Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~igogo/Term3/1sz1_e.out Дата изменения: Sun Nov 5 21:43:46 2006 Дата индексирования: Tue Oct 2 07:06:05 2012 Кодировка:

****************************************************************************
This structure has broken O3'[i] to P[i+1] linkages
****************************************************************************
3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
****************************************************************************
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.
****************************************************************************
File name: 1sz1_e.pdb
Date and time: Sun Nov 5 21:42:26 2006

Number of base-pairs: 29
Number of atoms: 1648
****************************************************************************
HEADER TRANSFERASE/RNA 02-APR-04 1SZ1
COMPND TRNA NUCLEOTIDYLTRANSFERASE;
EXPDTA X-RAY DIFFRACTION
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

Strand I Strand II Helix
1 (0.010) E:...1_:[..G]G-----C[..C]:..72_:E (0.013) |
2 (0.007) E:...2_:[..C]C-----G[..G]:..71_:E (0.008) |
3 (0.007) E:...3_:[..G]G-----C[..C]:..70_:E (0.027) |
4 (0.005) E:...4_:[..G]G-*---U[..U]:..69_:E (0.006) |
5 (0.008) E:...5_:[..A]A-----U[..U]:..68_:E (0.008) |
6 (0.009) E:...6_:[..U]U-----A[..A]:..67_:E (0.015) |
7 (0.008) E:...7_:[..U]Ux----A[..A]:..66_:E (0.011) |
8 (0.015) E:..49_:[5MC]c-----G[..G]:..65_:E (0.017) |
9 (0.014) E:..50_:[..U]U-----A[..A]:..64_:E (0.014) |
10 (0.009) E:..51_:[..G]G-----C[..C]:..63_:E (0.008) |
11 (0.013) E:..52_:[..U]U-----A[..A]:..62_:E (0.020) |
12 (0.014) E:..53_:[..G]G----xC[..C]:..61_:E (0.006) |
13 (0.010) E:..54_:[5MU]u-**-xa[1MA]:..58_:E (0.044) |
14 (0.019) E:..55_:[PSU]Px**+xG[..G]:..18_:E (0.024) x
15 (0.006) E:..36_:[..A]Ax*---U[..U]:..33_:E (0.008) |
16 (0.008) E:..38_:[..A]A-*---c[OMC]:..32_:E (0.006) |
17 (0.018) E:..39_:[PSU]P-*---A[..A]:..31_:E (0.005) |
18 (0.009) E:..40_:[5MC]c-----G[..G]:..30_:E (0.009) |
19 (0.006) E:..41_:[..U]U-----A[..A]:..29_:E (0.006) |
20 (0.012) E:..42_:[..G]G-----C[..C]:..28_:E (0.005) |
21 (0.011) E:..43_:[..G]G-----C[..C]:..27_:E (0.006) |
22 (0.008) E:..44_:[..A]Ax*---g[M2G]:..26_:E (0.009) |
23 (0.016) E:..10_:[2MG]g-----C[..C]:..25_:E (0.007) |
24 (0.006) E:..11_:[..C]C-----G[..G]:..24_:E (0.015) |
25 (0.009) E:..12_:[..U]U-----A[..A]:..23_:E (0.011) |
26 (0.011) E:..13_:[..C]C----xG[..G]:..22_:E (0.011) |
27 (0.016) E:..14_:[..A]A-**-xU[..U]:...8_:E (0.007) |
28 (0.017) E:..15_:[..G]Gx**+xC[..C]:..48_:E (0.011) x
29 (0.017) E:..19_:[..G]G-----C[..C]:..56_:E (0.011) +

Note: This structure contains 9[4] non-Watson-Crick base-pairs.
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 G-----C [3] O6 - N4 3.69 N1 - N3 3.52 N2 - O2 3.36
2 C-----G [3] O2 - N2 2.97 N3 - N1 3.44 N4 - O6 3.89
3 G-----C [3] O6 - N4 2.79 N1 - N3 2.85 N2 - O2 2.85
4 G-*---U [2] O6 - N3 2.97 N1 - O2 2.77
