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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.
****************************************************************************
File name: dna53.pdb
Date and time: Mon Oct 30 12:04:11 2006

Number of base-pairs: 22
Number of atoms: 980
****************************************************************************
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

Strand I Strand II Helix
1 (0.003) A:...1_:[..C]C-----G[..G]:..23_:B (0.006) |
2 (0.005) A:...2_:[..U]U-----A[..A]:..22_:B (0.011) |
3 (0.006) A:...3_:[..U]U-----A[..A]:..21_:B (0.005) |
4 (0.004) A:...4_:[..G]G-----C[..C]:..20_:B (0.003) |
5 (0.002) A:...5_:[..C]C-----G[..G]:..19_:B (0.003) |
6 (0.005) A:...6_:[..U]U-----A[..A]:..18_:B (0.004) |
7 (0.009) A:...7_:[..G]Gx----C[..C]:..17_:B (0.006) |
8 (0.009) A:...9_:[..G]G-*---A[..A]:..16_:B (0.004) |
9 (0.004) A:..10_:[..G]G-----C[..C]:..15_:B (0.002) |
10 (0.005) A:..11_:[..U]U-----A[..A]:..14_:B (0.004) |
11 (0.009) A:..12_:[..G]G-----C[..C]:..13_:B (0.003) |
12 (0.004) A:..13_:[..C]C-----G[..G]:..12_:B (0.007) |
13 (0.004) A:..14_:[..A]A-----U[..U]:..11_:B (0.003) |
14 (0.005) A:..15_:[..C]C----xG[..G]:..10_:B (0.008) |
15 (0.004) A:..16_:[..A]A-*--xG[..G]:...9_:B (0.009) |
16 (0.003) A:..17_:[..C]C-----G[..G]:...7_:B (0.005) |
17 (0.007) A:..18_:[..A]A-----U[..U]:...6_:B (0.006) |
18 (0.005) A:..19_:[..G]G-----C[..C]:...5_:B (0.004) |
19 (0.005) A:..20_:[..C]C-----G[..G]:...4_:B (0.006) |
20 (0.004) A:..21_:[..A]A-----U[..U]:...3_:B (0.006) |
21 (0.005) A:..22_:[..A]A-----U[..U]:...2_:B (0.006) |
22 (0.009) A:..23_:[..G]G-----C[..C]:...1_:B (0.005) |

Note: This structure contains 2[0] non-Watson-Crick base-pairs.
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 C-----G [3] O2 - N2 3.17 N3 - N1 3.12 N4 - O6 3.05
2 U-----A [2] N3 - N1 2.55 O4 - N6 2.81
3 U-----A [2] N3 - N1 2.89 O4 - N6 3.28
4 G-----C [3] O6 - N4 2.54 N1 - N3 2.76 N2 - O2 3.07
5 C-----G [3] O2 - N2 2.82 N3 - N1 3.06 N4 - O6 3.22
6 U-----A [2] N3 - N1 2.74 O4 - N6 2.74
7 G-----C [3] O6 - N4 3.53 N1 - N3 3.27 N2 - O2 2.92
8 G-*---A [2] O6 - N6 3.26 N1 - N1 2.65
9 G-----C [3] O6 - N4 2.87 N1 - N3 2.68 N2 - O2 2.47
10 U-----A [2] N3 - N1 2.67 O4 - N6 2.98
11 G-----C [3] O6 - N4 2.96 N1 - N3 2.72 N2 - O2 2.38
12 C-----G [3] O2 - N2 2.52 N3 - N1 2.52 N4 - O6 2.41
13 A-----U [2] N6 - O4 2.87 N1 - N3 2.76
14 C-----G [3] O2 - N2 2.55 N3 - N1 2.56 N4 - O6 2.47
