****************************************************************************
****************************************************************************
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: gatc-b.pdb
Date and time: Thu Nov 2 19:20:45 2006
Number of base-pairs: 16
Number of atoms: 656
****************************************************************************
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)
Strand I Strand II Helix
1 (0.009) A:...1_:[..G]G-----C[..C]:..32_:B (0.008) |
2 (0.009) A:...2_:[..A]A-----T[..T]:..31_:B (0.018) |
3 (0.018) A:...3_:[..T]T-----A[..A]:..30_:B (0.009) |
4 (0.008) A:...4_:[..C]C-----G[..G]:..29_:B (0.009) |
5 (0.009) A:...5_:[..G]G-----C[..C]:..28_:B (0.008) |
6 (0.009) A:...6_:[..A]A-----T[..T]:..27_:B (0.018) |
7 (0.018) A:...7_:[..T]T-----A[..A]:..26_:B (0.009) |
8 (0.008) A:...8_:[..C]C-----G[..G]:..25_:B (0.009) |
9 (0.009) A:...9_:[..G]G-----C[..C]:..24_:B (0.008) |
10 (0.009) A:..10_:[..A]A-----T[..T]:..23_:B (0.018) |
11 (0.018) A:..11_:[..T]T-----A[..A]:..22_:B (0.009) |
12 (0.008) A:..12_:[..C]C-----G[..G]:..21_:B (0.009) |
13 (0.009) A:..13_:[..G]G-----C[..C]:..20_:B (0.008) |
14 (0.009) A:..14_:[..A]A-----T[..T]:..19_:B (0.018) |
15 (0.018) A:..15_:[..T]T-----A[..A]:..18_:B (0.009) |
16 (0.008) A:..16_:[..C]C-----G[..G]:..17_:B (0.009) |
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 G-----C [3] O6 - N4 2.85 N1 - N3 2.85 N2 - O2 2.85
2 A-----T [2] N6 - O4 2.95 N1 - N3 2.88
3 T-----A [2] N3 - N1 2.88 O4 - N6 2.95
4 C-----G [3] O2 - N2 2.85 N3 - N1 2.85 N4 - O6 2.85
5 G-----C [3] O6 - N4 2.85 N1 - N3 2.85 N2 - O2 2.85
6 A-----T [2] N6 - O4 2.95 N1 - N3 2.88
7 T-----A [2] N3 - N1 2.88 O4 - N6 2.95
8 C-----G [3] O2 - N2 2.85 N3 - N1 2.85 N4 - O6 2.85
9 G-----C [3] O6 - N4 2.85 N1 - N3 2.85 N2 - O2 2.85
10 A-----T [2] N6 - O4 2.95 N1 - N3 2.88
11 T-----A [2] N3 - N1 2.88 O4 - N6 2.95
12 C-----G [3] O2 - N2 2.85 N3 - N1 2.85 N4 - O6 2.85
13 G-----C [3] O6 - N4 2.85 N1 - N3 2.85 N2 - O2 2.85
14 A-----T [2] N6 - O4 2.95 N1 - N3 2.88
15 T-----A [2] N3 - N1 2.88 O4 - N6 2.95
16 C-----G [3] O2 - N2 2.85 N3 - N1 2.85 N4 - O6 2.85
****************************************************************************
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 GA/TC 5.20( 2.22) 0.00( 0.00) 0.00( 0.00) 3.74( 0.14) 8.94( 2.36)
2 AT/AT 4.08( 0.41) 0.00( 0.00) 0.00( 0.00) 4.08( 0.41) 8.16( 0.82)
3 TC/GA 3.74( 0.14) 0.00( 0.00) 0.00( 0.00) 5.20( 2.22) 8.94( 2.36)
4 CG/CG 1.50( 0.00) 0.00( 0.00) 0.65( 0.00) 1.50( 0.00) 3.65( 0.00)
5 GA/TC 5.20( 2.22) 0.00( 0.00) 0.00( 0.00) 3.74( 0.14) 8.94( 2.36)
6 AT/AT 4.08( 0.41) 0.00( 0.00) 0.00( 0.00) 4.08( 0.41) 8.16( 0.82)
7 TC/GA 3.74( 0.14) 0.00( 0.00) 0.00( 0.00) 5.20( 2.22) 8.94( 2.37)
8 CG/CG 1.50( 0.00) 0.00( 0.00) 0.65( 0.00) 1.50( 0.00) 3.65( 0.00)
9 GA/TC 5.20( 2.22) 0.00( 0.00) 0.00( 0.00) 3.74( 0.14) 8.94( 2.37)
10 AT/AT 4.08( 0.41) 0.00( 0.00) 0.00( 0.00) 4.08( 0.41) 8.16( 0.82)