5 A-----U [2] N6 - O4 3.03 N1 - N3 2.68
6 U-----A [2] N3 - N1 2.60 O4 - N6 3.05
7 U-----A [2] N3 - N1 2.67 O4 - N6 2.86
8 c-----G [3] O2 - N2 2.75 N3 - N1 2.79 N4 - O6 2.69
9 U-----A [2] N3 - N1 2.73 O4 - N6 2.71
10 G-----C [3] O6 - N4 3.07 N1 - N3 2.83 N2 - O2 2.61
11 U-----A [2] N3 - N1 2.79 O4 - N6 2.84
12 G-----C [3] O6 - N4 2.96 N1 - N3 2.87 N2 - O2 2.67
13 u-**--a [2] N3 - N7 2.88 O2 - N6 2.44
14 P-**+-G [2] O4 * N2 2.80 O4'* O6 3.69
15 A-*---U [1] O2P* O2 2.31
16 A-*---c [1] N6 - O2 2.81
17 P-*---A [1] O2 * N1 2.71
18 c-----G [3] O2 - N2 2.79 N3 - N1 2.82 N4 - O6 2.78
19 U-----A [2] N3 - N1 2.87 O4 - N6 3.45
20 G-----C [3] O6 - N4 2.70 N1 - N3 2.71 N2 - O2 2.63
21 G-----C [3] O6 - N4 2.76 N1 - N3 2.74 N2 - O2 2.76
22 A-*---g [2] N6 - O6 2.92 N1 - N1 2.84
23 g-----C [3] O6 - N4 2.77 N1 - N3 2.72 N2 - O2 2.56
24 C-----G [3] O2 - N2 2.61 N3 - N1 2.75 N4 - O6 3.00
25 U-----A [2] N3 - N1 2.87 O4 - N6 2.87
26 C-----G [3] O2 - N2 2.72 N3 - N1 2.91 N4 - O6 3.01
27 A-**--U [3] O2P* O4 3.86 N7 - N3 2.77 N6 - O2 2.99
28 G-**+-C [2] N1 - O2 2.69 N2 - N3 2.89
29 G-----C [3] O6 - N4 3.21 N1 - N3 2.85 N2 - O2 2.53
****************************************************************************
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 GC/GC 4.90( 2.18) 0.00( 0.00) 0.00( 0.00) 3.14( 0.97) 8.04( 3.15)
2 CG/CG 0.46( 0.00) 0.00( 0.00) 2.70( 0.36) 1.22( 0.22) 4.38( 0.58)
3 GG/UC 2.29( 0.84) 0.00( 0.00) 0.10( 0.00) 0.24( 0.00) 2.63( 0.84)
4 GA/UU 3.70( 2.17) 0.00( 0.00) 0.00( 0.00) 2.45( 0.84) 6.16( 3.00)
5 AU/AU 4.87( 3.49) 0.00( 0.00) 0.00( 0.00) 3.06( 1.74) 7.93( 5.23)
6 UU/AA 1.15( 0.06) 0.00( 0.00) 0.00( 0.00) 3.11( 2.57) 4.26( 2.63)
7 Uc/GA 0.85( 0.00) 0.00( 0.00) 0.00( 0.00) 3.35( 1.83) 4.20( 1.83)
8 cU/AG 0.00( 0.00) 0.00( 0.00) 0.43( 0.00) 3.85( 2.83) 4.29( 2.83)
9 UG/CA 0.17( 0.00) 0.00( 0.00) 2.61( 1.29) 0.14( 0.00) 2.92( 1.29)
10 GU/AC 6.88( 3.89) 0.00( 0.00) 0.00( 0.00) 3.55( 1.99) 10.42( 5.88)
11 UG/CA 0.00( 0.00) 0.00( 0.00) 4.47( 2.21) 0.00( 0.00) 4.47( 2.21)
12 Gu/aC 8.84( 4.29) 0.00( 0.00) 0.00( 0.00) 4.76( 0.96) 13.60( 5.24)
13 uP/Ga 5.53( 1.75) 0.00( 0.00) 0.00( 0.00) 7.72( 3.51) 13.25( 5.26)
14 PA/UG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
15 AA/cU 0.67( 0.00) 0.00( 0.00) 0.00( 0.00) 2.79( 1.20) 3.46( 1.20)
16 AP/Ac 4.52( 1.97) 0.00( 0.00) 0.00( 0.00) 6.78( 3.74) 11.30( 5.71)
17 Pc/GA 1.78( 0.00) 0.00( 0.00) 0.00( 0.00) 5.13( 3.30) 6.91( 3.30)
18 cU/AG 0.07( 0.00) 0.00( 0.00) 0.72( 0.00) 0.72( 0.72) 1.51( 0.72)
19 UG/CA 0.08( 0.00) 0.00( 0.00) 3.08( 1.77) 0.04( 0.00) 3.20( 1.77)
20 GG/CC 2.98( 1.48) 0.00( 0.00) 0.37( 0.00) 0.19( 0.00) 3.54( 1.48)
21 GA/gC 3.67( 1.03) 0.00( 0.00) 0.00( 0.00) 5.46( 2.63) 9.13( 3.65)
22 Ag/Cg 0.00( 0.00) 0.00( 0.00) 1.28( 0.04) 0.34( 0.07) 1.61( 0.11)
23 gC/GC 3.39( 0.62) 0.00( 0.00) 0.00( 0.00) 7.16( 3.86) 10.54( 4.49)
24 CU/AG 1.06( 0.02) 0.00( 0.00) 0.03( 0.00) 2.48( 2.17) 3.57( 2.19)