15 A-*---G [3] N6 - O6 2.82 N1 - N1 2.39 N3 - N2 4.00
16 C-----G [3] O2 - N2 2.58 N3 - N1 2.66 N4 - O6 2.66
17 A-----U [2] N6 - O4 3.05 N1 - N3 2.72
18 G-----C [3] O6 - N4 2.58 N1 - N3 2.69 N2 - O2 2.74
19 C-----G [3] O2 - N2 2.71 N3 - N1 2.82 N4 - O6 2.99
20 A-----U [2] N6 - O4 3.12 N1 - N3 2.74
21 A-----U [2] N6 - O4 2.61 N1 - N3 2.50
22 G-----C [3] O6 - N4 3.49 N1 - N3 3.18 N2 - O2 2.90
****************************************************************************
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 CU/AG 0.00( 0.00) 0.00( 0.00) 0.68( 0.00) 1.80( 1.79) 2.49( 1.79)
2 UU/AA 0.68( 0.01) 0.00( 0.00) 0.00( 0.00) 1.38( 1.25) 2.07( 1.26)
3 UG/CA 0.00( 0.00) 0.00( 0.00) 2.59( 1.44) 0.27( 0.00) 2.87( 1.44)
4 GC/GC 5.92( 3.26) 0.00( 0.00) 0.00( 0.00) 6.23( 3.37) 12.15( 6.63)
5 CU/AG 0.27( 0.00) 0.00( 0.00) 0.08( 0.00) 1.91( 1.65) 2.26( 1.65)
6 UG/CA 0.00( 0.00) 0.00( 0.00) 3.48( 1.94) 0.00( 0.00) 3.48( 1.94)
7 GG/AC 3.67( 0.91) 0.00( 0.00) 0.00( 0.00) 5.27( 3.79) 8.94( 4.70)
8 GG/CA 0.72( 0.00) 0.00( 0.00) 3.06( 1.54) 0.07( 0.00) 3.86( 1.54)
9 GU/AC 4.91( 2.04) 0.00( 0.00) 0.00( 0.00) 5.48( 3.95) 10.40( 5.98)
10 UG/CA 0.60( 0.00) 0.00( 0.00) 1.92( 0.89) 0.65( 0.00) 3.17( 0.89)
11 GC/GC 5.31( 2.57) 0.00( 0.00) 0.00( 0.00) 6.73( 3.60) 12.04( 6.17)
12 CA/UG 0.23( 0.00) 0.00( 0.00) 2.96( 1.50) 0.14( 0.00) 3.32( 1.50)
13 AC/GU 3.55( 2.29) 0.00( 0.00) 0.00( 0.00) 4.88( 1.99) 8.44( 4.28)
14 CA/GG 0.08( 0.00) 0.00( 0.00) 3.05( 1.32) 1.65( 0.47) 4.79( 1.78)
15 AC/GG 5.73( 4.48) 0.00( 0.00) 0.00( 0.00) 2.97( 0.35) 8.70( 4.83)
16 CA/UG 0.29( 0.00) 0.00( 0.00) 2.58( 1.58) 0.00( 0.00) 2.87( 1.58)
17 AG/CU 0.92( 0.92) 0.00( 0.00) 0.25( 0.00) 1.27( 0.12) 2.45( 1.05)
18 GC/GC 7.05( 4.47) 0.00( 0.00) 0.00( 0.00) 5.00( 2.05) 12.05( 6.52)
19 CA/UG 0.48( 0.02) 0.00( 0.00) 1.84( 0.88) 0.35( 0.00) 2.66( 0.90)
20 AA/UU 0.80( 0.55) 0.00( 0.00) 0.00( 0.00) 2.42( 0.72) 3.22( 1.27)
21 AG/CU 3.55( 3.07) 0.00( 0.00) 0.18( 0.00) 0.00( 0.00) 3.73( 3.07)
****************************************************************************
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 C-G -27.13 -89.75 -15.49 -0.10 0.83 0.55
2 U-A -26.82 -88.12 -12.21 0.14 0.87 0.47
3 U-A -25.01 -85.89 -10.34 0.32 0.91 0.28
4 G-C -22.02 -82.81 -8.97 0.41 0.91 0.02
5 C-G -20.49 -80.18 -9.50 0.25 0.97 0.02
6 U-A -19.19 -77.22 -10.75 0.02 0.99 -0.11
7 G-C -20.20 -74.66 -13.05 -0.14 0.97 -0.19
8 G-A -19.93 -71.64 -14.27 -0.25 0.94 -0.25
