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General discussions (Q&As) / Helical parameters output of X3DNA
« on: August 22, 2007, 12:41:57 am »
Dear,
I wonder why that the number of helical parameters printed out of
'analyze' is one less than the number of base-pairs. Is there a reason why
or I am missing something fundamental?
Appended below is the a.out file.
Thanks,
kp
****************************************************************************
****************************************************************************
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: test.pdb
Date and time: Mon Aug 20 17:11:05 2007
Number of base-pairs: 10
Number of atoms: 3390
****************************************************************************
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)
Strand I Strand II Helix
1 (0.063) A:...1_:[..A]A-----T[..T]:..20_:A (0.051) |
2 (0.071) A:...2_:[..A]A-----T[..T]:..19_:A (0.042) |
3 (0.066) A:...3_:[..A]A-----T[..T]:..18_:A (0.046) |
4 (0.080) A:...4_:[..A]A-----T[..T]:..17_:A (0.074) |
5 (0.055) A:...5_:[..A]A-----T[..T]:..16_:A (0.040) |
6 (0.067) A:...6_:[..A]A-----T[..T]:..15_:A (0.041) |
7 (0.042) A:...7_:[..A]A-----T[..T]:..14_:A (0.059) |
8 (0.070) A:...8_:[..A]A-----T[..T]:..13_:A (0.064) |
9 (0.046) A:...9_:[..A]A-----T[..T]:..12_:A (0.061) |
10 (0.061) A:..10_:[..A]A-----T[..T]:..11_:A (0.076) |
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 A-----T [2] N6 - O4 2.90 N1 - N3 2.98
2 A-----T [2] N6 - O4 3.26 N1 - N3 3.07
3 A-----T [2] N6 - O4 3.09 N1 - N3 3.02
4 A-----T [2] N6 - O4 3.14 N1 - N3 2.94
5 A-----T [2] N6 - O4 3.03 N1 - N3 3.02
6 A-----T [2] N6 - O4 2.81 N1 - N3 2.95
7 A-----T [2] N6 - O4 2.75 N1 - N3 3.05
8 A-----T [2] N6 - O4 2.96 N1 - N3 2.89
9 A-----T [2] N6 - O4 3.54 N1 - N3 2.84
10 A-----T [2] N6 - O4 2.88 N1 - N3 3.06
****************************************************************************
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 AA/TT 4.74( 3.05) 0.00( 0.00) 0.00( 0.00) 5.23( 0.01) 9.96( 3.06)
2 AA/TT 0.39( 0.00) 0.00( 0.00) 0.00( 0.00) 8.19( 2.68) 8.58( 2.68)
3 AA/TT 3.24( 2.18) 0.00( 0.00) 0.00( 0.00) 4.08( 0.02) 7.31( 2.20)
4 AA/TT 2.56( 2.03) 0.00( 0.00) 0.00( 0.00) 3.14( 0.00) 5.69( 2.03)
5 AA/TT 2.08( 0.86) 0.00( 0.00) 0.00( 0.00) 7.48( 1.76) 9.56( 2.61)
6 AA/TT 4.10( 3.17) 0.00( 0.00) 0.00( 0.00) 3.60( 0.00) 7.70( 3.17)
7 AA/TT 2.63( 1.82) 0.00( 0.00) 0.00( 0.00) 4.59( 0.14) 7.22( 1.96)
8 AA/TT 3.96( 2.47) 0.00( 0.00) 0.00( 0.00) 4.46( 0.00) 8.43( 2.47)
9 AA/TT 1.82( 0.64) 0.00( 0.00) 0.00( 0.00) 7.77( 1.86) 9.59( 2.50)
****************************************************************************
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 A-T 37.60 35.96 24.86 -0.75 -0.59 0.30
2 A-T 35.23 34.08 25.15 -0.67 -0.74 0.07
3 A-T 32.07 31.79 27.06 -0.65 -0.75 0.14
4 A-T 29.66 29.31 26.84 -0.67 -0.73 0.14