25 UC/GA 1.26( 0.30) 0.00( 0.00) 0.00( 0.00) 1.01( 0.05) 2.27( 0.36)
26 CA/UG 0.00( 0.00) 1.99( 0.00) 2.25( 0.19) 0.00( 0.00) 4.25( 0.19)
27 AG/CU 2.41( 0.68) 0.00( 0.00) 0.16( 0.00) 0.00( 0.00) 2.57( 0.68)
28 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 128.81 42.89 39.20 0.94 -0.34 0.09
2 C-G 131.35 40.32 37.90 0.94 -0.33 0.10
3 G-C 134.00 38.11 37.45 0.96 -0.25 0.10
4 G-U 136.98 37.42 36.04 0.97 -0.14 0.19
5 A-U 140.49 37.38 35.28 0.98 -0.07 0.19
6 U-A 143.93 39.00 35.61 0.96 0.03 0.28
7 U-A 146.87 40.30 36.54 0.89 0.06 0.45
8 c-G 149.33 42.42 38.72 0.86 0.03 0.51
9 U-A 151.33 44.01 41.72 0.84 -0.10 0.53
10 G-C 153.30 43.12 44.63 0.82 -0.19 0.53
11 U-A 155.30 41.50 46.94 0.84 -0.23 0.49
12 G-C 157.75 38.47 47.99 0.87 -0.31 0.38
13 u-a 159.54 34.58 48.64 0.82 -0.37 0.44
14 P+G 163.84 35.94 48.84 0.90 -0.25 0.35
15 A-U 165.22 15.55 0.32 -0.38 0.13 0.91
16 A-c 165.70 14.09 5.85 0.03 0.24 0.97
17 P-A 166.92 14.49 8.95 -0.01 0.45 0.90
18 c-G 168.08 16.52 11.41 -0.07 0.54 0.84
19 U-A 167.73 20.01 13.43 -0.17 0.54 0.83
20 G-C 167.14 23.12 14.95 -0.30 0.51 0.81
21 G-C 165.21 25.63 16.70 -0.38 0.46 0.80
22 A-g 162.90 27.66 18.66 -0.49 0.36 0.79
23 g-C 157.83 28.18 19.54 -0.49 -0.01 0.87
24 C-G 155.70 26.54 22.03 -0.42 0.05 0.90
25 U-A 154.96 25.80 25.36 -0.34 0.15 0.93
26 C-G 156.57 27.17 28.66 -0.25 0.14 0.96
27 A-U 156.91 25.41 32.32 -0.22 0.05 0.97
28 G+C 158.56 29.22 35.71 -0.25 0.17 0.95
29 G-C 168.42 28.88 50.44 0.75 -0.58 0.32
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.22 0.54 0.18 7.73 -16.83 2.45
2 C-G 1.02 0.36 0.19 1.02 -15.76 10.10
3 G-C 0.08 -0.21 0.46 0.79 -12.19 -3.40
4 G-U -2.23 -0.46 0.67 9.64 -6.89 0.20
5 A-U 0.09 -0.21 0.32 4.52 -19.06 3.79
6 U-A -0.38 -0.25 0.19 -6.84 -21.62 7.74
7 U-A -0.02 -0.25 -0.11 -1.19 -5.53 2.48
8 c-G -0.10 -0.23 0.04 -0.73 -7.20 -2.20
9 U-A -0.13 -0.25 0.12 -3.48 -5.88 -2.35
10 G-C -0.31 -0.16 0.04 -4.60 -13.23 4.23
11 U-A -0.56 -0.16 0.08 -0.99 -6.85 -0.52
12 G-C -0.35 -0.15 -0.18 -10.71 -6.58 1.90
13 u-a 3.85 -1.70 0.05 4.01 4.09 -95.70
14 P+G 0.52 -5.73 0.31 17.12 1.13 -92.59
15 A-U -6.40 -7.28 1.47 -13.71 9.99 -38.88
16 A-c -6.41 -2.02 0.75 -3.62 1.31 -0.65
17 P-A -2.07 -0.14 0.30 6.58 -14.91 -5.09
18 c-G -0.76 -0.21 -0.05 4.83 -14.45 -1.77
19 U-A -0.06 0.05 0.36 -5.05 -8.85 12.11
20 G-C -0.01 -0.35 0.47 -4.80 -9.55 -1.52
21 G-C -0.19 -0.32 0.24 -9.47 -20.13 -2.97
22 A-g 0.45 1.38 -0.37 -20.23 -36.40 -14.66
23 g-C -0.22 -0.31 -0.05 -4.52 -8.19 1.11
24 C-G 0.22 -0.24 0.19 -6.79 -18.46 4.10
25 U-A -0.04 -0.12 0.42 -9.53 -3.80 -2.70
26 C-G 0.26 -0.10 -0.08 5.81 -2.36 1.58
27 A-U -4.12 -1.90 0.53 5.23 10.97 -101.14
28 G+C 0.12 3.91 0.11 1.83 0.55 152.11
29 G-C -0.16 -0.25 0.84 -18.85 -27.52 0.11
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.62 -0.58 0.26 -1.93 -9.45 -5.59
s.d. 2.03 1.94 0.36 8.38 10.53 43.25
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GC/GC 0.65 -2.16 3.11 -0.78 -0.03 41.01
2 CG/CG -0.76 -1.35 3.12 -2.34 3.58 20.19