9 G-C -22.56 -68.87 -15.13 -0.19 0.97 0.11
10 U-A -24.66 -66.03 -14.68 -0.13 0.98 0.17
11 G-C -25.57 -63.49 -13.28 -0.06 0.97 0.22
12 C-G -26.29 -61.07 -10.97 -0.01 0.94 0.34
13 A-U -25.57 -58.21 -8.69 0.15 0.97 0.18
14 C-G -23.63 -55.61 -7.34 0.20 0.97 0.15
15 A-G -20.84 -52.52 -7.36 0.25 0.97 -0.07
16 C-G -20.46 -49.58 -8.62 0.22 0.98 0.01
17 A-U -20.17 -46.71 -10.32 -0.05 1.00 -0.04
18 G-C -20.47 -43.40 -12.06 -0.25 0.97 -0.00
19 C-G -22.65 -40.90 -12.41 -0.37 0.93 -0.02
20 A-U -25.19 -38.11 -12.06 -0.40 0.88 0.24
21 A-U -27.39 -35.96 -11.58 -0.29 0.88 0.38
22 G-C -28.14 -34.23 -8.77 -0.14 0.84 0.53
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 C-G 0.53 0.02 -0.04 16.56 -17.06 -3.35
2 U-A -0.47 -0.35 -0.42 12.06 -6.74 4.88
3 U-A -0.48 0.00 -0.45 8.89 -14.34 9.15
4 G-C -0.96 -0.63 -0.80 -18.13 -22.90 -3.28
5 C-G 0.37 0.05 -0.02 -5.47 -6.28 4.10
6 U-A -0.39 -0.20 0.16 -10.17 -4.76 -2.38
7 G-C -1.40 -0.09 -0.19 4.37 -5.05 7.22
8 G-A 0.10 1.40 -0.54 18.89 -17.89 1.21
9 G-C -0.69 -0.44 0.15 -7.97 -15.03 3.12
10 U-A -0.36 -0.21 0.24 -5.62 -4.52 5.25
11 G-C -0.22 -0.28 0.38 -2.03 -7.70 5.10
12 C-G -0.21 -0.50 -0.23 8.80 -9.63 -2.52
13 A-U 0.58 -0.17 -0.11 0.64 -6.31 0.96
14 C-G -0.55 -0.47 -0.05 2.88 -10.21 -2.48
15 A-G 0.08 1.09 -0.49 -17.86 -10.28 -4.57
16 C-G 0.63 -0.50 0.03 3.16 -7.91 -0.38
17 A-U 0.17 -0.15 0.18 12.09 -7.09 6.76
18 G-C -1.09 -0.76 0.01 6.13 -9.23 -3.25
19 C-G -0.36 -0.15 -0.47 11.20 -18.36 5.34
20 A-U 0.56 -0.15 -0.12 2.65 -11.71 8.13
21 A-U 0.15 -0.41 0.23 12.85 1.13 1.23
22 G-C -0.18 0.27 0.29 18.90 -15.35 6.76
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.19 -0.12 -0.10 3.31 -10.33 2.14
s.d. 0.56 0.51 0.32 10.80 5.71 4.37
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 CU/AG -0.19 -1.99 3.09 -1.82 14.49 29.04
2 UU/AA 0.21 -1.40 3.12 -0.90 15.23 32.45
3 UG/CA -0.54 -1.71 4.13 3.41 15.16 29.30
4 GC/GC 0.30 -0.77 2.98 -9.00 4.47 37.10
5 CU/AG -0.20 -1.42 3.15 -0.30 15.47 30.06
6 UG/CA 0.91 -1.85 2.93 4.31 8.90 24.78
7 GG/AC -1.02 -0.01 3.11 6.69 3.65 40.64
8 GG/CA 0.08 -2.03 3.33 -10.51 18.39 33.56
9 GU/AC -0.39 -1.57 3.18 -2.53 4.06 34.40
10 UG/CA 0.08 -1.07 2.85 -0.27 5.16 33.24
11 GC/GC -0.39 -1.61 2.99 6.26 3.61 30.37
12 CA/UG -0.15 -1.53 3.39 -4.55 12.61 33.80
13 AC/GU 0.05 -1.67 3.09 1.40 2.63 28.63
14 CA/GG 0.12 -2.03 3.63 2.90 12.91 37.45
15 AC/GG 1.11 -0.48 2.98 -4.12 -2.52 36.98
16 CA/UG 0.45 -1.57 2.92 -2.00 15.89 31.19
17 AG/CU -0.53 -1.59 3.36 -0.17 11.52 25.00