11 TC/GA 3.74( 0.14) 0.00( 0.00) 0.00( 0.00) 5.20( 2.22) 8.94( 2.36)
12 CG/CG 1.50( 0.00) 0.00( 0.00) 0.65( 0.00) 1.50( 0.00) 3.65( 0.00)
13 GA/TC 5.20( 2.22) 0.00( 0.00) 0.00( 0.00) 3.74( 0.14) 8.94( 2.36)
14 AT/AT 4.08( 0.41) 0.00( 0.00) 0.00( 0.00) 4.08( 0.41) 8.16( 0.82)
15 TC/GA 3.74( 0.14) 0.00( 0.00) 0.00( 0.00) 5.20( 2.22) 8.94( 2.36)
****************************************************************************
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 -0.52 -0.03 0.01 0.00 -0.05 -1.00
2 A-T -0.39 0.29 -3.38 -0.03 -0.04 -1.00
3 T-A -0.16 0.46 -6.75 -0.05 -0.01 -1.00
4 C-G 0.19 0.48 -10.14 -0.05 0.01 -1.00
5 G-C 0.40 0.33 -13.49 -0.03 0.04 -1.00
6 A-T 0.48 -0.01 -16.88 0.00 0.05 -1.00
7 T-A 0.40 -0.28 -20.25 0.03 0.04 -1.00
8 C-G 0.13 -0.50 -23.64 0.05 0.01 -1.00
9 G-C -0.13 -0.50 -26.99 0.05 -0.01 -1.00
10 A-T -0.40 -0.28 -30.38 0.03 -0.04 -1.00
11 T-A -0.48 -0.01 -33.75 0.00 -0.05 -1.00
12 C-G -0.40 0.33 -37.14 -0.03 -0.04 -1.00
13 G-C -0.19 0.48 -40.49 -0.05 -0.01 -1.00
14 A-T 0.16 0.46 -43.88 -0.05 0.01 -1.00
15 T-A 0.39 0.29 -47.25 -0.03 0.04 -1.00
16 C-G 0.52 -0.03 -50.64 0.00 0.05 -1.00
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.14 -0.18 0.10 0.26 -15.15 -1.31
2 A-T 0.03 -0.10 0.09 -0.04 -15.13 -1.88
3 T-A -0.03 -0.10 0.09 0.04 -15.13 -1.87
4 C-G 0.14 -0.18 0.10 -0.26 -15.15 -1.29
5 G-C -0.14 -0.18 0.10 0.26 -15.15 -1.30
6 A-T 0.03 -0.10 0.09 -0.04 -15.13 -1.88
7 T-A -0.03 -0.10 0.09 0.04 -15.13 -1.88
8 C-G 0.14 -0.18 0.10 -0.26 -15.14 -1.29
9 G-C -0.14 -0.18 0.10 0.26 -15.14 -1.29
10 A-T 0.03 -0.10 0.09 -0.04 -15.13 -1.88
11 T-A -0.03 -0.10 0.09 0.04 -15.13 -1.88
12 C-G 0.14 -0.18 0.10 -0.26 -15.15 -1.30
13 G-C -0.14 -0.18 0.10 0.26 -15.15 -1.29
14 A-T 0.03 -0.10 0.09 -0.04 -15.13 -1.87
15 T-A -0.03 -0.10 0.09 0.04 -15.13 -1.88
16 C-G 0.14 -0.18 0.10 -0.26 -15.15 -1.31
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.00 -0.14 0.09 0.00 -15.14 -1.59
s.d. 0.11 0.05 0.00 0.19 0.01 0.30
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GA/TC -0.03 0.50 3.37 -0.01 1.71 37.13
2 AT/AT 0.00 0.44 3.35 0.00 1.71 35.67
3 TC/GA 0.03 0.50 3.37 0.01 1.71 37.13
4 CG/CG -0.00 0.41 3.34 -0.00 1.70 33.93
5 GA/TC -0.03 0.50 3.37 -0.01 1.72 37.12
6 AT/AT 0.00 0.44 3.35 -0.00 1.70 35.67
7 TC/GA 0.03 0.50 3.37 0.01 1.72 37.13
8 CG/CG -0.00 0.41 3.34 -0.00 1.70 33.92
9 GA/TC -0.03 0.50 3.37 -0.01 1.72 37.13
10 AT/AT -0.00 0.44 3.35 0.00 1.70 35.67
11 TC/GA 0.03 0.50 3.37 0.01 1.72 37.12
12 CG/CG 0.00 0.41 3.34 0.00 1.70 33.93
13 GA/TC -0.03 0.50 3.37 -0.01 1.71 37.13
14 AT/AT -0.00 0.44 3.35 -0.00 1.71 35.67
15 TC/GA 0.03 0.50 3.37 0.01 1.71 37.13
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.00 0.47 3.36 -0.00 1.71 36.10
s.d. 0.02 0.04 0.01 0.01 0.01 1.29
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GA/TC 0.55 0.04 3.39 2.69 0.02 37.17
2 AT/AT 0.46 -0.00 3.37 2.78 -0.00 35.71
3 TC/GA 0.55 -0.04 3.39 2.69 -0.02 37.16
4 CG/CG 0.43 0.00 3.35 2.91 0.00 33.97