3 GG/UC 0.24 -1.83 2.82 -5.74 5.42 23.25
4 GA/UU -0.21 -1.43 3.29 1.37 3.87 42.98
5 AU/AU 0.51 -1.69 3.38 2.05 7.49 29.25
6 UU/AA -0.20 -1.16 3.13 1.98 10.39 34.05
7 Uc/GA -0.47 -2.06 3.30 0.37 4.42 33.75
8 cU/AG -0.91 -2.10 3.21 -1.55 7.56 29.04
9 UG/CA 0.27 -1.43 3.33 1.14 5.06 31.52
10 GU/AC 0.26 -1.31 3.19 -1.10 3.49 28.72
11 UG/CA 0.98 -1.98 3.38 2.01 7.63 33.74
12 Gu/aC -1.77 -2.45 3.09 -0.32 -5.80 89.14
13 uP/Ga 1.93 -2.30 3.38 8.70 4.37 45.86
14 PA/UG ---- ---- ---- ---- ---- ----
15 AA/cU 0.70 -2.76 4.98 0.98 25.04 60.84
16 AP/Ac -0.24 -1.36 3.06 -6.81 11.08 47.89
17 Pc/GA 0.00 -1.41 3.09 -0.67 7.08 38.71
18 cU/AG 0.78 -1.66 3.61 -2.08 4.98 41.00
19 UG/CA -0.30 -1.78 3.02 -0.14 7.73 26.01
20 GG/CC -0.08 -1.52 3.28 1.46 5.66 36.20
21 GA/gC -0.67 -1.10 3.41 5.61 6.02 38.42
22 Ag/Cg -2.88 -2.66 3.38 14.66 16.08 58.73
23 gC/GC -0.95 -1.61 3.14 -2.68 4.59 38.16
24 CU/AG -0.28 -1.20 3.26 -1.16 7.46 32.31
25 UC/GA 1.74 -2.07 2.84 5.60 0.96 27.20
26 CA/UG -2.38 -0.29 3.29 -0.33 -5.29 57.85
27 AG/CU 2.42 -3.45 3.31 0.94 7.17 -63.66
28 GG/CC ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.06 -1.77 3.28 0.81 6.00 35.47
s.d. 1.20 0.64 0.39 4.28 5.93 24.90
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GC/GC -3.08 -1.01 3.10 -0.04 1.11 41.01
2 CG/CG -5.22 1.17 2.91 10.08 6.58 20.63
3 GG/UC -5.64 -1.96 2.22 12.97 13.75 24.54
4 GA/UU -2.32 0.41 3.14 5.26 -1.86 43.17
5 AU/AU -4.72 -0.56 2.90 14.52 -3.97 30.25
6 UU/AA -3.27 0.58 2.66 17.23 -3.28 35.61
7 Uc/GA -4.20 0.86 3.00 7.58 -0.64 34.03
8 cU/AG -5.46 1.47 2.64 14.75 3.03 30.03
9 UG/CA -3.50 -0.29 3.07 9.24 -2.07 31.94
10 GU/AC -3.35 -0.75 3.00 7.00 2.21 28.94
11 UG/CA -4.47 -1.34 2.93 12.92 -3.41 34.63
12 Gu/aC -1.63 1.25 3.22 -4.13 0.23 89.29
13 uP/Ga -3.27 -1.67 3.45 5.54 -11.02 46.83
14 PA/UG ---- ---- ---- ---- ---- ----
15 AA/cU -4.00 -0.59 3.73 23.68 -0.93 65.34
16 AP/Ac -2.36 -0.16 2.71 13.37 8.22 49.53
17 Pc/GA -2.85 -0.07 2.80 10.57 1.00 39.33
18 cU/AG -2.92 -1.34 3.35 7.07 2.95 41.34
19 UG/CA -5.45 0.62 2.41 16.71 0.30 27.12
20 GG/CC -3.16 0.32 3.01 9.04 -2.34 36.66
21 GA/gC -2.35 1.67 3.09 9.02 -8.41 39.26
22 Ag/Cg -3.19 3.36 1.96 15.82 -14.42 62.29
23 gC/GC -2.97 1.13 3.00 6.98 4.07 38.52
24 CU/AG -3.31 0.30 2.93 13.18 2.05 33.15
25 UC/GA -4.52 -2.39 3.06 2.01 -11.75 27.78
26 CA/UG -0.02 2.44 3.32 -5.46 0.34 58.07
27 AG/CU 2.93 2.33 3.61 -6.78 0.88 -64.03
28 GG/CC ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -3.24 0.22 2.97 8.77 -0.67 36.36
s.d. 1.79 1.42 0.39 7.28 6.09 25.28
****************************************************************************
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 51.7 54.7 11.4 9.6 10.5
2 C-G 63.6 53.9 10.8 9.2 10.4
3 G-C 52.5 48.2 10.8 8.9 9.8
4 G-U 42.6 68.8 10.5 8.9 9.8
5 A-U 56.4 58.0 10.3 8.7 9.7
6 U-A 55.9 59.9 10.1 8.6 9.7
7 U-A 55.3 54.0 10.4 8.7 9.7
8 c-G 52.3 55.2 10.7 8.9 9.8
9 U-A 54.0 55.9 10.5 8.8 9.7
10 G-C 56.0 56.7 10.5 8.8 9.9