18 GC/GC 0.77 -1.09 3.06 5.54 4.88 35.38
19 CA/UG 0.24 -1.23 3.58 -0.79 15.07 35.54
20 AA/UU -0.82 -1.05 2.81 -2.83 10.07 30.10
21 AG/CU 0.71 -1.52 2.94 3.67 11.68 32.91
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.04 -1.39 3.17 -0.27 9.68 32.47
s.d. 0.56 0.51 0.31 4.58 5.75 4.05
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 CU/AG -5.62 0.08 1.92 26.86 3.37 32.43
2 UU/AA -4.18 -0.46 2.25 25.56 1.50 35.77
3 UG/CA -5.91 1.60 2.85 27.65 -6.21 33.09
4 GC/GC -1.67 -1.45 2.73 6.87 13.84 38.39
5 CU/AG -4.62 0.31 2.19 27.64 0.53 33.72
6 UG/CA -5.94 -1.05 2.26 19.77 -9.57 26.65
7 GG/AC -0.38 2.11 2.90 5.20 -9.53 41.32
8 GG/CA -4.90 -1.19 1.91 28.60 16.34 39.52
9 GU/AC -3.21 0.29 3.00 6.82 4.25 34.72
10 UG/CA -2.57 -0.17 2.66 8.95 0.47 33.63
11 GC/GC -3.59 1.76 2.66 6.77 -11.74 31.20
12 CA/UG -4.16 -0.37 2.67 20.70 7.48 36.28
13 AC/GU -3.90 0.18 2.93 5.30 -2.82 28.78
14 CA/GG -4.53 0.17 2.81 19.38 -4.36 39.64
15 AC/GG -0.45 -2.22 2.87 -3.96 6.47 37.29
16 CA/UG -4.49 -0.98 1.89 27.40 3.44 34.97
17 AG/CU -5.97 1.07 2.41 24.99 0.36 27.49
18 GC/GC -2.40 -0.52 2.97 7.92 -8.99 36.11
19 CA/UG -3.77 -0.46 2.84 23.43 1.23 38.51
20 AA/UU -3.43 1.07 2.41 18.69 5.25 31.82
21 AG/CU -3.99 -0.72 2.35 19.78 -6.22 35.06
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -3.79 -0.05 2.55 16.87 0.24 34.59
s.d. 1.61 1.11 0.37 9.89 7.53 3.96
****************************************************************************
Structure classification:

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 C-G 54.1 51.6 10.9 9.1 9.9
2 U-A 54.3 60.3 10.1 8.5 9.6
3 U-A 56.1 61.4 10.3 8.8 9.9
4 G-C 48.5 56.6 10.3 8.5 9.3
5 C-G 57.7 54.8 10.7 9.0 10.1
6 U-A 52.1 54.7 10.6 8.8 9.7
7 G-C 50.6 64.6 10.5 8.9 10.0
8 G-A 55.8 55.4 12.0 10.3 11.1
9 G-C 52.4 58.3 10.2 8.6 9.6
10 U-A 55.5 59.1 10.2 8.7 9.7
11 G-C 56.6 57.5 10.3 8.7 9.7
12 C-G 51.0 54.6 10.4 8.6 9.5
13 A-U 58.3 52.1 10.5 8.8 9.8
14 C-G 49.3 55.4 10.5 8.7 9.6
15 A-G 53.3 51.3 11.9 10.1 10.8
16 C-G 56.9 51.2 10.3 8.6 9.5
17 A-U 58.9 58.3 10.2 8.6 9.7
18 G-C 45.8 57.9 10.3 8.5 9.3
19 C-G 53.8 59.1 10.4 8.8 9.8
20 A-U 61.6 55.9 10.2 8.7 9.8
21 A-U 55.6 55.2 10.2 8.5 9.5
22 G-C 56.2 58.6 10.7 9.1 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 CU/AG -1.68 8.21 2.51 -7.04 6.28 5.85 A
2 UU/AA -2.02 8.29 2.16 -5.97 6.65 5.40 A
3 UG/CA -1.74 8.21 2.02 -7.35 6.45 5.40 A
4 GC/GC -1.36 8.56 1.81 -3.05 8.30 2.78 A
5 CU/AG -1.45 8.40 2.65 -5.87 6.32 6.14 A