5 GA/TC 0.55 0.04 3.39 2.69 0.02 37.16
6 AT/AT 0.46 -0.00 3.37 2.78 0.00 35.71
7 TC/GA 0.55 -0.04 3.39 2.69 -0.02 37.17
8 CG/CG 0.43 0.00 3.35 2.91 0.00 33.96
9 GA/TC 0.55 0.04 3.39 2.69 0.02 37.17
10 AT/AT 0.46 0.00 3.37 2.78 -0.00 35.71
11 TC/GA 0.55 -0.04 3.39 2.69 -0.02 37.16
12 CG/CG 0.43 -0.00 3.35 2.91 -0.00 33.97
13 GA/TC 0.55 0.04 3.39 2.69 0.02 37.16
14 AT/AT 0.46 0.00 3.37 2.78 0.00 35.71
15 TC/GA 0.55 -0.04 3.39 2.69 -0.02 37.17
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.50 -0.00 3.38 2.76 0.00 36.14
s.d. 0.06 0.03 0.01 0.09 0.02 1.29
****************************************************************************
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 G-C 54.2 54.2 10.7 8.9 9.8
2 A-T 54.2 54.2 10.7 8.9 9.9
3 T-A 54.1 54.2 10.7 8.9 9.9
4 C-G 54.2 54.1 10.7 8.9 9.8
5 G-C 54.2 54.2 10.7 8.9 9.8
6 A-T 54.2 54.2 10.7 8.9 9.9
7 T-A 54.2 54.2 10.7 8.9 9.9
8 C-G 54.1 54.2 10.7 8.9 9.8
9 G-C 54.2 54.1 10.7 8.9 9.8
10 A-T 54.2 54.2 10.7 8.9 9.9
11 T-A 54.2 54.2 10.7 8.9 9.9
12 C-G 54.2 54.2 10.7 8.9 9.8
13 G-C 54.1 54.2 10.7 8.9 9.8
14 A-T 54.2 54.1 10.7 8.9 9.9
15 T-A 54.2 54.2 10.7 8.9 9.9
16 C-G 54.2 54.2 10.7 8.9 9.8
****************************************************************************
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 GA/TC -2.98 8.86 -0.57 -2.45 8.88 -0.17 B
2 AT/AT -2.97 8.86 -0.57 -2.54 8.88 -0.16 B
3 TC/GA -2.98 8.86 -0.57 -2.45 8.88 -0.17 B
4 CG/CG -3.01 8.86 -0.57 -2.60 8.88 -0.14 B
5 GA/TC -2.98 8.86 -0.57 -2.45 8.88 -0.17 B
6 AT/AT -2.97 8.86 -0.57 -2.54 8.88 -0.16 B
7 TC/GA -2.98 8.86 -0.57 -2.46 8.88 -0.17 B
8 CG/CG -3.01 8.86 -0.57 -2.60 8.88 -0.14 B
9 GA/TC -2.98 8.86 -0.57 -2.46 8.88 -0.17 B
10 AT/AT -2.97 8.86 -0.57 -2.54 8.88 -0.16 B
11 TC/GA -2.98 8.86 -0.57 -2.45 8.88 -0.17 B
12 CG/CG -3.01 8.86 -0.57 -2.60 8.88 -0.14 B
13 GA/TC -2.98 8.86 -0.57 -2.45 8.88 -0.17 B
14 AT/AT -2.97 8.86 -0.57 -2.54 8.88 -0.16 B
15 TC/GA -2.98 8.86 -0.57 -2.45 8.88 -0.17 B
****************************************************************************
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 GA/TC --- --- --- ---
2 AT/AT --- --- --- ---
3 TC/GA 11.7 --- 17.2 ---
4 CG/CG 11.7 11.7 17.2 17.2
5 GA/TC 11.7 11.7 17.2 17.2
6 AT/AT 11.7 11.7 17.2 17.2
7 TC/GA 11.7 11.7 17.2 17.2
8 CG/CG 11.7 11.7 17.2 17.2
9 GA/TC 11.7 11.7 17.2 17.2
10 AT/AT 11.7 11.7 17.2 17.2
11 TC/GA 11.7 11.7 17.2 17.2
12 CG/CG 11.7 11.7 17.2 17.2
13 GA/TC 11.7 --- 17.2 ---
14 AT/AT --- --- --- ---
15 TC/GA --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.38(0.00)
Helix: -0.000 -0.000 -1.000
HETATM 9998 XS X X 999 -0.000 0.000 0.000
HETATM 9999 XE X X 999 -0.000 0.000 -50.625
Average and standard deviation of helix radius:
P: 9.23(0.00), O4': 6.15(0.00), C1': 5.68(0.00)
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 G-C 1.91 -0.17 36.00 3.38
2 A-T 1.91 -0.17 36.00 3.38
3 T-A 1.91 -0.17 36.00 3.38
4 C-G 1.91 -0.17 36.00 3.38
5 G-C 1.91 -0.17 36.00 3.38
6 A-T 1.91 -0.17 36.00 3.38
