70( 2.34) 0.00( 0.00) 0.22( 0.00) 0.00( 0.00) 3.92( 2.34)
11 GG/CC 4.13( 2.67) 0.00( 0.00) 0.48( 0.00) 0.00( 0.00) 4.61( 2.67)
12 GU/AC 5.77( 2.83) 0.00( 0.00) 0.00( 0.00) 1.12( 0.02) 6.89( 2.85)
13 UU/GA 5.05( 2.64) 0.00( 0.00) 0.00( 0.00) 3.74( 1.24) 8.78( 3.88)
14 UA/CG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
15 AG/CC 3.93( 2.16) 0.00( 0.00) 0.00( 0.00) 5.20( 2.36) 9.13( 4.52)
16 GG/CC 2.92( 1.44) 0.00( 0.00) 0.51( 0.00) 0.38( 0.00) 3.81( 1.44)
17 GC/GC 6.19( 3.17) 0.00( 0.00) 0.00( 0.00) 6.51( 3.37) 12.69( 6.53)
18 CC/GG 0.20( 0.01) 0.00( 0.00) 0.69( 0.00) 2.95( 1.47) 3.84( 1.48)
19 CG/CG 0.00( 0.00) 0.00( 0.00) 5.02( 2.28) 0.00( 0.00) 5.02( 2.28)
20 GA/GC 1.66( 0.00) 0.00( 0.00) 0.00( 0.00) 4.93( 2.24) 6.59( 2.24)
21 AG/CG 0.00( 0.00) 0.00( 0.00) 0.47( 0.00) 1.50( 0.92) 1.97( 0.92)
22 GU/AC 5.06( 2.37) 0.00( 0.00) 0.00( 0.00) 3.41( 2.04) 8.47( 4.41)
23 UC/GA 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 3.87( 2.43) 3.87( 2.43)
24 CU/GG 1.30( 0.05) 0.00( 0.00) 0.00( 0.00) 2.71( 1.19) 4.01( 1.24)
25 UA/UG 0.00( 0.00) 2.33( 0.10) 5.78( 4.47) 0.00( 0.00) 8.11( 4.57)
26 AG/CU 3.49( 1.30) 0.00( 0.00) 0.04( 0.00) 0.00( 0.00) 3.53( 1.30)
27 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
28 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
29 GG/UC 1.12( 0.10) 0.00( 0.00) 0.00( 0.00) 0.89( 0.00) 2.01( 0.10)
30 GC/GU 7.17( 4.39) 0.00( 0.00) 0.00( 0.00) 6.49( 4.01) 13.66( 8.40)
31 CC/GG 0.46( 0.07) 0.00( 0.00) 0.23( 0.00) 2.74( 1.29) 3.43( 1.37)
32 CC/GG 0.00( 0.00) 0.00( 0.00) 0.16( 0.00) 3.79( 2.48) 3.95( 2.48)
33 CC/GG 0.41( 0.05) 0.00( 0.00) 0.24( 0.00) 3.03( 1.62) 3.68( 1.66)
34 CA/UG 0.13( 0.00) 0.00( 0.00) 1.79( 0.40) 0.72( 0.21) 2.64( 0.60)
35 AG/CU 0.00( 0.00) 0.00( 0.00) 0.35( 0.00) 0.16( 0.01) 0.51( 0.01)
36 GG/CC 2.15( 0.69) 0.00( 0.00) 0.27( 0.00) 0.59( 0.19) 3.01( 0.87)
37 GG/CC 4.21( 2.85) 0.00( 0.00) 0.02( 0.00) 0.41( 0.00) 4.64( 2.85)
38 GG/CC 3.65( 2.27) 0.00( 0.00) 0.23( 0.00) 0.00( 0.00) 3.88( 2.27)
39 GG/CC 4.02( 2.55) 0.00( 0.00) 0.51( 0.00) 0.00( 0.00) 4.53( 2.55)
40 GU/AC 5.36( 2.50) 0.00( 0.00) 0.00( 0.00) 1.20( 0.04) 6.56( 2.54)
41 UU/GA 5.06( 2.66) 0.00( 0.00) 0.00( 0.00) 2.70( 0.67) 7.76( 3.33)
42 UA/CG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
43 AG/CC 4.74( 2.33) 0.00( 0.00) 0.00( 0.00) 5.68( 2.31) 10.42( 4.64)
44 GG/CC 3.18( 1.72) 0.00( 0.00) 0.50( 0.00) 0.28( 0.00) 3.96( 1.72)
45 GC/GC 5.94( 3.02) 0.00( 0.00) 0.00( 0.00) 6.44( 3.32) 12.38( 6.34)
46 CC/GG 0.29( 0.02) 0.00( 0.00) 0.68( 0.00) 2.92( 1.48) 3.89( 1.50)
47 CG/CG 0.00( 0.00) 0.00( 0.00) 5.05( 2.31) 0.00( 0.00) 5.05( 2.31)
48 GA/GC 1.80( 0.04) 0.00( 0.00) 0.00( 0.00) 4.75( 2.12) 6.55( 2.16)
49 AG/CG 0.00( 0.00) 0.00( 0.00) 0.45( 0.00) 1.01( 0.58) 1.46( 0.58)
50 GU/AC 5.06( 2.37) 0.00( 0.00) 0.00( 0.00) 3.42( 2.07) 8.48( 4.45)
51 UC/GA 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 3.72( 2.24) 3.72( 2.24)
52 CU/GG 1.11( 0.01) 0.00( 0.00) 0.00( 0.00) 2.61( 1.08) 3.72( 1.09)
53 UA/UG 0.00( 0.00) 2.26( 0.07) 6.03( 4.70) 0.00( 0.00) 8.29( 4.77)
54 AG/CU 3.81( 1.57) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 3.82( 1.57)
55 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
****************************************************************************
Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in
the coordinate system of the given structure