6 UG/CA -1.39 8.37 2.38 -7.10 7.14 4.87 A
7 GG/AC -2.15 8.77 3.58 -2.81 8.44 4.07
8 GG/CA -2.14 8.12 2.75 -6.52 5.96 6.14 A
9 GU/AC -1.93 8.19 2.53 -5.03 7.84 3.49 A
10 UG/CA -1.70 8.28 2.73 -4.17 7.78 3.93 A
11 GC/GC -1.44 8.29 2.47 -4.89 7.96 3.35 A
12 CA/UG -1.38 8.35 2.47 -5.28 7.03 5.12 A
13 AC/GU -1.24 8.09 2.59 -5.02 7.82 3.30 A
14 CA/GG -1.41 8.03 3.04 -5.61 6.67 5.40 A
15 AC/GG -1.82 8.38 3.66 -2.45 8.60 2.98
16 CA/UG -1.76 8.38 2.29 -6.01 6.50 5.75 A
17 AG/CU -1.44 8.29 2.53 -7.23 6.51 5.72 A
18 GC/GC -1.48 8.43 2.13 -3.80 8.08 3.12 A
19 CA/UG -1.85 8.34 2.06 -5.40 6.94 5.06 A
20 AA/UU -1.62 8.40 2.28 -4.89 7.29 4.72 A
21 AG/CU -1.74 8.25 2.59 -5.61 6.96 5.14 A
****************************************************************************
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 CU/AG --- --- --- ---
2 UU/AA --- --- --- ---
3 UG/CA 16.8 --- 15.6 ---
4 GC/GC 17.3 15.5 15.3 10.5
5 CU/AG 19.7 17.4 15.4 11.6
6 UG/CA 19.8 18.0 15.7 12.1
7 GG/AC 17.1 16.0 15.5 13.0
8 GG/CA 16.4 15.0 14.7 13.4
9 GU/AC 16.8 15.4 15.3 9.9
10 UG/CA 17.0 15.8 15.8 9.6
11 GC/GC 17.1 15.9 16.5 12.6
12 CA/UG 16.9 15.7 15.7 11.7
13 AC/GU 16.7 15.5 15.0 11.6
14 CA/GG 16.5 15.3 15.0 14.1
15 AC/GG 17.4 16.3 14.8 12.7
16 CA/UG 19.8 17.7 15.0 11.6
17 AG/CU 19.2 16.6 15.4 11.7
18 GC/GC 17.1 15.4 16.4 13.0
19 CA/UG 17.4 --- 15.7 ---
20 AA/UU --- --- --- ---
21 AG/CU --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 2.67(0.55)
Helix: -0.025 0.986 0.164
HETATM 9998 XS X X 999 -22.575 -88.946 -15.605
HETATM 9999 XE X X 999 -23.993 -33.759 -6.431
Average and standard deviation of helix radius:
P: 9.16(1.16), O4': 8.97(1.12), C1': 8.34(1.12)

Global parameters based on C1'-C1' vectors:

disp.: displacement of the middle C1'-C1' point from the helix
angle: inclination between C1'-C1' vector and helix (subtracted from 90)
twist: helical twist angle between consecutive C1'-C1' vectors
rise: helical rise by projection of the vector connecting consecutive
C1'-C1' middle points onto the helical axis

bp disp. angle twist rise
1 C-G 6.92 20.28 36.70 1.91
2 U-A 8.01 17.36 35.05 2.51
3 U-A 8.10 14.32 33.70 2.11
4 G-C 7.93 17.63 31.90 2.57
5 C-G 7.72 15.45 35.60 2.78
6 U-A 6.95 15.85 31.97 2.87
7 G-C 5.47 19.46 35.27 2.81
8 G-A 5.85 19.07 37.43 1.78
9 G-C 5.43 6.38 32.99 3.05
10 U-A 5.91 5.47 32.66 3.09
11 G-C 5.67 4.61 30.51 3.25
12 C-G 5.33 6.60 30.04 3.12
13 A-U 5.33 5.07 34.99 2.76
14 C-G 4.97 9.69 34.74 2.12
15 A-G 5.51 14.56 35.00 3.01