7 T-A 1.91 -0.17 36.00 3.38
8 C-G 1.91 -0.17 36.00 3.38
9 G-C 1.91 -0.17 36.00 3.38
10 A-T 1.91 -0.17 36.00 3.38
11 T-A 1.91 -0.17 36.00 3.38
12 C-G 1.91 -0.17 36.00 3.38
13 G-C 1.91 -0.17 36.00 3.38
14 A-T 1.91 -0.17 36.00 3.38
15 T-A 1.91 -0.17 36.00 3.38
16 C-G 1.91 -0.17 --- ---
****************************************************************************
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 --- 136.4 31.1 143.4 -140.8 -160.5 -98.0
2 A -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
3 T -29.9 136.3 31.1 143.3 -140.8 -160.5 -97.9
4 C -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
5 G -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
6 A -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
7 T -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
8 C -29.9 136.3 31.1 143.3 -140.8 -160.5 -97.9
9 G -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
10 A -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
11 T -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
12 C -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
13 G -29.9 136.3 31.1 143.3 -140.8 -160.5 -98.0
14 A -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
15 T -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
16 C -29.9 136.4 31.1 143.4 --- --- -98.0
Strand II
base alpha beta gamma delta epsilon zeta chi
1 C -29.9 136.4 31.1 143.4 --- --- -98.0
2 T -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
3 A -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
4 G -29.9 136.3 31.1 143.3 -140.8 -160.5 -98.0
5 C -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
6 T -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
7 A -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
8 G -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
9 C -29.9 136.3 31.1 143.3 -140.8 -160.5 -97.9
10 T -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
11 A -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
12 G -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
13 C -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0
14 T -29.9 136.3 31.1 143.3 -140.8 -160.5 -97.9
15 A -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0
16 G --- 136.4 31.1 143.4 -140.8 -160.5 -98.0
****************************************************************************
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 -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
2 A -33.0 44.7 -40.2 23.1 5.9 44.7 153.9 C2'-endo
3 T -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
4 C -33.0 44.7 -40.2 23.0 6.0 44.8 153.9 C2'-endo
5 G -33.1 44.8 -40.2 23.1 5.9 44.8 153.9 C2'-endo
6 A -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
7 T -33.0 44.7 -40.2 23.1 5.9 44.7 153.9 C2'-endo
8 C -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
9 G -33.0 44.7 -40.2 23.0 6.0 44.8 153.9 C2'-endo
10 A -33.1 44.8 -40.2 23.1 5.9 44.8 153.9 C2'-endo
11 T -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