11 U-A 52.3 57.4 10.6 8.9 9.8
12 G-C 53.8 55.7 10.6 8.9 9.8
13 u-a 30.6 17.7 9.9 7.3 6.3
14 P+G 110.9 31.3 8.6 8.2 9.6
15 A-U 24.2 90.3 7.9 6.9 6.9
16 A-c 19.5 89.7 10.9 9.5 10.2
17 P-A 42.8 64.6 10.9 9.2 10.0
18 c-G 48.3 57.0 10.7 9.0 9.8
19 U-A 62.5 61.8 10.1 8.7 9.9
20 G-C 55.7 53.5 10.5 8.8 9.7
21 G-C 52.5 52.0 10.6 8.8 9.7
22 A-g 49.5 42.2 12.6 10.6 11.0
23 g-C 52.7 55.6 10.5 8.8 9.7
24 C-G 56.3 56.2 10.4 8.7 9.8
25 U-A 53.4 52.5 10.7 8.9 9.8
26 C-G 55.2 54.5 10.6 9.0 9.9
27 A-U 19.8 29.6 9.7 7.1 6.1
28 G+C 37.3 61.0 10.4 8.8 10.4
29 G-C 57.9 52.4 10.4 8.7 9.7
****************************************************************************
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 GC/GC -2.58 8.11 2.62 -5.46 8.11 2.62 A
2 CG/CG -1.14 8.48 2.46 -6.29 7.93 3.83 A
3 GG/UC -1.17 8.04 3.04 -6.54 7.16 4.77 A
4 GA/UU -1.77 8.15 2.64 -3.95 7.90 3.31 A
5 AU/AU -2.16 8.31 2.47 -6.71 7.47 4.40 A
6 UU/AA -2.19 8.23 2.15 -5.27 7.29 4.36 A
7 Uc/GA -1.43 7.57 3.37 -5.44 7.09 4.30 A
8 cU/AG -1.11 8.04 2.93 -6.39 7.06 4.83 A
9 UG/CA -1.30 8.25 2.50 -4.65 7.77 3.74 A
10 GU/AC -1.43 8.41 2.34 -4.67 8.08 3.32 A
11 UG/CA -1.72 8.01 2.85 -5.97 7.21 4.49 A
12 Gu/aC -1.09 7.11 3.22 -2.25 7.26 2.84
13 uP/Ga 3.81 4.78 0.33 0.32 4.70 1.30
14 PA/UG --- --- --- --- --- --- ---
15 AA/cU -0.81 5.48 4.38 -4.19 3.63 5.94
16 AP/Ac -1.06 8.08 2.79 -3.11 7.27 4.72 A
17 Pc/GA -1.24 8.16 2.76 -3.91 7.56 4.15 A
18 cU/AG -1.89 8.04 2.68 -4.62 7.68 3.60 A
19 UG/CA -1.61 8.23 2.82 -6.91 7.11 5.01 A
20 GG/CC -1.55 8.12 2.69 -4.53 7.62 3.86 A
21 GA/gC -1.09 8.80 2.17 -3.12 8.38 3.46 A
22 Ag/Cg -2.76 6.53 4.49 -5.53 5.33 5.49
23 gC/GC -1.86 8.08 2.57 -4.68 7.72 3.51 A
24 CU/AG -1.50 8.37 2.54 -4.70 7.61 4.32 A
25 UC/GA -1.68 8.51 2.54 -5.92 8.42 2.70 A
26 CA/UG -1.39 8.31 2.22 -1.40 8.46 1.50
27 AG/CU 2.97 1.67 2.35 5.45 1.91 2.25
28 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 GC/GC --- --- --- ---
2 CG/CG --- --- --- ---
3 GG/UC 16.7 --- 18.2 ---
4 GA/UU 16.7 15.3 15.8 13.6
5 AU/AU 17.0 15.0 14.6 11.3
6 UU/AA 17.3 15.6 16.1 13.1
7 Uc/GA 16.6 15.2 17.8 15.4
8 cU/AG 16.8 15.4 18.1 17.2
9 UG/CA 17.3 16.3 15.0 12.1
10 GU/AC 17.0 15.8 15.1 12.2
11 UG/CA 16.4 --- 13.7 ---
12 Gu/aC --- --- --- ---
13 uP/Ga --- --- --- ---
14 PA/UG --- --- --- ---
15 AA/cU --- --- --- ---
16 AP/Ac --- --- --- ---
17 Pc/GA 17.4 --- 13.7 ---
18 cU/AG 16.6 15.1 14.8 10.7
19 UG/CA 16.4 15.3 15.2 9.3
20 GG/CC 18.2 15.4 14.4 9.0
21 GA/gC 19.0 14.8 12.2 9.5
22 Ag/Cg 17.0 14.1 11.3 9.3
23 gC/GC 16.7 14.8 11.0 10.9
24 CU/AG 17.1 16.0 15.1 10.2
25 UC/GA 16.7 --- 8.9 ---
26 CA/UG --- --- --- ---
27 AG/CU --- --- --- ---
28 GG/CC --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 0.04(3.20)
****************************************************************************
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 --- --- -108.0 101.8 -121.2 -57.4 170.6
2 C -37.7 -175.0 9.3 73.7 -149.0 -75.6 -149.0