16 C-G 5.46 14.20 34.70 3.37
17 A-U 6.49 10.93 32.87 2.89
18 G-C 7.26 12.86 32.66 2.43
19 C-G 7.51 15.84 32.54 2.52
20 A-U 7.86 19.01 34.45 2.62
21 A-U 8.38 21.45 38.16 2.38
22 G-C 7.41 21.94 --- ---
****************************************************************************
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 C --- --- 62.1 82.0 -155.8 -66.2 -161.2
2 U -70.4 -165.9 42.4 82.9 -155.6 -67.6 -153.3
3 U -67.8 178.8 47.4 81.0 -160.3 -63.3 -154.4
4 G -64.1 -173.2 49.7 79.9 -166.5 -63.9 -156.0
5 C -74.3 179.9 54.2 82.9 -156.8 -68.7 -159.1
6 U -73.9 -176.5 50.0 79.3 -159.6 -60.9 -163.0
7 G -70.9 -167.3 48.0 78.2 --- --- -145.6
8 G --- -150.8 48.9 79.9 -158.3 -64.3 -168.8
9 G -77.2 -164.6 54.2 82.1 -141.0 -72.8 -176.3
10 U -68.9 177.8 49.2 80.6 -166.1 -64.5 -158.9
11 G -77.7 177.8 55.3 80.7 -153.2 -77.5 -164.0
12 C -54.5 170.5 51.2 80.9 -168.8 -60.3 -151.2
13 A -76.9 -173.8 50.2 80.8 -153.8 -74.5 -162.5
14 C -56.7 169.6 51.2 77.8 -165.2 -61.3 -161.2
15 A -72.4 -174.7 53.9 83.1 -150.7 -66.1 -166.6
16 C -57.9 170.1 53.7 81.1 -155.6 -65.2 -155.8
17 A -70.0 -174.3 44.5 81.2 -162.7 -70.2 -147.9
18 G -61.6 173.6 51.9 77.8 -153.5 -67.8 -158.8
19 C -63.9 170.4 52.3 79.5 -154.6 -67.5 -150.6
20 A -66.7 -174.3 49.5 83.0 -166.6 -68.8 -148.8
21 A -78.0 -172.3 52.2 83.2 -166.2 -56.5 -150.3
22 G -77.8 -171.9 49.3 73.7 --- --- -143.6

Strand II
base alpha beta gamma delta epsilon zeta chi
1 G -59.4 172.3 56.7 75.2 --- --- -165.3
2 A -71.1 177.3 50.3 80.9 -160.1 -69.4 -161.5
3 A -58.6 171.4 51.6 82.2 -139.7 -75.8 -168.1
4 C -62.5 159.0 56.7 78.7 -153.9 -74.4 -147.5
5 G -73.6 172.9 53.5 82.9 -141.1 -81.4 -162.7
6 A -63.1 178.9 51.0 81.9 -152.9 -71.2 -156.2
7 C -68.9 179.7 51.5 83.8 -159.7 -73.7 -158.4
8 A -65.8 176.9 48.1 82.9 -160.6 -61.1 -158.5
9 C -50.6 160.3 54.1 80.8 -150.8 -77.4 -161.1
10 A -57.9 163.2 46.1 78.9 -147.7 -78.2 -162.9
11 C -62.8 173.8 53.7 80.1 -149.9 -79.5 -161.7
12 G -58.8 169.8 55.8 79.1 -158.9 -68.6 -162.5
13 U -62.0 178.5 47.5 81.1 -144.8 -71.2 -162.3
14 G --- -155.0 45.4 81.6 -156.1 -72.9 -166.6
15 G --- -161.4 59.0 86.0 --- --- -176.8
16 G -80.7 -164.5 50.6 80.2 --- --- -147.9
17 U -62.2 172.1 52.2 81.1 -156.9 -65.7 -165.9
18 C -62.0 176.2 46.4 79.0 -153.9 -71.3 -160.6
19 G -68.8 177.9 57.0 83.4 -159.1 -70.5 -160.3
20 U -63.3 165.0 52.1 77.9 -157.5 -71.5 -160.3
21 U -73.0 -173.3 49.7 82.8 -150.2 -69.6 -163.8
22 C --- --- -54.2 85.0 -144.1 -73.2 -179.5