bp Ox Oy Oz Nx Ny Nz
1 G-C 26.04 89.66 67.92 -0.63 -0.15 -0.76
2 G-U 25.32 89.13 65.11 -0.75 -0.18 -0.64
3 C-G 23.36 87.41 62.74 -0.77 -0.27 -0.58
4 C-G 20.86 84.73 61.51 -0.79 -0.27 -0.55
5 C-G 18.44 82.25 60.85 -0.83 -0.31 -0.46
6 C-G 14.87 81.12 60.96 -0.87 -0.15 -0.47
7 A-U 11.26 80.40 60.74 -0.89 0.12 -0.44
8 G-C 7.24 80.16 61.19 -0.88 -0.01 -0.47
9 G-C 4.21 82.13 60.16 -0.86 0.01 -0.51
10 G-C 2.20 83.02 57.63 -0.84 -0.03 -0.54
11 G-C 0.63 83.07 54.20 -0.74 -0.15 -0.65
12 G-C -0.21 81.66 51.05 -0.83 -0.18 -0.52
13 U-A -1.22 78.85 47.09 -0.83 -0.19 -0.52
14 U+G -5.17 78.57 47.64 -0.84 -0.31 -0.43
15 A-C 21.24 36.94 54.79 -0.56 0.77 -0.31
16 G-C 18.27 38.97 53.89 -0.61 0.78 -0.13
17 G-C 15.27 41.04 54.75 -0.55 0.83 -0.03
18 C-G 13.00 43.50 56.04 -0.49 0.87 -0.04
19 C-G 12.16 46.78 57.56 -0.39 0.92 -0.04
20 G-C 12.69 50.82 58.39 -0.15 0.97 -0.17
21 A-G 13.34 54.23 59.07 -0.11 0.97 -0.23
22 G-C 16.57 57.94 59.04 -0.02 0.84 -0.54
23 U-A 16.42 59.78 55.50 -0.12 0.82 -0.57
24 C-G 15.64 61.48 52.25 -0.27 0.82 -0.50
25 U-G 12.15 63.16 51.30 -0.37 0.81 -0.46
26 A-U 10.00 64.90 49.31 -0.36 0.79 -0.50
27 G+C 6.56 68.13 50.50 -0.37 0.90 -0.21
28 G-C -7.53 73.48 40.43 -0.63 -0.35 -0.69
29 G-C 85.54 90.39 130.48 -0.69 -0.22 -0.69
30 G-U 84.45 89.78 127.66 -0.80 -0.26 -0.54
31 C-G 82.51 87.93 125.64 -0.78 -0.38 -0.49
32 C-G 80.20 85.08 124.80 -0.82 -0.39 -0.42
33 C-G 77.84 82.30 124.44 -0.87 -0.37 -0.32
34 C-G 74.41 80.91 125.09 -0.92 -0.24 -0.30
35 A-U 71.00 79.79 125.44 -0.96 0.02 -0.28
36 G-C 67.41 80.10 126.79 -0.96 -0.04 -0.29
37 G-C 64.21 82.10 126.41 -0.95 0.01 -0.31
38 G-C 61.67 83.01 124.35 -0.93 -0.04 -0.35
39 G-C 59.44 83.12 121.34 -0.87 -0.14 -0.47
40 G-C 57.93 81.68 118.35 -0.91 -0.23 -0.35
41 U-A 56.03 78.93 114.55 -0.94 -0.16 -0.31
42 U+G 52.33 78.70 115.73 -0.92 -0.30 -0.23
43 A-C 79.37 37.36 117.11 -0.62 0.75 -0.22
44 G-C 76.47 39.48 116.82 -0.64 0.77 -0.01
45 G-C 73.72 41.49 118.28 -0.55 0.83 0.07
46 C-G 71.69 43.83 120.06 -0.49 0.87 0.09
47 C-G 71.23 46.98 121.87 -0.37 0.93 0.08
48 G-C 71.80 50.87 122.79 -0.22 0.97 -0.09
49 A-G 72.52 54.34 123.48 -0.16 0.97 -0.18
50 G-C 75.79 58.10 122.83 -0.15 0.84 -0.52
51 U-A 74.97 59.99 119.37 -0.20 0.83 -0.52
52 C-G 73.64 61.67 116.40 -0.36 0.83 -0.43
53 U-G 69.96 63.32 116.05 -0.43 0.82 -0.38
54 A-U 67.45 65.06 114.47 -0.45 0.79 -0.41
55 G+C 64.21 68.34 116.32 -0.37 0.92 -0.13
56 G-C 48.38 73.55 109.16 -0.77 -0.34 -0.53
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.15 -0.26 0.16 0.60 -14.22 -5.98
2 G-U -2.40 -0.51 0.78 17.41 -7.44 -4.89
3 C-G -0.01 -0.08 0.26 13.48 -13.12 -3.93
4 C-G 0.11 0.07 0.30 8.40 -4.65 0.00
5 C-G 0.16 -0.09 -0.16 11.57 -15.50 -2.92
6 C-G 0.17 -0.15 0.34 2.18 -13.11 0.79
7 A-U 0.64 0.10 -0.11 -4.70 -9.00 -5.82
8 G-C -0.75 0.15 0.06 -9.58 -9.89 4.68
9 G-C -0.14 -0.11 -0.19 -5.95 -10.34 -0.39
10 G-C 0.12 0.13 -0.12 -2.33 1.09 5.41
11 G-C -0.22 -0.10 -0.53 -4.07 -8.05 4.65
12 G-C 0.11 0.15 0.77 3.16 7.01 2.25
13 U-A 4.18 -1.62 0.86 -0.30 2.30 -97.20
14 U+G 0.15 -6.06 0.82 16.83 -0.54 -95.17
15 A-C -4.81 -0.77 1.44 15.24 7.22 4.12
16 G-C -0.36 -0.14 0.34 8.87 -12.89 2.44
17 G-C -0.63 -0.17 -0.04 3.32 -9.96 6.59
18 C-G 0.19 -0.28 0.01 5.49 -8.47 0.53
19 C-G 0.30 -0.34 0.04 -0.26 -10.07 1.74
20 G-C 0.05 -0.06 -0.15 -18.59 -22.49 0.64
21 A-G -0.14 1.56 -0.08 -20.24 -22.60 -12.70
22 G-C -0.54 -0.04 0.21 8.55 2.14 0.91
23 U-A -0.19 -0.13 -0.02 -1.23 -8.34 6.51
24 C-G 0.02 -0.09 0.18 -6.04 -6.76 1.26
25 U-G 2.31 -0.45 -0.20 5.46 -1.73 6.67
26 A-U -3.98 -2.06 0.92 9.05 16.26 -94.19
27 G+C -0.11 3.42 -0.43 0.39 4.31 164.86
28 G-C -0.11 -0.02 -0.67 -29.07 -32.91 -2.62
29 G-C -0.07 -0.23 0.34 5.35 -14.48 -5.65
30 G-U -2.38 -0.52 0.90 17.52 -7.42 -5.78
31 C-G -0.02 -0.12 0.05 17.53 -15.45 -4.54
32 C-G 0.16 0.03 -0.05 14.99 -6.39 0.71
33 C-G 0.14 -0.14 -0.03 15.09 -12.54 -3.56
34 C-G 0.31 -0.11 0.22 5.12 -13.99 1.34
35 A-U 0.79 0.02 -0.14 -0.48 -9.71 -6.35
36 G-C -0.80 0.15 0.24 -4.37 -11.55 4.10
37 G-C -0.09 -0.12 -0.19 -3.21 -9.13 -0.24
38 G-C 0.19 0.13 -0.12 -1.06 1.80 4.70
39 G-C -0.14 -0.09 -0.50 -2.87 -7.04 3.94
40 G-C 0.10 0.18 0.53 1.42 7.52 2.40
41 U-A 4.17 -1.64 0.93 -0.14 3.26 -96.97
42 U+G 0.23 -6.55 0.86 16.73 1.77 -96.46
43 A-C -4.86 -0.83 1.35 16.58 0.02 1.63
44 G-C -0.38 -0.17 0.30 8.52 -12.77 1.61
45 G-C -0.58 -0.17 0.18 2.71 -11.21 6.95
46 C-G 0.18 -0.33 0.02 4.52 -13.19 0.39
47 C-G 0.19 -0.32 -0.07 0.23 -12.31 3.27
48 G-C -0.07 -0.13 0.15 -14.65 -21.03 1.67
49 A-G -0.27 1.55 0.02 -19.32 -19.49 -13.55
50 G-C -0.56 -0.04 0.15 8.42 2.17 1.14
51 U-A -0.17 -0.12 0.15 -0.10 -8.59 7.75
52 C-G 0.14 -0.13 0.09 -4.42 -3.74 1.01
53 U-G 2.26 -0.48 -0.04 4.90 -3.53 6.52
54 A-U -4.03 -1.95 0.85 8.48 14.11 -96.06
55 G+C -0.17 3.79 -0.35 0.89 -0.62 162.99
56 G-C 0.07 0.51 -0.66 -34.26 -35.79 -0.76
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.21 -0.28 0.18 1.64 -7.52 -4.10
s.d. 1.58 1.49 0.46 11.24 9.96 44.56
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GG/UC -0.31 -1.43 2.56 -8.63 4.67 29.48
2 GC/GU 0.08 -1.15 3.32 2.25 5.50 43.63
3 CC/GG 0.38 -1.86 3.37 0.06 2.15 32.82
4 CC/GG -0.40 -1.79 3.01 5.34 3.04 31.36
5 CC/GG 0.30 -1.82 3.26 -2.48 9.04 31.23
6 CA/UG -0.95 -1.28 3.33 5.10 14.66 35.29
7 AG/CU -2.04 -1.01 3.35 -7.02 -3.07 47.10
8 GG/CC -0.72 -1.94 3.14 1.49 2.53 34.00
9 GG/CC 0.34 -1.40 3.03 -0.64 3.02 30.67
10 GG/CC 0.43 -1.78 3.29 5.06 9.59 28.23
11 GG/CC 0.75 -2.12 2.77 -8.63 3.15 32.88
12 GU/AC -1.91 -3.02 3.43 0.34 0.66 93.65
13 UU/GA 1.96 -1.52 3.13 7.85 -2.58 45.15
14 UA/CG ---- ---- ---- ---- ---- ----
15 AG/CC -0.10 -1.15 3.52 1.82 10.76 48.31
16 GG/CC 0.12 -1.66 3.36 -0.29 7.04 31.71
17 GC/GC -0.17 -1.55 3.22 -1.86 3.38 35.58
18 CC/GG 0.23 -1.79 3.26 2.06 6.36 32.60
19 CG/CG 0.24 -2.01 3.62 4.84 15.34 30.14
20 GA/GC -1.05 -1.36 3.09 1.31 3.84 35.06
21 AG/CG -3.01 -2.21 3.20 14.53 13.67 57.50
22 GU/AC 0.32 -1.89 3.50 0.76 6.05 36.36
23 UC/GA -0.59 -1.71 3.29 0.24 9.84 34.74
24 CU/GG 1.54 -2.20 2.94 3.60 4.45 27.92
25 UA/UG -1.02 -0.89 3.12 -0.78 -2.92 66.33
26 AG/CU 1.97 -2.61 3.61 3.15 17.66 -78.84
27 GG/CC ---- ---- ---- ---- ---- ----
28 GG/CC ---- ---- ---- ---- ---- ----
29 GG/UC -0.36 -1.44 2.70 -9.50 4.75 29.27
30 GC/GU 0.07 -1.07 3.18 4.24 6.17 42.71
31 CC/GG 0.44 -1.70 3.34 0.39 4.29 33.48
32 CC/GG -0.43 -1.75 3.18 2.69 6.23 30.77
33 CC/GG 0.31 -1.75 3.32 -1.09 7.88 31.75
34 CA/UG -1.01 -1.16 3.25 4.51 14.41 35.47
35 AG/CU -1.63 -1.68 3.06 -2.97 -1.53 47.72
36 GG/CC -0.72 -2.00 3.14 3.00 1.05 34.09
37 GG/CC 0.33 -1.42 3.06 -0.87 3.91 31.15
38 GG/CC 0.38 -1.82 3.27 4.86 8.41 28.29
39 GG/CC 0.72 -2.17 2.84 -7.13 5.87 32.22
40 GU/AC -2.05 -2.97 3.54 -4.11 0.92 94.26
41 UU/GA 1.78 -1.36 3.18 8.39 -3.78 46.31
42 UA/CG ---- ---- ---- ---- ---- ----
43 AG/CC 0.07 -0.88 3.49 1.08 12.61 50.50
44 GG/CC 0.27 -1.67 3.30 -1.87 7.69 32.15
45 GC/GC -0.20 -1.60 3.19 0.62 3.86 35.35
46 CC/GG 0.30 -1.79 3.18 2.06 7.44 30.97
47 CG/CG 0.26 -1.93 3.54 1.59 13.08 30.77
48 GA/GC -1.00 -1.47 3.15 2.69 5.22 34.62
49 AG/CG -3.00 -2.49 3.16 14.25 16.16 60.12
50 GU/AC 0.36 -1.91 3.53 -0.39 2.82 36.00
51 UC/GA -0.55 -1.72 3.19 1.41 10.53 35.93
52 CU/GG 1.53 -2.31 2.96 2.88 3.89 27.27
53 UA/UG -1.07 -0.93 3.12 0.49 -2.93 66.22
54 AG/CU 1.89 -2.73 3.69 1.38 18.74 -75.06
55 GG/CC ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.14 -1.74 3.23 1.16 6.11 35.11
s.d. 1.13 0.50 0.23 4.76 5.58 27.36
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GG/UC -3.36 -0.69 2.31 8.88 16.39 31.03
2 GC/GU -2.05 0.10 3.16 7.36 -3.02 44.02
3 CC/GG -3.66 -0.65 3.24 3.80 -0.10 32.88
4 CC/GG -3.73 1.59 2.73 5.56 -9.76 31.94
5 CC/GG -4.69 -0.93 2.61 16.33 4.48 32.57
6 CA/UG -3.64 2.03 2.47 22.87 -7.96 38.46
7 AG/CU -0.98 1.91 3.66 -3.81 8.72 47.69
8 GG/CC -3.68 1.45 2.96 4.31 -2.54 34.13
9 GG/CC -3.17 -0.76 2.88 5.70 1.21 30.82
10 GG/CC -5.23 0.13 2.60 18.82 -9.92 30.20
11 GG/CC -4.00 -2.36 2.30 5.43 14.89 34.11
12 GU/AC -2.08 1.32 3.41 0.45 -0.23 93.65
13 UU/GA -1.73 -1.82 3.49 -3.33 -10.13 45.86
14 UA/CG ---- ---- ---- ---- ---- ----
15 AG/CC -2.21 0.26 3.20 12.95 -2.20 49.46
16 GG/CC -4.18 -0.27 2.93 12.69 0.52 32.47
17 GC/GC -2.98 0.01 3.07 5.51 3.03 35.78
18 CC/GG -4.13 -0.08 2.87 11.18 -3.62 33.26
19 CG/CG -5.82 0.34 2.36 27.20 -8.57 34.08
20 GA/GC -2.77 1.92 2.89 6.36 -2.16 35.29
21 AG/CG -2.73 3.56 1.94 13.77 -14.63 60.58
22 GU/AC -3.83 -0.41 3.17 9.61 -1.21 36.85
23 UC/GA -4.07 0.99 2.72 16.08 -0.39 36.07
24 CU/GG -5.37 -2.41 2.74 9.09 -7.37 28.49
25 UA/UG -0.70 0.90 3.16 -2.67 0.71 66.39
26 AG/CU 1.47 1.62 3.96 -13.74 2.45 -80.53
27 GG/CC ---- ---- ---- ---- ---- ----
28 GG/CC ---- ---- ---- ---- ---- ----
29 GG/UC -3.43 -0.80 2.44 9.03 18.06 31.09
30 GC/GU -2.03 0.30 3.00 8.39 -5.77 43.33
31 CC/GG -3.61 -0.69 3.11 7.40 -0.67 33.74
32 CC/GG -4.29 1.26 2.73 11.56 -4.99 31.49
33 CC/GG -4.40 -0.74 2.80 14.13 1.95 32.71
34 CA/UG -3.41 2.04 2.47 22.44 -7.02 38.46
35 AG/CU -1.95 1.78 3.20 -1.89 3.67 47.83
36 GG/CC -3.56 1.67 3.01 1.79 -5.10 34.23
37 GG/CC -3.29 -0.75 2.86 7.24 1.61 31.40
38 GG/CC -5.15 0.20 2.66 16.59 -9.59 29.88
39 GG/CC -4.53 -2.18 2.21 10.31 12.53 33.49
40 GU/AC -2.04 1.32 3.59 0.62 2.80 94.33
41 UU/GA -1.38 -1.51 3.53 -4.76 -10.55 47.16
42 UA/CG ---- ---- ---- ---- ---- ----
43 AG/CC -1.89 -0.01 3.20 14.52 -1.24 51.96
44 GG/CC -4.16 -0.78 2.81 13.63 3.31 33.09
45 GC/GC -3.16 0.41 3.00 6.33 -1.02 35.56
46 CC/GG -4.49 -0.20 2.70 13.67 -3.79 31.89
47 CG/CG -5.46 -0.19 2.54 23.36 -2.84 33.42
48 GA/GC -3.15 2.03 2.82 8.70 -4.48 35.10
49 AG/CG -2.92 3.34 1.83 15.60 -13.76 63.52
50 GU/AC -3.51 -0.64 3.37 4.55 0.63 36.11
51 UC/GA -3.93 1.03 2.58 16.62 -2.23 37.42
52 CU/GG -5.64 -2.59 2.75 8.16 -6.06 27.69
53 UA/UG -0.74 0.99 3.15 -2.68 -0.45 66.28
54 AG/CU 1.53 1.57 4.15 -15.15 1.11 -77.04
55 GG/CC ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -3.20 0.29 2.91 8.21 -1.31 35.99
s.d. 1.58 1.42 0.46 8.73 6.99 27.77
****************************************************************************
Structure classification:

This structure contains more than one helical regions
This is a right-handed nucleic acid structure
****************************************************************************
lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the
base-pair C1'-C1' line

C1'-C1': distance between C1' atoms for each base-pair
RN9-YN1: distance between RN9-YN1 atoms for each base-pair
RC8-YC6: distance between RC8-YC6 atoms for each base-pair

bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6
1 G-C 50.6 51.8 10.8 9.0 9.8
2 G-U 39.5 67.0 10.6 8.9 9.7
3 C-G 51.5 53.2 10.8 9.0 9.9
4 C-G 54.0 54.6 10.8 9.1 10.1
5 C-G 52.0 52.8 10.8 9.0 9.9
6 C-G 55.1 53.7 10.6 8.9 9.9
7 A-U 55.6 48.5 11.0 9.2 10.1
8 G-C 52.4 59.7 10.8 9.1 10.2
9 G-C 53.2 53.8 10.7 9.0 9.9
10 G-C 58.1 56.0 10.7 9.1 10.1
11 G-C 55.3 56.9 10.5 8.9 9.9
12 G-C 55.9 54.0 10.9 9.2 10.2
13 U-A 31.8 18.6 10.1 7.6 6.6
14 U+G 111.9 34.3 8.6 8.2 9.8
15 A-C 29.8 82.4 11.0 9.5 10.4
16 G-C 52.9 57.8 10.6 8.9 9.9
17 G-C 54.7 60.2 10.4 8.8 9.9
18 C-G 55.3 54.3 10.5 8.8 9.7
19 C-G 56.1 53.4 10.4 8.7 9.7
20 G-C 56.7 53.1 10.6 8.9 9.8
21 A-G 50.2 48.1 12.6 10.7 11.2
22 G-C 51.8 57.5 10.7 9.0 10.0
23 U-A 57.8 60.0 10.2 8.7 9.8
24 C-G 55.2 54.7 10.6 9.0 9.9
25 U-G 72.3 45.7 10.2 8.7 9.8
26 A-U 16.4 32.0 9.7 7.1 6.2
27 G+C 40.9 54.3 10.9 9.2 10.6
28 G-C 55.1 49.6 10.7 8.9 9.7
29 G-C 50.1 51.4 10.8 9.0 9.8
30 G-U 37.9 66.3 10.6 8.9 9.7
31 C-G 51.2 53.1 10.8 9.0 9.8
32 C-G 55.1 54.5 10.7 9.0 10.0
33 C-G 52.0 53.0 10.7 9.0 9.8
34 C-G 55.7 53.6 10.6 8.9 9.9
35 A-U 56.7 47.4 11.0 9.2 10.0
36 G-C 52.1 59.8 10.8 9.2 10.2
37 G-C 53.2 53.7 10.7 9.0 9.9
38 G-C 58.1 54.9 10.7 9.1 10.2
39 G-C 55.9 56.3 10.6 8.9 9.9
40 G-C 55.9 53.5 11.0 9.3 10.2
41 U-A 31.3 18.6 10.1 7.6 6.6
42 U+G 113.1 36.4 8.9 8.6 10.2
43 A-C 29.0 81.3 11.0 9.5 10.3
44 G-C 52.0 56.8 10.6 8.9 9.9
45 G-C 54.2 59.9 10.4 8.8 9.9
46 C-G 55.1 53.5 10.5 8.8 9.7
47 C-G 55.6 54.0 10.4 8.7 9.7
48 G-C 56.7 53.9 10.5 8.8 9.8
49 A-G 49.8 48.2 12.6 10.7 11.2
50 G-C 52.1 58.2 10.7 9.0 10.0
51 U-A 58.9 60.1 10.2 8.7 9.8
52 C-G 54.9 53.5 10.7 8.9 9.9
53 U-G 71.1 46.3 10.2 8.7 9.8
54 A-U 17.3 32.6 9.7 7.2 6.2
55 G+C 41.1 56.6 10.9 9.3 10.8
56 G-C 57.6 49.3 11.1 9.3 10.1
****************************************************************************
Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases

step Xp Yp Zp XpH YpH ZpH Form
1 GG/UC -1.34 8.10 2.44 -4.25 7.64 3.65 A
2 GC/GU -1.20 8.30 2.86 -3.14 7.91 3.81 A
3 CC/GG -1.28 8.15 2.93 -4.80 7.95 3.45 A
4 CC/GG -1.15 8.15 2.80 -4.79 7.85 3.55 A
5 CC/GG -1.36 8.21 2.73 -5.84 7.17 4.84 A
6 CA/UG -1.57 8.42 2.46 -4.92 6.92 5.33 A
7 AG/CU -2.55 7.77 2.56 -3.43 7.92 2.22 A
8 GG/CC -1.58 8.16 2.70 -5.08 7.95 3.26 A
9 GG/CC -1.21 8.29 2.61 -4.27 8.00 3.39 A
10 GG/CC -1.61 8.24 2.50 -6.60 7.05 4.89 A
11 GG/CC -1.82 7.88 3.18 -5.58 7.56 3.79 A
12 GU/AC -1.04 6.43 4.58 -2.46 6.41 4.62
13 UU/GA 3.75 4.40 0.55 1.75 4.44 0.82
14 UA/CG --- --- --- --- --- --- ---
15 AG/CC -1.56 8.28 3.08 -3.60 7.48 4.66 A
16 GG/CC -1.86 8.13 2.62 -5.86 7.39 4.28 A
17 GC/GC -1.65 8.19 2.56 -4.47 7.92 3.29 A
18 CC/GG -1.63 8.14 2.76 -5.59 7.49 4.23 A
19 CG/CG -1.89 8.29 2.64 -7.36 6.28 5.98 A
20 GA/GC -1.29 8.68 2.14 -3.88 8.41 3.04 A
21 AG/CG -2.46 7.07 4.55 -4.95 6.01 5.47
22 GU/AC -1.76 7.84 2.97 -5.41 7.27 4.17 A
23 UC/GA -1.70 8.03 2.80 -5.57 7.00 4.82 A
24 CU/GG -1.74 8.37 2.58 -6.90 7.88 3.81 A
25 UA/UG -1.40 6.52 2.49 -1.98 6.61 2.20
26 AG/CU 2.22 1.41 1.05 3.37 1.60 0.98
27 GG/CC --- --- --- --- --- --- ---
28 GG/CC --- --- --- --- --- --- ---
29 GG/UC -1.31 8.12 2.54 -4.19 7.64 3.70 A
30 GC/GU -1.13 8.39 2.75 -3.11 7.94 3.81 A
31 CC/GG -1.30 8.24 2.62 -4.76 7.85 3.62 A
32 CC/GG -1.15 8.21 2.67 -5.33 7.54 4.21 A
33 CC/GG -1.24 8.18 2.73 -5.45 7.31 4.56 A
34 CA/UG -1.46 8.33 2.44 -4.64 6.88 5.27 A
35 AG/CU -2.63 7.41 2.87 -4.39 7.50 2.70
36 GG/CC -1.53 8.06 2.82 -4.90 7.97 3.04 A
37 GG/CC -1.22 8.27 2.68 -4.40 7.88 3.66 A
38 GG/CC -1.63 8.23 2.55 -6.56 7.21 4.67 A
39 GG/CC -1.86 7.91 3.18 -6.15 7.25 4.43 A
40 GU/AC -1.04 6.50 4.49 -2.45 6.47 4.42
41 UU/GA 3.80 4.38 0.54 2.12 4.43 0.74
42 UA/CG --- --- --- --- --- --- ---
43 AG/CC -1.56 8.44 2.88 -3.27 7.57 4.70 A
44 GG/CC -1.84 8.22 2.67 -5.80 7.40 4.46 A
45 GC/GC -1.66 8.13 2.64 -4.67 7.81 3.48 A
46 CC/GG -1.58 8.19 2.64 -5.91 7.38 4.44 A
47 CG/CG -1.91 8.22 2.64 -7.12 6.59 5.57 A
48 GA/GC -1.31 8.68 2.34 -4.21 8.26 3.54 A
49 AG/CG -2.48 6.93 4.58 -5.08 5.72 5.64
50 GU/AC -1.76 7.75 3.05 -5.09 7.50 3.63 A
51 UC/GA -1.72 7.97 2.93 -5.43 6.87 4.99 A
52 CU/GG -1.75 8.37 2.70 -7.20 7.92 3.81 A
53 UA/UG -1.41 6.55 2.55 -2.04 6.65 2.31
54 AG/CU 2.18 1.48 1.16 3.39 1.70 0.93
55 GG/CC --- --- --- --- --- --- ---
****************************************************************************
Minor and major groove widths: direct P-P distances and refined P-P distances
which take into account the directions of the sugar-phosphate backbones

(Subtract 5.8 Angstrom from the values to take account of the vdw radii
of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

Minor Groove Major Groove
P-P Refined P-P Refined
1 GG/UC --- --- --- ---
2 GC/GU --- --- --- ---
3 CC/GG 16.2 --- 14.8 ---
4 CC/GG 16.0 15.2 16.1 13.1
5 CC/GG 16.5 14.9 15.4 12.8
6 CA/UG 16.6 14.5 13.8 11.8
7 AG/CU 16.1 14.5 13.2 11.7
8 GG/CC 16.3 15.0 13.4 12.4
9 GG/CC 16.9 15.8 15.4 11.5
10 GG/CC 17.1 15.8 16.1 13.2
11 GG/CC 16.7 --- 13.4 ---
12 GU/AC --- --- --- ---
13 UU/GA --- --- --- ---
14 UA/CG --- --- --- ---
15 AG/CC --- --- --- ---
16 GG/CC --- --- --- ---
17 GC/GC 16.6 --- 15.9 ---
18 CC/GG 16.4 15.2 15.9 9.9
19 CG/CG 18.4 15.1 15.4 10.0
20 GA/GC 19.6 15.3 13.8 10.2
21 AG/CG 18.0 15.2 12.2 9.9
22 GU/AC 17.2 15.1 11.4 11.2
23 UC/GA 17.1 15.3 15.0 10.5
24 CU/GG 16.8 --- 8.8 ---
25 UA/UG --- --- --- ---
26 AG/CU --- --- --- ---
27 GG/CC --- --- --- ---
28 GG/CC --- --- --- ---
29 GG/UC --- --- --- ---
30 GC/GU --- --- --- ---
31 CC/GG 16.4 --- 14.4 ---
32 CC/GG 16.3 15.5 15.9 12.2
33 CC/GG 16.7 15.1 15.2 11.3
34 CA/UG 16.5 14.3 13.3 10.5
35 AG/CU 15.5 13.9 12.9 11.2
36 GG/CC 15.5 14.3 13.5 12.5
37 GG/CC 16.5 15.5 15.4 11.6
38 GG/CC 17.0 15.8 16.0 13.2
39 GG/CC 16.6 --- 13.4 ---
40 GU/AC --- --- --- ---
41 UU/GA --- --- --- ---
42 UA/CG --- --- --- ---
43 AG/CC --- --- --- ---
44 GG/CC --- --- --- ---
45 GC/GC 16.5 --- 15.9 ---
46 CC/GG 16.3 15.2 16.0 9.9
47 CG/CG 18.4 15.1 15.4 9.7
48 GA/GC 19.7 15.3 13.6 9.6
49 AG/CG 18.1 15.2 12.1 9.4
50 GU/AC 17.1 15.0 11.3 11.0
51 UC/GA 17.0 15.3 15.1 10.5
52 CU/GG 16.7 --- 8.3 ---
53 UA/UG --- --- --- ---
54 AG/CU --- --- --- ---
55 GG/CC --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 0.43(3.57)
****************************************************************************
Main chain and chi torsion angles:

Note: alpha: O3'(i-1)-P-O5'-C5'
beta: P-O5'-C5'-C4'
gamma: O5'-C5'-C4'-C3'
delta: C5'-C4'-C3'-O3'
epsilon: C4'-C3'-O3'-P(i+1)
zeta: C3'-O3'-P(i+1)-O5'(i+1)

chi for pyrimidines(Y): O4'-C1'-N1-C2
chi for purines(R): O4'-C1'-N9-C4

Strand I
base alpha beta gamma delta epsilon zeta chi
1 G --- 168.7 43.2 92.0 -145.9 -81.2 -172.5
2 G -76.0 -178.5 53.6 84.9 -144.7 -70.2 -161.4
3 C -63.1 171.3 49.2 83.6 -152.0 -71.1 -159.4
4 C -65.7 171.7 54.7 80.1 -155.2 -77.1 -166.0
5 C -57.3 171.9 50.1 81.8 -156.3 -67.8 -155.4
6 C -67.0 174.4 61.6 86.5 -159.4 -72.0 -166.2
7 A -53.4 -167.3 46.9 116.0 --- --- -118.4
8 G --- 144.5 40.9 83.8 -149.2 -70.5 -179.1
9 G -60.4 -174.5 44.8 80.6 -158.1 -68.8 -160.4
10 G -61.9 177.2 46.9 81.4 -166.4 -85.9 -162.1
11 G 164.7 -152.3 161.8 84.0 -107.3 -85.3 179.7
12 G -71.2 134.7 85.0 79.1 -131.9 -84.8 168.5
13 U -46.9 166.6 38.9 80.5 -118.3 -76.0 -168.2
14 U -54.4 157.4 53.3 79.2 --- --- -150.9
15 A --- 171.6 44.7 85.8 -147.2 -57.9 -166.0
16 G -71.8 176.9 54.7 82.0 -153.4 -73.5 -165.4
17 G -64.7 177.9 51.0 82.5 -148.3 -74.1 -162.9
18 C -60.2 171.1 52.9 81.2 -151.3 -70.9 -162.7
19 C -68.3 171.9 57.5 79.8 -152.8 -69.6 -165.4
20 G -55.9 169.0 55.0 79.3 -152.4 -85.9 -165.8
21 A -58.2 169.5 47.7 82.0 --- --- -154.4
22 G --- -179.2 57.5 89.4 -146.9 -67.9 -177.1
23 U -68.9 -174.7 48.8 84.1 -157.2 -71.2 -164.9
24 C -66.7 -170.6 43.9 80.9 -153.9 -57.2 -158.5
25 U 155.4 -169.2 -174.8 83.3 -152.4 -80.4 -173.1
26 A -56.0 -178.3 46.7 80.0 -140.6 -60.4 -167.4
27 G -52.2 166.4 60.8 129.0 --- --- -120.0
28 G --- -121.3 51.6 116.2 --- --- -61.8
29 G --- 176.1 45.2 88.9 -145.7 -76.5 -168.7
30 G -66.6 179.8 47.6 83.9 -144.6 -68.1 -162.1
31 C -62.8 170.6 47.1 83.5 -151.4 -72.7 -155.6
32 C -64.2 173.3 51.2 80.7 -154.5 -75.6 -157.9
33 C -62.0 175.8 51.6 79.4 -159.2 -65.0 -154.6
34 C -65.8 175.4 57.7 83.5 -165.4 -67.3 -163.4
35 A -56.0 -163.8 47.6 109.9 --- --- -119.1
36 G --- 147.6 39.1 82.8 -147.5 -71.8 -178.4
37 G -57.7 -175.9 45.3 81.5 -157.6 -69.1 -159.7
38 G -61.9 176.4 47.7 82.8 -165.0 -87.4 -163.0
39 G 163.8 -151.6 161.3 83.9 -106.5 -85.2 178.9
40 G -74.4 130.9 91.0 81.8 -131.3 -84.0 166.4
41 U -51.2 169.7 39.1 81.3 -118.6 -75.5 -169.3
42 U -56.5 159.5 54.4 79.8 --- --- -151.2
43 A --- 170.7 48.9 85.8 -143.6 -60.3 -164.8
44 G -67.1 172.8 50.3 80.6 -150.4 -74.6 -164.1
45 G -57.4 171.9 48.1 79.4 -148.8 -72.6 -166.0
46 C -60.7 171.7 51.3 80.5 -152.6 -69.8 -160.8
47 C -67.5 171.1 58.8 80.2 -152.0 -71.2 -166.1
48 G -55.9 170.0 54.2 80.1 -151.4 -84.6 -165.0
49 A -61.8 168.4 52.5 80.4 --- --- -157.4
50 G --- -178.4 58.1 90.1 -147.6 -68.1 -175.9
51 U -66.5 -177.3 48.3 81.9 -155.4 -72.2 -166.1
52 C -63.3 -175.5 43.7 80.5 -157.9 -53.4 -158.6
53 U 158.9 -170.2 -178.8 80.8 -150.4 -83.7 -174.7
54 A -52.7 177.7 48.7 81.6 -144.5 -56.3 -167.2
55 G -55.4 168.5 58.8 127.6 --- --- -122.7
56 G --- -120.7 52.2 116.8 --- --- -62.5

Strand II
base alpha beta gamma delta epsilon zeta chi
1 C -176.8 -151.8 138.1 81.0 --- --- -160.2
2 U -56.3 167.6 48.8 84.4 -172.1 -82.9 -163.8
3 G -56.0 173.3 51.5 84.9 -153.6 -69.9 -169.6
4 G -51.4 164.3 51.2 82.8 -156.7 -74.8 -174.8
5 G -61.3 174.4 50.7 79.7 -149.4 -76.1 -168.3
6 G -59.3 172.1 46.1 76.6 -149.2 -72.9 -167.6
7 U -69.4 175.5 53.5 82.0 -154.6 -63.6 -153.8
8 C -53.7 164.4 54.7 81.6 -153.3 -63.9 -163.1
9 C -58.7 165.1 52.5 81.2 -145.3 -75.6 -165.1
10 C -70.1 -172.2 48.6 84.1 -158.6 -75.5 -160.6
11 C -69.4 -170.1 49.5 84.7 -161.4 -69.6 -156.9
12 C --- -173.3 42.5 81.6 -153.6 -72.3 172.1
13 A --- -99.4 -166.4 104.9 --- --- -125.1
14 G --- -179.2 -43.4 111.4 --- --- -95.6
15 C -61.5 172.5 52.7 87.5 --- --- -160.4
16 C -68.8 174.2 57.3 81.4 -141.7 -70.1 -162.5
17 C -67.2 173.7 59.3 84.0 -154.2 -70.1 -163.9
18 G -65.9 174.3 52.9 81.3 -152.7 -71.9 -170.7
19 G -57.9 171.1 47.2 77.6 -153.1 -73.2 -168.5
20 C -66.0 -177.8 48.1 80.4 -141.4 -77.1 -157.4
21 G -68.6 170.9 50.1 82.4 -149.1 -65.8 -164.2
22 C -64.5 178.9 52.1 85.1 -147.4 -60.9 -165.3
23 A -65.3 175.1 51.2 82.6 -154.7 -75.2 -166.8
24 G -42.2 165.1 48.1 81.5 -150.8 -70.2 -165.6
25 G --- 142.0 46.1 78.3 -145.4 -86.6 -171.0
26 U --- 176.6 39.2 83.0 --- --- -149.1
27 C --- 101.5 173.5 130.8 --- --- -127.6
28 C --- 163.0 53.6 82.1 --- --- -159.8
29 C 174.3 -144.1 145.3 80.1 --- --- -162.6
30 U -59.4 167.9 53.3 84.2 -172.3 -86.3 -165.2
31 G -52.3 173.8 48.8 86.1 -153.7 -69.6 -166.3
32 G -54.0 169.2 49.6 83.4 -160.2 -74.1 -173.1
33 G -62.0 178.9 49.5 79.5 -152.8 -72.2 -169.3
34 G -61.2 175.9 44.2 77.4 -155.8 -68.2 -165.8
35 U -83.8 -163.8 50.6 81.3 -155.5 -62.8 -155.1
36 C -48.9 161.6 52.1 84.8 -170.9 -52.2 -169.1
37 C -59.2 166.1 52.2 80.6 -147.3 -75.0 -166.7
38 C -68.6 -175.1 50.1 83.9 -157.5 -75.7 -163.2
39 C -72.3 -169.0 50.0 84.3 -161.0 -71.7 -158.6
40 C --- -174.4 45.2 84.0 -154.7 -71.4 175.6
41 A --- -99.3 -166.6 105.1 --- --- -125.1
42 G --- 179.4 -44.3 111.8 --- --- -94.9
43 C -64.8 168.5 52.6 86.4 --- --- -159.1
44 C -69.7 172.2 60.3 82.4 -142.6 -68.9 -163.0
45 C -62.8 171.6 56.8 85.8 -153.3 -69.9 -164.9
46 G -67.4 173.5 56.1 80.6 -150.0 -73.6 -170.8
47 G -56.2 172.3 43.6 79.3 -153.5 -72.4 -164.9
48 C -72.5 -175.9 51.3 79.5 -144.0 -77.3 -160.9
49 G -70.9 176.3 49.6 82.9 -153.0 -61.9 -163.5
50 C -66.4 -178.6 52.6 86.6 -145.8 -60.7 -166.7
51 A -70.6 178.3 51.4 81.5 -156.4 -72.5 -168.5
52 G -44.5 168.9 48.2 82.9 -153.8 -68.1 -168.1
53 G --- 141.1 42.9 77.9 -148.7 -82.4 -170.2
54 U --- -171.4 36.6 84.9 --- --- -148.8
55 C --- 106.7 168.6 134.2 --- --- -129.0
56 C --- 163.8 53.9 83.3 --- --- -157.2
****************************************************************************
Sugar conformational parameters:

Note: v0: C4'-O4'-C1'-C2'
v1: O4'-C1'-C2'-C3'
v2: C1'-C2'-C3'-C4'
v3: C2'-C3'-C4'-O4'
v4: C3'-C4'-O4'-C1'

tm: amplitude of pseudorotation of the sugar ring
P: phase angle of pseudorotation of the sugar ring

Strand I
base v0 v1 v2 v3 v4 tm P Puckering
1 G 9.1 -28.1 35.5 -31.0 13.8 35.5 4.0 C3'-endo
2 G 6.2 -29.1 39.8 -37.2 19.6 40.4 9.9 C3'-endo
3 C 5.1 -28.8 40.1 -38.2 20.9 40.9 11.5 C3'-endo
4 C 5.6 -30.6 42.6 -40.4 22.0 43.4 11.3 C3'-endo
5 C 5.2 -28.4 40.1 -37.7 20.4 40.9 11.2 C3'-endo
6 C -0.3 -22.5 35.5 -36.5 23.3 37.6 19.0 C3'-endo
7 A -5.4 16.9 -21.6 19.3 -8.7 21.6 184.9 C3'-exo
8 G 8.8 -30.5 39.4 -35.4 16.8 39.6 6.0 C3'-endo
9 G 5.1 -29.5 41.5 -39.4 21.6 42.4 11.7 C3'-endo
10 G 6.2 -29.2 40.1 -37.6 19.7 40.8 10.1 C3'-endo
11 G 11.0 -32.0 39.8 -34.6 14.9 39.9 3.1 C3'-endo
12 G -3.4 -21.8 37.5 -40.4 27.7 40.9 23.3 C3'-endo
13 U 4.6 -27.2 38.3 -36.8 20.4 39.2 12.2 C3'-endo
14 U -0.5 -24.4 38.9 -40.0 25.6 41.2 19.2 C3'-endo
15 A 9.7 -30.8 39.2 -34.8 15.8 39.3 4.8 C3'-endo
16 G 3.1 -28.6 41.9 -41.0 23.8 43.3 14.4 C3'-endo
17 G 2.7 -26.4 38.7 -38.2 22.2 40.0 14.7 C3'-endo
18 C -0.3 -24.8 38.7 -40.0 25.4 40.9 19.0 C3'-endo
19 C 0.2 -24.6 38.2 -39.0 24.6 40.2 18.3 C3'-endo
20 G -4.1 -20.7 36.3 -39.6 27.6 39.8 24.4 C3'-endo
21 A 1.5 -25.6 38.7 -38.8 23.5 40.4 16.5 C3'-endo
22 G 8.3 -30.6 40.0 -36.2 17.5 40.3 6.8 C3'-endo
23 U 6.4 -29.3 39.6 -36.9 19.3 40.2 9.6 C3'-endo
24 C 4.1 -27.0 38.6 -37.2 20.9 39.6 12.8 C3'-endo
25 U 5.1 -27.8 38.8 -36.9 20.2 39.6 11.5 C3'-endo
26 A -1.2 -23.8 38.3 -40.0 26.2 40.8 20.2 C3'-endo
27 G -13.7 24.6 -25.7 19.0 -3.4 26.2 168.6 C2'-endo
28 G 0.8 12.9 -21.3 22.5 -14.4 22.8 200.7 C3'-exo
29 G 12.8 -31.6 37.2 -31.1 11.7 37.3 359.3 C2'-exo
30 G 5.8 -28.5 38.8 -36.7 19.6 39.4 10.4 C3'-endo
31 C 4.7 -28.7 40.2 -38.6 21.4 41.1 12.1 C3'-endo
32 C 4.9 -29.1 41.3 -39.3 21.7 42.2 12.0 C3'-endo
33 C 4.5 -30.2 43.2 -41.4 23.2 44.3 12.6 C3'-endo
34 C 1.8 -25.5 38.0 -38.2 23.1 39.6 16.2 C3'-endo
35 A -2.3 14.1 -20.5 19.8 -10.8 21.0 192.7 C3'-exo
36 G 9.8 -32.1 41.2 -36.5 16.9 41.3 5.2 C3'-endo
37 G 6.0 -29.8 41.0 -38.5 20.5 41.7 10.4 C3'-endo
38 G 5.9 -28.5 39.2 -36.7 19.4 39.9 10.2 C3'-endo
39 G 10.0 -31.4 39.6 -35.0 15.9 39.7 4.4 C3'-endo
40 G -3.7 -20.3 35.4 -38.6 26.6 38.7 24.0 C3'-endo
41 U 3.6 -26.1 37.5 -36.6 20.8 38.6 13.5 C3'-endo
42 U -1.7 -23.4 38.2 -40.1 26.3 40.9 20.8 C3'-endo
43 A 4.8 -28.3 39.5 -38.0 21.0 40.4 12.0 C3'-endo
44 G 3.0 -28.5 41.8 -40.9 23.9 43.2 14.5 C3'-endo
45 G 4.1 -27.6 39.4 -38.0 21.4 40.4 12.9 C3'-endo
46 C 0.4 -25.7 39.8 -40.6 25.3 41.8 18.0 C3'-endo
47 C -1.5 -24.5 39.6 -41.4 27.2 42.3 20.5 C3'-endo
48 G -4.9 -19.7 35.6 -39.4 27.9 39.5 25.6 C3'-endo
49 A 0.2 -24.4 38.1 -38.8 24.5 40.1 18.3 C3'-endo
50 G 12.1 -33.3 40.1 -34.2 14.0 40.1 1.4 C3'-endo
51 U 6.3 -30.3 41.3 -38.6 20.5 41.9 10.0 C3'-endo
52 C 3.2 -26.8 39.2 -38.2 22.1 40.4 14.1 C3'-endo
53 U 1.4 -25.6 38.9 -38.9 23.7 40.6 16.5 C3'-endo
54 A -4.0 -20.5 35.8 -39.1 27.3 39.3 24.4 C3'-endo
55 G -15.0 25.6 -26.1 18.7 -2.5 26.9 166.5 C2'-endo
56 G -0.2 13.9 -22.1 22.7 -13.9 23.3 198.3 C3'-exo

Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 C 1.1 -25.6 39.1 -39.5 24.2 40.9 17.1 C3'-endo
2 U 3.0 -24.0 34.9 -34.1 19.7 36.0 14.1 C3'-endo
3 G 0.1 -24.2 37.5 -38.4 24.2 39.5 18.3 C3'-endo
4 G 0.9 -24.1 36.7 -37.4 22.9 38.5 17.3 C3'-endo
5 G 2.9 -28.7 42.1 -41.5 24.3 43.5 14.8 C3'-endo
6 G 3.5 -29.3 42.8 -41.6 24.0 44.1 14.0 C3'-endo
7 U 2.9 -27.6 40.4 -39.7 23.3 41.8 14.7 C3'-endo
8 C 1.3 -24.5 36.9 -37.2 22.8 38.6 16.8 C3'-endo
9 C 1.9 -26.2 39.5 -39.4 23.6 41.1 16.0 C3'-endo
10 C 3.4 -25.4 36.5 -35.6 20.4 37.5 13.6 C3'-endo
11 C 4.2 -26.2 37.0 -35.6 19.8 37.9 12.4 C3'-endo
12 C 6.1 -28.7 39.2 -36.6 19.4 39.8 10.0 C3'-endo
13 A 3.1 9.3 -18.0 20.1 -14.3 20.2 207.1 C3'-exo
14 G -2.1 14.8 -21.5 21.1 -11.7 22.1 193.5 C3'-exo
15 C 4.6 -26.1 36.2 -34.8 19.2 37.0 11.8 C3'-endo
16 C 0.4 -25.1 39.0 -39.6 24.7 41.0 18.0 C3'-endo
17 C 5.5 -27.8 38.0 -36.0 19.3 38.7 10.7 C3'-endo
18 G 0.8 -25.8 39.7 -40.3 24.8 41.6 17.5 C3'-endo
19 G -0.9 -24.7 39.5 -41.0 26.3 41.9 19.7 C3'-endo
20 C 4.2 -29.1 41.3 -40.0 22.7 42.4 13.0 C3'-endo
21 G 4.3 -29.6 42.1 -40.4 22.6 43.1 12.7 C3'-endo
22 C 5.3 -26.7 36.7 -34.7 18.6 37.4 10.6 C3'-endo
23 A 3.7 -27.2 39.1 -37.8 21.7 40.2 13.4 C3'-endo
24 G 4.9 -30.0 42.1 -40.2 22.3 43.1 12.0 C3'-endo
25 G 6.7 -31.2 42.8 -39.8 20.9 43.5 9.8 C3'-endo
26 U 7.2 -30.2 40.4 -37.2 19.0 40.8 8.6 C3'-endo
27 C -10.8 22.4 -25.1 20.1 -5.9 25.2 174.6 C2'-endo
28 C 0.5 -24.5 37.9 -38.6 24.0 39.8 17.9 C3'-endo
29 C -2.7 -22.5 37.9 -40.7 27.1 41.0 22.4 C3'-endo
30 U 2.2 -23.9 35.2 -35.0 20.8 36.5 15.3 C3'-endo
31 G -0.9 -21.6 34.6 -36.0 23.2 36.8 20.0 C3'-endo
32 G 1.1 -23.9 36.5 -36.8 22.5 38.2 17.0 C3'-endo
33 G 3.3 -27.9 40.5 -39.6 22.9 41.8 14.1 C3'-endo
34 G 2.9 -28.8 42.5 -41.7 24.5 43.9 14.8 C3'-endo
35 U 2.9 -26.7 39.1 -38.4 22.4 40.4 14.5 C3'-endo
36 C -0.2 -24.2 38.2 -39.2 24.7 40.3 18.8 C3'-endo
37 C 2.9 -27.2 40.1 -39.3 23.0 41.4 14.6 C3'-endo
38 C 1.7 -24.6 36.9 -37.0 22.2 38.4 16.1 C3'-endo
39 C 3.1 -25.3 37.0 -36.1 20.7 38.1 14.0 C3'-endo
40 C 5.5 -27.8 38.2 -36.1 19.3 38.9 10.7 C3'-endo
41 A 2.8 9.4 -17.8 19.8 -13.9 19.9 206.3 C3'-exo
42 G -1.2 13.8 -20.9 20.9 -12.2 21.7 195.8 C3'-exo
43 C 1.9 -23.8 35.3 -35.3 21.2 36.7 15.8 C3'-endo
44 C -2.9 -22.0 37.2 -39.9 27.0 40.3 22.6 C3'-endo
45 C 4.2 -26.1 36.9 -35.5 19.9 37.8 12.5 C3'-endo
46 G 0.0 -25.9 40.6 -41.4 26.2 42.8 18.5 C3'-endo
47 G 2.6 -28.1 41.7 -40.8 24.1 43.2 14.9 C3'-endo
48 C 3.8 -27.9 40.2 -39.1 22.2 41.4 13.5 C3'-endo
49 G 6.1 -31.0 42.6 -40.0 21.4 43.3 10.5 C3'-endo
50 C 5.0 -27.0 37.6 -35.8 19.4 38.4 11.3 C3'-endo
51 A 5.6 -28.9 39.8 -37.5 20.2 40.5 10.7 C3'-endo
52 G 0.8 -25.7 39.2 -39.7 24.6 41.1 17.4 C3'-endo
53 G 7.3 -31.9 43.0 -39.9 20.5 43.5 9.1 C3'-endo
54 U 10.5 -32.3 40.3 -35.3 15.7 40.4 3.8 C3'-endo
55 C -8.1 20.6 -24.7 21.2 -8.4 24.7 180.6 C3'-exo
56 C 0.8 -24.3 37.1 -37.6 23.3 38.9 17.4 C3'-endo
****************************************************************************
Same strand P--P and C1'--C1' virtual bond distances

Strand I Strand II
base P--P C1'--C1' base P--P C1'--C1'
1 G/G 5.7 6.1 1 C/U 6.1 5.4
2 G/C 5.6 5.3 2 U/G 5.9 5.2
3 C/C 5.8 5.4 3 G/G 6.0 5.4
4 C/C 6.0 5.5 4 G/G 5.7 5.2
5 C/C 5.9 5.3 5 G/G 5.6 5.4
6 C/A 6.2 5.9 6 G/U 5.8 5.0
7 A/G 10.6 8.4 7 U/C 6.1 5.2
8 G/G 5.8 6.0 8 C/C 5.8 5.3
9 G/G 5.6 5.3 9 C/C 5.6 5.0
10 G/G 5.8 5.4 10 C/C 5.6 5.7
11 G/G 6.1 5.3 11 C/C 5.4 6.1
12 G/U 6.3 5.8 12 C/A 13.7 9.1
13 U/U 4.9 5.5 13 A/G 14.0 6.9
14 U/A --- --- 14 G/C --- ---
15 A/G 5.7 5.4 15 C/C 5.7 5.4
16 G/G 5.8 5.6 16 C/C 6.1 5.5
17 G/C 5.6 5.4 17 C/G 5.8 5.5
18 C/C 5.9 5.4 18 G/G 5.8 5.5
19 C/G 6.0 5.3 19 G/C 5.4 5.7
20 G/A 5.9 5.6 20 C/G 5.7 5.6
21 A/G 15.0 12.7 21 G/C 5.6 5.0
22 G/U 5.7 5.8 22 C/A 5.8 5.8
23 U/C 5.7 5.9 23 A/G 5.8 5.5
24 C/U 5.4 5.2 24 G/G 5.8 5.6
25 U/A 6.9 6.1 25 G/U 16.5 11.3
26 A/G 5.3 5.3 26 U/C 11.1 4.5
27 G/G --- --- 27 C/C --- ---
28 G/G --- --- 28 C/C --- ---
29 G/G 5.6 6.0 29 C/U 6.3 5.4
30 G/C 5.5 5.2 30 U/G 5.9 5.1
31 C/C 5.7 5.4 31 G/G 6.0 5.5
32 C/C 5.8 5.5 32 G/G 5.7 5.3
33 C/C 5.8 5.2 33 G/G 5.5 5.4
34 C/A 6.1 5.9 34 G/U 5.5 5.0
35 A/G 10.5 8.5 35 U/C 6.2 5.6
36 G/G 5.6 6.0 36 C/C 5.8 5.1
37 G/G 5.6 5.3 37 C/C 5.7 5.1
38 G/G 5.9 5.4 38 C/C 5.6 5.6
39 G/G 6.1 5.3 39 C/C 5.6 6.1
40 G/U 6.4 5.9 40 C/A 13.7 9.1
41 U/U 4.8 5.5 41 A/G 14.4 7.1
42 U/A --- --- 42 G/C --- ---
43 A/G 5.6 5.4 43 C/C 5.9 5.3
44 G/G 5.8 5.5 44 C/C 6.1 5.5
45 G/C 5.7 5.4 45 C/G 5.9 5.5
46 C/C 5.8 5.3 46 G/G 5.7 5.4
47 C/G 6.0 5.4 47 G/C 5.4 5.7
48 G/A 5.8 5.5 48 C/G 5.7 5.7
49 A/G 15.0 12.9 49 G/C 5.6 5.3
50 G/U 5.8 5.8 50 C/A 5.8 5.7
51 U/C 5.6 5.9 51 A/G 5.9 5.6
52 C/U 5.4 5.2 52 G/G 5.8 5.5
53 U/A 6.9 6.1 53 G/U 16.4 11.4
54 A/G 5.6 5.2 54 U/C 11.2 4.3
55 G/G --- --- 55 C/C --- ---
****************************************************************************
Helix radius (radial displacement of P, O4', and C1' atoms in local helix
frame of each dimer)