3 G -64.1 151.0 69.7 75.3 -143.2 -84.2 -169.6
4 G -67.2 163.1 64.8 81.2 -152.8 -65.9 -174.1
5 A -74.4 -175.9 54.6 82.7 -148.1 -67.0 -162.0
6 U -68.8 166.0 65.0 78.3 -150.2 -75.2 -168.3
7 U -58.8 177.7 63.6 134.5 --- --- -129.1
8 c --- 172.3 41.1 85.2 -152.4 -77.5 -172.0
9 U -48.4 177.8 37.6 84.7 -149.6 -79.4 -165.4
10 G -42.7 174.4 31.9 86.7 -154.5 -73.0 -155.4
11 U -62.7 166.6 50.7 80.8 -159.5 -66.4 -167.6
12 G -59.9 172.7 55.0 83.2 -166.4 -61.2 -173.2
13 u -84.7 -167.8 58.1 80.7 -136.5 -68.1 -156.1
14 P -55.7 172.1 45.4 79.8 --- --- -153.0
15 A --- 148.5 58.3 80.3 --- --- -154.6
16 A --- -175.0 58.8 75.3 -146.2 -62.1 -173.0
17 P -83.6 -179.8 70.7 84.8 -150.8 -70.1 -172.6
18 c -89.2 169.2 73.4 81.7 -142.0 -96.2 -176.1
19 U 41.0 161.9 -46.2 98.3 -152.4 -68.5 -156.3
20 G -57.6 161.7 58.7 82.6 -156.6 -80.5 -170.2
21 G -53.0 168.1 51.7 83.8 -150.9 -78.2 -159.9
22 A -71.5 156.3 69.9 84.0 --- --- -158.6
23 g --- 147.9 57.8 91.8 -135.0 -76.6 173.5
24 C -74.2 179.2 57.7 89.4 -146.0 -71.2 -161.4
25 U -69.6 172.8 49.8 82.5 -162.1 -73.3 -160.1
26 C 137.5 -155.5 -163.4 79.6 -169.5 -79.5 -168.3
27 A 130.6 177.4 -152.5 91.3 -117.2 -65.3 -175.3
28 G -51.0 160.1 42.3 80.3 --- --- -166.8
29 G --- 176.4 59.6 156.7 --- --- -79.7

Strand II
base alpha beta gamma delta epsilon zeta chi
1 C -92.1 -144.3 58.3 74.0 --- --- -157.4
2 G -63.8 142.7 74.2 79.9 -174.0 -58.2 -179.5
3 C -55.5 155.7 50.2 69.3 -141.4 -81.5 -163.3
4 U -89.0 -176.1 76.4 77.3 -147.7 -87.7 -165.0
5 U -55.2 169.5 41.4 82.2 -150.4 -59.2 -161.2
6 A -63.3 171.5 49.3 88.2 -152.4 -75.1 -156.3
7 A -65.9 175.5 58.8 80.2 -148.1 -73.9 -166.2
8 G -42.1 157.7 48.9 79.5 -154.9 -74.0 -172.5
9 A -57.4 176.4 38.8 76.9 -145.8 -75.8 -160.7
10 C -81.1 175.3 62.6 81.9 -150.9 -75.1 -157.2
11 A -73.3 -173.2 51.5 83.2 -157.1 -68.1 -161.9
12 C --- 179.5 33.9 83.6 -157.4 -70.0 -169.9
13 a --- -150.5 69.5 155.7 --- --- -85.4
14 G --- 136.4 -67.4 177.3 --- --- -95.2
15 U -96.4 -149.4 55.1 88.6 --- --- -144.9
16 c -70.4 -179.1 48.0 85.6 -163.4 -50.5 -145.5
17 A -70.9 -175.9 49.4 87.6 -142.9 -62.5 -158.3
18 G -59.1 -176.9 39.3 81.8 -166.0 -57.0 -157.3
19 A -56.9 165.1 52.7 82.8 -159.9 -72.2 -164.5
20 C -72.2 175.0 54.1 81.1 -147.3 -76.2 -162.6
21 C -59.4 171.6 48.2 81.8 -147.8 -73.5 -163.4
22 g -83.2 -177.5 62.2 82.1 -136.5 -72.0 -163.2
23 C -57.8 168.9 48.7 78.0 -160.4 -50.2 -161.6
24 G -52.1 174.7 32.5 87.9 -147.2 -66.8 -158.6
25 A -60.3 -179.8 47.6 84.0 -152.0 -73.4 -161.4
26 G --- 161.3 178.1 87.4 -148.6 -78.5 -177.0
27 U --- -141.3 50.8 80.7 --- --- -159.3
28 C --- -175.2 152.8 139.3 --- --- -143.0
29 C --- 175.3 52.2 85.7 --- --- -169.1
****************************************************************************
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 23.5 -31.1 27.8 -14.9 -5.3 31.4 332.2 C2'-exo
2 C 4.7 -30.8 45.1 -44.0 24.1 46.3 13.2 C3'-endo
3 G 2.0 -27.8 42.0 -41.8 25.0 43.7 15.9 C3'-endo
4 G 2.9 -27.8 40.9 -40.3 23.6 42.3 14.8 C3'-endo