****************************************************************************
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 C 1.6 -25.4 38.3 -38.2 23.1 39.9 16.2 C3'-endo
2 U 3.0 -25.4 36.9 -36.4 21.0 38.1 14.3 C3'-endo
3 U 2.2 -26.3 39.1 -38.8 23.1 40.6 15.5 C3'-endo
4 G -5.1 -20.2 36.3 -40.3 28.6 40.3 25.8 C3'-endo
5 C 2.4 -25.6 38.0 -37.7 22.2 39.4 15.2 C3'-endo
6 U 0.4 -25.4 39.4 -40.2 25.1 41.5 18.0 C3'-endo
7 G -3.2 -22.8 38.6 -41.5 28.3 41.9 22.9 C3'-endo
8 G 0.3 -25.3 39.3 -40.1 25.0 41.3 18.1 C3'-endo
9 G 0.8 -24.2 37.0 -37.7 23.4 38.9 17.6 C3'-endo
10 U -1.2 -22.5 36.3 -38.1 24.8 38.8 20.4 C3'-endo
11 G 2.6 -26.7 39.3 -38.8 22.9 40.7 15.0 C3'-endo
12 C -1.3 -23.4 37.9 -39.8 25.9 40.5 20.5 C3'-endo
13 A 2.1 -26.3 39.4 -39.1 23.3 40.9 15.7 C3'-endo
14 C 1.0 -25.8 39.5 -39.9 24.6 41.4 17.3 C3'-endo
15 A 4.3 -26.7 37.9 -36.4 20.3 38.8 12.4 C3'-endo
16 C -0.2 -24.2 38.2 -39.4 24.9 40.4 18.9 C3'-endo
17 A 1.1 -25.0 38.0 -38.6 23.6 39.8 17.1 C3'-endo
18 G -4.6 -22.2 39.2 -42.7 29.9 43.1 24.5 C3'-endo
19 C 0.1 -25.3 39.6 -40.6 25.4 41.7 18.4 C3'-endo
20 A 4.2 -26.7 37.8 -36.5 20.4 38.8 12.6 C3'-endo
21 A 4.7 -27.1 38.0 -36.3 20.1 38.8 11.9 C3'-endo
22 G 3.6 -27.3 39.2 -38.3 21.9 40.4 13.7 C3'-endo

Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 G -1.5 -23.9 38.7 -40.7 26.6 41.4 20.7 C3'-endo
2 A -0.3 -24.7 38.9 -40.1 25.4 41.1 18.9 C3'-endo
3 A 5.8 -28.5 39.2 -37.0 19.6 39.9 10.4 C3'-endo
4 C 1.1 -26.6 40.7 -40.9 25.2 42.6 17.0 C3'-endo
5 G 2.2 -25.2 37.3 -37.2 22.0 38.7 15.4 C3'-endo
6 A 1.7 -24.8 37.1 -37.3 22.6 38.7 16.3 C3'-endo
7 C 6.8 -28.9 38.9 -36.0 18.5 39.4 8.9 C3'-endo
8 A 4.4 -27.0 38.3 -36.7 20.3 39.2 12.3 C3'-endo
9 C 0.8 -25.4 39.2 -39.7 24.5 41.1 17.5 C3'-endo
10 A 3.5 -27.3 39.5 -38.5 22.1 40.7 13.8 C3'-endo
11 C -0.4 -24.3 38.5 -39.7 25.3 40.7 19.2 C3'-endo
12 G -2.0 -23.4 38.5 -40.5 26.9 41.3 21.3 C3'-endo
13 U 4.0 -27.8 39.8 -38.5 21.6 40.9 13.0 C3'-endo
14 G 5.2 -28.1 39.3 -37.3 20.2 40.0 11.3 C3'-endo
15 G 1.8 -23.8 35.5 -35.6 21.3 37.0 16.0 C3'-endo
16 G -0.6 -23.7 37.7 -39.1 25.0 40.0 19.4 C3'-endo
17 U 2.0 -25.7 38.6 -38.5 22.9 40.1 15.8 C3'-endo
18 C 1.8 -25.8 39.0 -39.0 23.4 40.6 16.1 C3'-endo
19 G 2.4 -25.7 37.7 -37.4 22.1 39.1 15.1 C3'-endo
20 U -2.7 -23.6 39.5 -41.9 28.1 42.6 22.0 C3'-endo
21 U 3.0 -25.7 37.3 -36.8 21.3 38.5 14.3 C3'-endo
22 C 6.9 -28.6 38.1 -35.2 17.9 38.5 8.5 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 C/U --- 6.0 1 G/A 5.8 5.3