5 A-T 27.08 26.55 26.22 -0.67 -0.74 0.11
6 A-T 24.53 24.26 26.06 -0.62 -0.76 0.20
7 A-T 23.12 21.15 26.43 -0.63 -0.76 0.13
8 A-T 21.78 18.24 27.04 -0.59 -0.81 0.03
9 A-T 19.56 16.18 27.53 -0.61 -0.79 -0.01
10 A-T 18.52 12.87 27.38 -0.64 -0.76 -0.09
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 A-T -0.10 -0.27 -0.81 12.69 -25.71 7.98
2 A-T -0.20 0.22 0.47 24.48 -9.98 7.73
3 A-T 0.38 0.10 0.38 1.16 -16.25 1.81
4 A-T 0.21 0.13 0.18 -4.00 -16.93 5.81
5 A-T 0.21 0.14 -0.25 -18.33 -3.53 -2.54
6 A-T 0.50 0.03 -0.08 -9.36 -12.22 -4.65
7 A-T 0.10 -0.02 -0.06 2.81 -2.71 -10.65
8 A-T -0.06 -0.05 -0.12 12.01 -14.90 -0.77
9 A-T 0.06 0.11 0.80 15.69 -27.91 15.23
10 A-T 0.11 0.09 0.64 14.73 -14.33 -8.04
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.12 0.05 0.12 5.19 -14.45 1.19
s.d. 0.21 0.14 0.48 13.11 8.16 8.06
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 AA/TT 0.34 -0.17 3.02 -11.74 11.19 32.23
2 AA/TT -1.71 -0.22 3.98 -3.17 -3.15 40.48
3 AA/TT 0.23 -0.68 3.39 0.81 -1.24 32.38
4 AA/TT -0.10 -1.08 3.67 1.81 0.00 34.47
5 AA/TT -0.75 -0.30 3.33 -2.83 5.37 33.25
6 AA/TT 0.19 -0.89 3.31 1.29 -3.94 28.47
7 AA/TT 0.24 -0.78 3.16 2.91 -6.07 35.57
8 AA/TT 0.70 0.04 2.99 -2.95 -0.16 41.95
9 AA/TT -1.27 -0.18 3.22 -5.25 1.58 29.06
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.24 -0.48 3.34 -2.12 0.40 34.21
s.d. 0.82 0.39 0.32 4.55 5.23 4.59
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 AA/TT -1.72 -2.05 2.56 18.74 19.67 35.99
2 AA/TT 0.12 2.02 4.11 -4.54 4.57 40.71
3 AA/TT -0.99 -0.27 3.42 -2.23 -1.44 32.41
4 AA/TT -1.82 0.48 3.66 0.00 -3.05 34.52
5 AA/TT -1.41 0.82 3.29 9.30 4.90 33.78
6 AA/TT -0.89 -0.09 3.41 -7.95 -2.61 28.77
7 AA/TT -0.41 0.02 3.25 -9.82 -4.71 36.18
8 AA/TT 0.06 -1.25 2.94 -0.22 4.11 42.05
9 AA/TT -0.69 1.35 3.38 3.12 10.35 29.56
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.86 0.12 3.33 0.71 3.53 34.88
s.d. 0.71 1.25 0.43 8.86 7.78 4.49
****************************************************************************
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 A-T 57.8 59.3 10.2 8.6 9.7
2 A-T 58.6 61.9 10.3 8.8 10.0
3 A-T 57.6 53.6 10.7 9.1 10.1
4 A-T 63.2 55.8 10.5 9.0 10.2
5 A-T 57.6 52.5 10.8 9.1 10.0
6 A-T 58.3 49.0 10.9 9.1 10.0
7 A-T 53.8 51.2 10.9 9.1 9.9
8 A-T 56.9 57.4 10.5 8.9 9.9
9 A-T 58.6 63.4 10.0 8.6 10.0
10 A-T 50.0 52.6 11.1 9.2 10.0
****************************************************************************
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 AA/TT -4.31 8.40 -0.82 -5.70 8.18 2.19 B
2 AA/TT -3.79 8.82 -0.03 -3.61 8.79 -0.71 B
3 AA/TT -3.80 9.11 -0.42 -4.74 9.09 -0.76 B
4 AA/TT -3.41 9.03 -0.04 -5.11 9.03 -0.05 B
5 AA/TT -2.16 9.02 0.77 -3.60 8.79 2.18
6 AA/TT -2.18 9.46 0.84 -3.02 9.48 -0.44
7 AA/TT -2.57 8.91 0.46 -3.01 8.87 -0.97 B
8 AA/TT -3.16 8.75 0.08 -3.04 8.75 0.05 B