Strand I Strand II
step P O4' C1' P O4' C1'
1 GG/UC 7.5 7.9 7.4 10.0 8.4 7.7
2 GC/GU 8.5 8.1 7.3 8.6 7.3 6.4
3 CC/GG 8.5 8.2 7.7 10.1 9.3 8.6
4 CC/GG 10.6 10.1 9.3 7.9 7.8 7.3
5 CC/GG 8.2 8.6 8.1 10.3 10.1 9.5
6 CA/UG 10.7 10.1 9.3 6.3 7.1 6.7
7 AG/CU 10.1 9.0 8.1 7.2 5.6 4.9
8 GG/CC 10.8 10.1 9.4 8.1 7.7 7.2
9 GG/CC 8.4 8.0 7.4 9.7 9.2 8.4
10 GG/CC 10.3 10.2 9.6 9.0 9.7 9.1
11 GG/CC 7.3 7.4 7.1 11.6 11.0 10.2
12 GU/AC 9.1 8.3 7.3 7.0 5.5 5.0
13 UU/GA 5.7 3.6 2.3 6.0 7.5 7.2
14 UA/CG ---- ---- ---- ---- ---- ----
15 AG/CC 8.7 8.7 8.0 8.2 6.9 5.9
16 GG/CC 9.1 9.1 8.6 9.8 9.2 8.6
17 GC/GC 9.1 8.5 7.7 9.1 8.3 7.6
18 CC/GG 9.3 8.9 8.3 9.3 9.2 8.5
19 CG/CG 10.7 10.3 9.9 8.7 9.6 9.2
20 GA/GC 11.6 10.0 9.1 7.0 6.9 6.3
21 AG/CG 10.9 11.6 10.7 4.8 5.3 5.0
22 GU/AC 8.8 8.8 8.2 9.4 9.2 8.4
23 UC/GA 9.9 9.8 9.1 8.0 8.3 7.8
24 CU/GG 9.5 8.2 7.9 11.6 12.1 11.4
25 UA/UG 7.7 6.8 5.8 7.4 6.4 5.5
26 AG/CU 9.2 6.3 5.4 11.2 7.6 6.7
27 GG/CC ---- ---- ---- ---- ---- ----
28 GG/CC ---- ---- ---- ---- ---- ----
29 GG/UC 7.1 7.7 7.2 10.3 8.5 7.8
30 GC/GU 8.7 8.1 7.4 8.4 7.1 6.2
31 CC/GG 8.3 8.1 7.6 10.0 9.3 8.6
32 CC/GG 10.1 10.0 9.3 8.4 8.4 7.9
33 CC/GG 8.2 8.5 8.0 10.0 9.8 9.2
34 CA/UG 10.3 9.9 9.1 6.4 7.0 6.6
35 AG/CU 9.9 9.2 8.4 7.5 6.3 5.7
36 GG/CC 11.0 10.2 9.5 7.8 7.5 7.0
37 GG/CC 8.4 8.1 7.4 9.7 9.3 8.5
38 GG/CC 10.4 10.1 9.5 9.1 9.7 9.1
39 GG/CC 7.6 7.9 7.6 11.5 11.1 10.4
40 GU/AC 9.2 8.3 7.3 7.1 5.5 5.0
41 UU/GA 6.2 4.0 2.7 5.7 7.2 6.9
42 UA/CG ---- ---- ---- ---- ---- ----
43 AG/CC 8.3 8.2 7.5 8.4 6.9 6.0
44 GG/CC 8.5 8.7 8.2 10.4 9.5 8.9
45 GC/GC 9.5 8.9 8.1 8.7 8.1 7.4
46 CC/GG 9.4 9.1 8.5 9.5 9.5 8.9
47 CG/CG 10.0 9.8 9.4 9.4 9.9 9.4
48 GA/GC 11.9 10.3 9.5 6.7 6.9 6.4
49 AG/CG 10.6 11.5 10.6 4.9 5.5 5.2
50 GU/AC 8.5 8.4 7.8 9.6 9.2 8.4
51 UC/GA 9.8 9.7 9.0 7.8 8.2 7.7
52 CU/GG 9.6 8.3 8.1 12.0 12.4 11.7
53 UA/UG 7.8 6.9 5.9 7.4 6.4 5.5
54 AG/CU 9.3 6.3 5.4 11.3 7.7 6.8
55 GG/CC ---- ---- ---- ---- ---- ----
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step

bp Px Py Pz Hx Hy Hz
1 GG/UC 24.35 86.51 67.40 -0.74 0.14 -0.66
2 GC/GU 23.68 87.13 65.30 -0.83 -0.16 -0.53
3 CC/GG 19.92 86.87 64.82 -0.79 -0.21 -0.58
4 CC/GG 17.79 84.44 64.47 -0.88 -0.12 -0.46
5 CC/GG 15.27 86.06 61.06 -0.69 -0.19 -0.70
6 CA/UG 12.26 84.52 61.67 -0.64 0.03 -0.77
7 AG/CU 9.17 82.21 61.29 -0.95 0.02 -0.32
8 GG/CC 7.53 82.29 57.56 -0.85 -0.08 -0.52
9 GG/CC 4.30 80.18 57.18 -0.88 -0.08 -0.46
10 GG/CC 3.75 78.71 54.78 -0.85 -0.36 -0.37
11 GG/CC -1.51 78.82 54.67 -0.83 0.09 -0.54
12 GU/AC -1.05 78.95 50.08 -0.84 -0.19 -0.52
13 UU/GA -3.42 80.96 46.91 -0.92 -0.16 -0.35
14 UA/CG ---- ---- ---- ---- ---- ----
15 AG/CC 19.27 38.11 56.29 -0.42 0.89 -0.17
16 GG/CC 18.82 41.75 57.31 -0.43 0.88 -0.21
17 GC/GC 16.33 43.83 56.29 -0.53 0.83 -0.14
18 CC/GG 16.11 46.55 55.71 -0.42 0.87 -0.24
19 CG/CG 16.70 48.97 54.42 -0.44 0.75 -0.50
20 GA/GC 15.39 52.49 56.57 -0.22 0.94 -0.26
21 AG/CG 16.34 54.85 55.65 -0.35 0.83 -0.44
22 GU/AC 12.88 58.31 57.14 -0.12 0.90 -0.42
23 UC/GA 12.15 60.55 54.77 -0.09 0.94 -0.32
24 CU/GG 13.22 63.98 57.19 -0.26 0.91 -0.31
25 UA/UG 10.51 64.20 51.06 -0.40 0.78 -0.47
26 AG/CU 7.10 65.46 49.36 -0.54 0.78 -0.33
27 GG/CC ---- ---- ---- ---- ---- ----
28 GG/CC ---- ---- ---- ---- ---- ----
29 GG/UC 83.93 87.05 130.14 -0.82 0.09 -0.57
30 GC/GU 83.29 87.55 128.02 -0.88 -0.28 -0.38
31 CC/GG 79.53 87.13 128.17 -0.84 -0.27 -0.47
32 CC/GG 77.02 84.92 128.23 -0.88 -0.18 -0.43
33 CC/GG 74.62 85.57 125.32 -0.82 -0.24 -0.52
34 CA/UG 71.65 83.82 126.21 -0.77 -0.06 -0.63
35 AG/CU 69.25 82.32 125.69 -0.97 -0.02 -0.22
36 GG/CC 67.06 82.49 123.35 -0.92 -0.05 -0.38
37 GG/CC 63.68 80.10 123.38 -0.97 -0.10 -0.24
38 GG/CC 62.54 78.80 121.22 -0.91 -0.34 -0.22
39 GG/CC 57.79 78.33 122.25 -0.96 0.04 -0.28
40 GU/AC 56.84 79.01 117.46 -0.92 -0.18 -0.36
41 UU/GA 53.95 80.64 114.77 -0.98 -0.15 -0.12
42 UA/CG ---- ---- ---- ---- ---- ----
43 AG/CC 77.88 38.60 118.64 -0.44 0.89 -0.10
44 GG/CC 77.78 42.44 119.88 -0.48 0.86 -0.17
45 GC/GC 75.20 44.08 120.15 -0.49 0.87 -0.02
46 CC/GG 75.08 46.96 119.19 -0.45 0.88 -0.15
47 CG/CG 74.50 49.50 118.08 -0.54 0.80 -0.27
48 GA/GC 74.34 52.71 120.30 -0.32 0.92 -0.22
49 AG/CG 74.73 55.10 119.59 -0.46 0.83 -0.33
50 GU/AC 72.06 58.72 121.72 -0.17 0.87 -0.46
51 UC/GA 70.75 60.62 119.35 -0.16 0.95 -0.26
52 CU/GG 72.08 64.34 121.95 -0.31 0.91 -0.28
53 UA/UG 68.23 64.34 116.17 -0.47 0.80 -0.37
54 AG/CU 64.53 65.64 115.00 -0.59 0.79 -0.19
55 GG/CC ---- ---- ---- ---- ---- ----