12 C -33.0 44.7 -40.2 23.1 5.9 44.7 153.9 C2'-endo
13 G -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
14 A -33.0 44.7 -40.2 23.0 6.0 44.8 153.9 C2'-endo
15 T -33.1 44.8 -40.2 23.1 5.9 44.8 153.9 C2'-endo
16 C -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 C -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
2 T -33.1 44.8 -40.2 23.1 5.9 44.8 153.9 C2'-endo
3 A -33.0 44.7 -40.2 23.0 6.0 44.8 153.9 C2'-endo
4 G -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
5 C -33.0 44.7 -40.2 23.1 5.9 44.7 153.9 C2'-endo
6 T -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
7 A -33.1 44.8 -40.2 23.1 5.9 44.8 153.9 C2'-endo
8 G -33.0 44.7 -40.2 23.0 6.0 44.8 153.9 C2'-endo
9 C -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
10 T -33.0 44.7 -40.2 23.1 5.9 44.7 153.9 C2'-endo
11 A -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
12 G -33.1 44.8 -40.2 23.1 5.9 44.8 153.9 C2'-endo
13 C -33.0 44.7 -40.2 23.0 6.0 44.8 153.9 C2'-endo
14 T -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-endo
15 A -33.0 44.7 -40.2 23.1 5.9 44.7 153.9 C2'-endo
16 G -33.0 44.7 -40.2 23.1 5.9 44.8 153.9 C2'-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/A 6.6 4.9 1 C/T 6.6 4.9
2 A/T 6.6 4.9 2 T/A 6.6 4.9
3 T/C 6.6 4.9 3 A/G 6.6 4.9
4 C/G 6.6 4.9 4 G/C 6.6 4.9
5 G/A 6.6 4.9 5 C/T 6.6 4.9
6 A/T 6.6 4.9 6 T/A 6.6 4.9
7 T/C 6.6 4.9 7 A/G 6.6 4.9
8 C/G 6.6 4.9 8 G/C 6.6 4.9
9 G/A 6.6 4.9 9 C/T 6.6 4.9
10 A/T 6.6 4.9 10 T/A 6.6 4.9
11 T/C 6.6 4.9 11 A/G 6.6 4.9
12 C/G 6.6 4.9 12 G/C 6.6 4.9
13 G/A 6.6 4.9 13 C/T 6.6 4.9
14 A/T 6.6 4.9 14 T/A 6.6 4.9
15 T/C 6.6 4.9 15 A/G 6.6 4.9
****************************************************************************
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 GA/TC 9.3 6.2 5.7 9.2 6.1 5.6
2 AT/AT 9.2 6.2 5.7 9.2 6.2 5.7
3 TC/GA 9.2 6.1 5.6 9.3 6.2 5.7
4 CG/CG 9.3 6.2 5.7 9.2 6.2 5.7
5 GA/TC 9.3 6.2 5.7 9.2 6.1 5.6
6 AT/AT 9.2 6.2 5.7 9.2 6.2 5.7
7 TC/GA 9.2 6.1 5.6 9.3 6.2 5.7
8 CG/CG 9.3 6.2 5.7 9.3 6.2 5.7
9 GA/TC 9.3 6.2 5.7 9.2 6.1 5.6
10 AT/AT 9.2 6.2 5.7 9.2 6.2 5.7
11 TC/GA 9.2 6.1 5.6 9.3 6.2 5.7
12 CG/CG 9.2 6.2 5.7 9.3 6.2 5.7
13 GA/TC 9.3 6.2 5.7 9.2 6.1 5.6
14 AT/AT 9.2 6.2 5.7 9.2 6.2 5.7
15 TC/GA 9.2 6.1 5.6 9.3 6.2 5.7
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
bp Px Py Pz Hx Hy Hz
1 GA/TC 0.04 -0.07 -1.68 -0.00 -0.00 -1.00
2 AT/AT -0.02 0.02 -5.06 0.00 0.00 -1.00
3 TC/GA 0.05 -0.06 -8.44 -0.00 0.00 -1.00
4 CG/CG 0.05 0.07 -11.81 0.00 -0.00 -1.00
5 GA/TC -0.07 0.03 -15.18 -0.00 0.00 -1.00
6 AT/AT 0.03 -0.01 -18.56 -0.00 -0.00 -1.00
7 TC/GA -0.07 0.01 -21.94 0.00 0.00 -1.00
8 CG/CG 0.00 -0.09 -25.31 -0.00 0.00 -1.00
9 GA/TC 0.07 0.01 -28.68 0.00 -0.00 -1.00
10 AT/AT -0.03 -0.01 -32.06 -0.00 0.00 -1.00
11 TC/GA 0.07 0.03 -35.44 -0.00 -0.00 -1.00
12 CG/CG -0.05 0.07 -38.81 0.00 0.00 -1.00
13 GA/TC -0.05 -0.06 -42.18 -0.00 -0.00 -1.00
14 AT/AT 0.02 0.02 -45.56 0.00 -0.00 -1.00
15 TC/GA -0.04 -0.07 -48.94 -0.00 0.00 -1.00