5 A 10.3 -33.7 42.9 -37.8 17.6 43.1 4.9 C3'-endo
6 U -0.5 -25.2 39.8 -40.9 26.3 42.1 19.2 C3'-endo
7 U -24.2 33.1 -28.7 15.6 5.2 32.5 152.1 C2'-endo
8 c 6.3 -30.4 41.9 -39.0 20.4 42.5 10.0 C3'-endo
9 U 7.9 -32.6 43.3 -39.7 20.1 43.8 8.2 C3'-endo
10 G 8.0 -28.7 37.2 -33.6 16.3 37.5 6.6 C3'-endo
11 U -2.0 -26.4 43.2 -45.2 29.7 46.2 20.8 C3'-endo
12 G -7.9 -18.2 35.7 -40.8 30.7 40.8 29.1 C3'-endo
13 u 1.3 -27.0 41.1 -41.3 25.2 42.9 16.8 C3'-endo
14 P 0.8 -26.0 40.0 -40.4 25.1 42.0 17.4 C3'-endo
15 A 7.5 -32.0 43.6 -40.1 20.6 44.1 9.0 C3'-endo
16 A -2.9 -25.4 42.9 -45.5 30.3 46.2 22.0 C3'-endo
17 P -1.7 -21.6 35.3 -37.2 24.7 37.8 21.1 C3'-endo
18 c -0.5 -25.2 40.2 -41.3 26.3 42.5 19.2 C3'-endo
19 U 26.5 -42.7 42.1 -27.9 1.0 44.1 342.7 C2'-exo
20 G -3.0 -23.3 39.2 -41.7 28.2 42.4 22.3 C3'-endo
21 G 2.0 -25.3 37.8 -37.7 22.8 39.3 15.9 C3'-endo
22 A 0.1 -24.4 38.3 -39.3 24.7 40.4 18.5 C3'-endo
23 g 13.1 -32.7 38.8 -32.0 12.1 38.8 359.2 C2'-exo
24 C 2.8 -20.9 30.0 -29.4 16.9 30.9 13.7 C3'-endo
25 U -7.1 -19.2 36.6 -41.6 30.5 41.5 28.0 C3'-endo
26 C -2.5 -21.6 36.0 -38.5 26.0 38.9 22.3 C3'-endo
27 A 15.1 -34.0 39.3 -31.7 10.3 39.4 356.6 C2'-exo
28 G 2.6 -28.4 42.4 -42.0 24.8 44.0 15.3 C3'-endo
29 G -18.9 36.8 -39.8 29.6 -7.1 40.3 171.2 C2'-endo

Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 C 11.4 -37.6 47.9 -42.6 20.1 48.1 5.3 C3'-endo
2 G 10.8 -35.6 46.2 -40.5 19.1 46.4 5.3 C3'-endo
3 C -0.9 -28.3 46.9 -47.3 30.4 49.7 19.2 C3'-endo
4 U 1.3 -22.5 32.7 -33.6 20.6 34.2 16.8 C3'-endo
5 U -0.9 -19.8 34.0 -35.1 21.7 36.2 19.9 C3'-endo
6 A 3.9 -29.0 41.8 -40.4 23.0 43.0 13.3 C3'-endo
7 A 0.0 -25.9 40.7 -41.4 26.2 42.9 18.4 C3'-endo
8 G -1.4 -26.3 42.1 -43.9 28.6 44.8 20.2 C3'-endo
9 A 4.8 -30.7 43.3 -41.6 23.4 44.4 12.4 C3'-endo
10 C 3.7 -29.3 42.3 -41.1 23.7 43.6 13.7 C3'-endo
11 A 6.6 -31.4 43.2 -40.0 21.2 43.9 9.9 C3'-endo
12 C 2.7 -26.2 38.4 -37.6 22.2 39.7 14.7 C3'-endo
13 a -24.3 43.4 -44.5 31.2 -4.5 45.7 166.9 C2'-endo
14 G -14.0 36.9 -43.2 37.1 -14.6 43.2 180.3 C3'-exo
15 U -1.5 -20.0 32.6 -34.3 22.6 34.9 20.9 C3'-endo
16 c 6.3 -28.8 39.0 -36.3 19.0 39.6 9.5 C3'-endo
17 A 8.2 -29.6 38.5 -34.9 16.9 38.8 6.7 C3'-endo
18 G 7.1 -30.1 40.8 -37.6 19.3 41.3 8.9 C3'-endo
19 A 5.6 -28.4 38.9 -36.8 19.9 39.6 10.7 C3'-endo
20 C 4.5 -30.3 43.1 -41.6 23.4 44.2 12.8 C3'-endo
21 C 2.5 -27.4 40.5 -39.8 23.6 41.9 15.0 C3'-endo
22 g 4.9 -29.5 41.8 -40.0 22.1 42.8 12.2 C3'-endo
23 C 1.9 -28.0 41.6 -41.6 25.2 43.3 16.1 C3'-endo
24 G 10.1 -32.8 41.5 -37.0 17.0 41.7 5.0 C3'-endo
25 A 8.5 -31.6 41.0 -37.3 18.2 41.3 7.0 C3'-endo
26 G 15.0 -33.4 37.6 -30.0 9.7 37.7 355.8 C2'-exo
27 U 11.4 -36.0 45.3 -39.8 18.1 45.4 4.3 C3'-endo
28 C -28.7 39.9 -35.7 19.6 5.6 39.9 153.6 C2'-endo
29 C 3.7 -27.2 38.9 -38.2 21.8 40.1 13.7 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/C --- 5.9 1 C/G 6.7 6.1
2 C/G 4.3 4.7 2 G/C 5.6 4.6
3 G/G 6.1 5.5 3 C/U 6.2 5.4
4 G/A 6.1 5.6 4 U/U 5.6 5.2
5 A/U 5.7 5.2 5 U/A 5.8 5.4