2 U/U 5.3 5.4 2 A/A 5.6 5.8
3 U/G 5.8 5.7 3 A/C 6.1 5.3
4 G/C 5.8 5.2 4 C/G 5.7 5.3
5 C/U 5.8 5.6 5 G/A 5.7 5.4
6 U/G 5.7 5.8 6 A/C 5.8 5.6
7 G/G 10.3 5.9 7 C/A 5.8 5.1
8 G/G 5.3 6.1 8 A/C 5.9 5.6
9 G/U 5.3 5.9 9 C/A 5.6 5.1
10 U/G 6.0 5.1 10 A/C 5.7 5.1
11 G/C 5.9 5.5 11 C/G 6.1 5.3
12 C/A 6.1 5.2 12 G/U 5.4 5.4
13 A/C 5.5 5.3 13 U/G 5.2 5.5
14 C/A 6.0 5.4 14 G/G 4.6 6.2
15 A/C 5.6 5.2 15 G/G 10.4 5.8
16 C/A 5.9 5.6 16 G/U 5.9 6.1
17 A/G 5.5 5.3 17 U/C 5.6 5.3
18 G/C 5.8 5.1 18 C/G 6.0 5.4
19 C/A 5.9 5.7 19 G/U 5.9 5.5
20 A/A 5.8 5.6 20 U/U 5.5 5.0
21 A/G 5.8 5.4 21 U/C --- 6.2
****************************************************************************
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 CU/AG 8.9 9.7 9.3 9.9 10.0 9.6
2 UU/AA 8.5 8.8 8.3 9.4 9.3 8.6
3 UG/CA 12.0 11.6 11.0 7.7 8.9 8.6
4 GC/GC 7.6 6.5 5.8 10.1 8.8 7.8
5 CU/AG 9.1 9.4 8.8 8.2 8.8 8.3
6 UG/CA 10.5 10.2 9.9 9.8 10.5 9.9
7 GG/AC 11.2 9.5 8.4 6.7 5.4 4.4
8 GG/CA 7.0 8.3 8.0 10.8 10.5 9.9
9 GU/AC 10.1 8.9 8.2 8.6 8.1 7.4
10 UG/CA 8.9 8.1 7.3 8.8 8.1 7.3
11 GC/GC 11.0 10.1 9.3 7.7 7.3 6.8
12 CA/UG 7.9 8.4 7.8 9.6 9.3 8.7
13 AC/GU 9.6 9.0 8.3 9.0 8.7 8.1
14 CA/GG 9.5 9.5 9.0 7.9 8.9 8.4
15 AC/GG 6.9 5.0 4.2 11.1 9.3 8.3
16 CA/UG 7.6 8.1 7.6 10.2 10.0 9.3
17 AG/CU 10.6 10.9 10.4 8.9 9.4 9.1
18 GC/GC 8.9 7.7 7.0 9.1 8.2 7.3
19 CA/UG 8.2 8.4 7.8 9.4 9.3 8.6
20 AA/UU 9.1 9.1 8.2 8.6 8.0 7.4
21 AG/CU 8.4 8.4 7.9 9.5 9.5 8.8
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step

bp Px Py Pz Hx Hy Hz
1 CU/AG -21.70 -88.16 -14.72 -0.13 0.99 0.11
2 UU/AA -23.45 -86.43 -14.37 -0.09 0.99 0.11
3 UG/CA -21.11 -84.30 -15.01 -0.07 1.00 -0.02
4 GC/GC -22.99 -80.64 -10.02 0.32 0.91 0.28
5 CU/AG -23.48 -78.14 -12.59 -0.10 0.93 0.35
6 UG/CA -25.32 -77.44 -11.10 -0.23 0.96 0.18
7 GG/AC -21.36 -73.62 -15.12 -0.28 0.96 -0.06
8 GG/CA -21.80 -69.35 -10.08 0.31 0.94 -0.15
9 GU/AC -23.09 -67.55 -11.87 -0.07 1.00 0.04
10 UG/CA -23.14 -64.87 -12.50 -0.01 1.00 0.08
11 GC/GC -22.79 -63.25 -10.12 0.17 0.97 0.20
12 CA/UG -22.50 -59.01 -11.71 -0.18 0.98 -0.00
13 AC/GU -22.40 -56.95 -11.10 0.13 0.99 0.08
14 CA/GG -22.14 -54.17 -11.61 -0.09 1.00 -0.03
15 AC/GG -22.45 -50.40 -7.02 0.35 0.94 0.01
16 CA/UG -24.68 -47.97 -9.91 -0.01 0.91 0.42
17 AG/CU -26.19 -45.48 -11.02 -0.06 0.92 0.38
18 GC/GC -22.75 -42.94 -10.39 -0.33 0.93 0.18
19 CA/UG -24.11 -40.11 -8.70 -0.01 0.99 0.17
20 AA/UU -25.89 -37.38 -8.41 -0.11 0.99 0.11
21 AG/CU -24.13 -35.55 -8.93 0.04 0.97 0.25