6 U/U 6.0 5.8 6 A/A 5.7 5.3
7 U/c 7.8 6.0 7 A/G 6.1 5.6
8 c/U 5.5 5.9 8 G/A 5.3 5.0
9 U/G 5.5 5.5 9 A/C 5.9 5.5
10 G/U 5.6 5.0 10 C/A 5.6 5.4
11 U/G 5.9 5.3 11 A/C 5.5 5.9
12 G/u 6.2 5.8 12 C/a 14.6 8.6
13 u/P 5.3 5.5 13 a/G 14.2 6.5
14 P/A --- --- 14 G/U --- ---
15 A/A 11.8 10.0 15 U/c 5.8 6.1
16 A/P 5.5 5.6 16 c/A 5.5 5.6
17 P/c 6.1 5.4 17 A/G 5.6 5.1
18 c/U 6.0 6.2 18 G/A 6.2 5.7
19 U/G 5.3 4.9 19 A/C 5.7 5.3
20 G/G 6.2 5.4 20 C/C 5.8 5.7
21 G/A 5.7 4.9 21 C/g 5.5 5.6
22 A/g 15.2 12.8 22 g/C 6.0 5.3
23 g/C 6.1 6.2 23 C/G 5.4 5.2
24 C/U 5.8 5.5 24 G/A 5.6 5.3
25 U/C 5.9 5.1 25 A/G 6.7 6.0
26 C/A 6.9 6.0 26 G/U 17.1 9.3
27 A/G 5.8 5.2 27 U/C 10.8 4.1
28 G/G --- --- 28 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 GC/GC 9.4 7.8 7.2 10.2 9.7 8.9
2 CG/CG 10.9 10.6 9.9 9.5 9.5 9.1
3 GG/UC 7.8 9.0 8.8 11.7 11.0 10.4
4 GA/UU 9.1 8.6 7.8 8.6 7.2 6.4
5 AU/AU 9.8 9.3 8.8 10.3 9.9 9.2
6 UU/AA 10.1 9.0 8.3 7.9 7.9 7.3
7 Uc/GA 9.3 9.8 9.1 8.5 8.4 7.9
8 cU/AG 10.6 10.9 10.3 8.5 8.9 8.6
9 UG/CA 8.9 8.5 7.9 9.2 8.8 8.0
10 GU/AC 8.7 8.2 7.6 10.0 9.0 8.3
11 UG/CA 8.7 8.6 8.2 10.1 10.0 9.3
12 Gu/aC 9.8 8.1 7.1 7.7 5.2 4.6
13 uP/Ga 4.2 2.8 2.2 7.4 8.7 8.2
14 PA/UG ---- ---- ---- ---- ---- ----
15 AA/cU 9.0 9.0 9.1 5.4 4.9 3.9
16 AP/Ac 8.4 8.6 8.1 8.0 6.6 5.6
17 Pc/GA 8.7 8.5 7.8 8.4 7.8 7.0
18 cU/AG 7.9 7.6 7.0 10.1 9.4 8.5
19 UG/CA 10.5 10.5 9.9 9.4 9.6 9.2
20 GG/CC 9.4 8.6 7.9 8.4 8.0 7.3
21 GA/gC 11.0 9.4 8.6 6.9 6.6 6.0
22 Ag/Cg 10.6 11.4 10.5 4.8 5.8 5.6
23 gC/GC 9.9 9.2 8.4 8.1 7.5 6.9
24 CU/AG 9.8 8.7 8.0 8.1 8.2 7.6
25 UC/GA 9.7 7.7 7.5 11.2 11.2 10.4
26 CA/UG 10.2 8.4 7.5 7.9 5.5 4.4
27 AG/CU 9.5 7.1 5.9 12.9 9.3 8.2
28 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 GC/GC 131.06 43.62 36.50 0.93 -0.34 0.11
2 CG/CG 134.88 42.54 34.24 0.91 -0.29 0.30
3 GG/UC 137.31 43.17 37.94 0.84 -0.37 0.39
4 GA/UU 138.86 39.54 36.11 0.95 -0.11 0.28
5 AU/AU 140.87 40.24 39.33 0.89 -0.19 0.41
6 UU/AA 144.23 40.25 38.95 0.88 -0.24 0.41
7 Uc/GA 146.40 39.83 41.03 0.90 -0.07 0.42
8 cU/AG 148.93 39.00 43.39 0.95 -0.10 0.29
9 UG/CA 152.07 40.30 42.35 0.90 -0.17 0.39
10 GU/AC 155.22 40.13 43.45 0.88 -0.11 0.45
11 UG/CA 157.95 39.67 43.25 0.94 -0.09 0.33
12 Gu/aC 159.26 36.59 46.99 0.85 -0.38 0.38
13 uP/Ga 160.82 37.71 50.88 0.83 -0.17 0.53
14 PA/UG ---- ---- ---- ---- ---- ----
15 AA/cU 168.57 16.20 3.17 -0.25 0.50 0.83
16 AP/Ac 166.89 16.30 6.92 -0.23 0.29 0.93
17 Pc/GA 166.39 17.62 8.96 -0.19 0.41 0.89
18 cU/AG 164.93 18.18 12.03 -0.13 0.43 0.89
19 UG/CA 162.21 21.00 13.32 -0.19 0.28 0.94
20 GG/CC 163.79 22.53 15.85 -0.28 0.37 0.89
21 GA/gC 162.24 24.62 17.64 -0.33 0.28 0.90
22 Ag/Cg 160.10 24.05 19.88 -0.20 0.21 0.96
23 gC/GC 159.20 26.67 22.41 -0.52 0.13 0.84
24 CU/AG 157.68 28.10 24.65 -0.53 0.24 0.82
25 UC/GA 155.51 31.11 25.22 -0.25 0.34 0.91
26 CA/UG 158.69 27.11 30.70 -0.16 0.12 0.98
27 AG/CU 160.37 25.64 34.61 -0.14 0.13 0.98
28 GG/CC ---- ---- ---- ---- ---- ----