9 AA/TT -4.05 8.81 -1.27 -4.72 8.87 -0.76 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 AA/TT --- --- --- ---
2 AA/TT --- --- --- ---
3 AA/TT 10.8 --- 18.9 ---
4 AA/TT 11.3 11.1 18.2 18.1
5 AA/TT 12.9 12.9 21.3 21.1
6 AA/TT 13.2 13.2 20.6 20.6
7 AA/TT 10.7 --- 21.3 ---
8 AA/TT --- --- --- ---
9 AA/TT --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.36(0.50)
Helix: -0.630 -0.763 0.142
HETATM 9998 XS X X 999 36.556 36.152 24.444
HETATM 9999 XE X X 999 17.508 13.084 28.739
Average and standard deviation of helix radius:
P: 9.85(0.67), O4': 6.92(0.71), C1': 6.32(0.68)
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 A-T 3.82 2.16 33.56 3.82
2 A-T 3.13 4.54 36.57 2.73
3 A-T 4.33 -2.32 32.44 2.92
4 A-T 3.94 -3.48 35.36 3.18
5 A-T 3.55 -2.90 31.94 4.13
6 A-T 4.04 -5.26 30.09 3.63
7 A-T 3.07 -0.86 36.64 3.15
8 A-T 3.15 -4.43 40.17 3.09
9 A-T 3.06 -14.65 30.16 3.57
10 A-T 3.22 -11.90 --- ---
****************************************************************************
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 A --- --- 48.5 136.9 -134.9 -69.1 -131.4
2 A -99.1 178.1 44.1 140.5 -89.8 161.2 -77.4
3 A -96.7 141.7 65.9 119.1 172.4 -71.1 -116.3
4 A -74.6 174.2 57.2 111.9 -170.8 -103.0 -129.0
5 A -43.3 165.4 37.6 116.9 -160.9 -103.2 -146.8
6 A -83.6 165.2 74.7 110.0 -166.9 -91.9 -128.2
7 A -51.8 170.9 50.5 135.7 171.7 -118.8 -116.0
8 A -56.5 -178.8 61.3 139.0 172.7 -94.9 -102.0
9 A -46.4 -178.9 60.1 145.5 -167.4 -73.4 -91.9
10 A -94.0 169.0 44.6 126.5 --- --- -84.2
Strand II
base alpha beta gamma delta epsilon zeta chi
1 T -56.3 158.2 78.8 122.3 --- --- -120.7
2 T -64.9 163.6 55.0 96.0 179.2 -96.0 -141.3
3 T -61.9 -178.2 44.6 136.2 -176.5 -91.2 -106.9
4 T -65.7 -170.7 49.8 132.5 173.9 -90.3 -112.1
5 T -61.5 170.1 78.6 140.0 176.4 -98.7 -115.6
6 T -83.7 170.9 61.7 76.9 -169.8 -69.0 -142.4
7 T -80.0 174.1 55.4 89.4 167.9 -67.0 -146.1
8 T -66.5 176.6 69.7 120.7 -175.6 -89.6 -128.2
9 T -74.9 161.6 69.3 86.5 177.1 -93.0 -146.5
10 T --- --- 60.1 112.7 -179.3 -86.7 -121.1
****************************************************************************
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 A -27.0 31.5 -22.9 8.4 10.9 30.3 139.2 C1'-exo
2 A -34.1 43.4 -37.2 17.9 10.8 43.7 148.4 C2'-endo
3 A -25.4 36.7 -34.2 18.8 4.6 37.6 155.5 C2'-endo
4 A -41.8 39.4 -19.0 -5.4 29.0 42.1 116.8 C1'-exo
5 A -35.6 29.5 -13.0 -7.7 29.8 35.8 111.2 C1'-exo
6 A -27.3 31.5 -21.0 6.7 12.9 29.8 134.9 C1'-exo
7 A -35.5 43.1 -31.5 11.3 15.4 41.4 139.5 C1'-exo
8 A -6.9 21.3 -24.8 24.4 -11.1 24.9 185.4 C3'-exo
9 A -11.1 28.7 -31.7 28.7 -12.3 31.7 180.7 C3'-exo
10 A -35.3 35.5 -21.4 -0.1 23.2 37.3 125.0 C1'-exo
Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 T -31.2 31.9 -21.5 3.7 17.2 32.9 130.9 C1'-exo
2 T -40.2 22.2 2.2 -24.3 39.0 40.9 86.9 O4'-endo
3 T -29.2 43.8 -38.6 22.7 4.1 42.5 155.4 C2'-endo
4 T -10.0 23.5 -26.4 20.9 -7.3 26.4 176.3 C2'-endo
5 T -24.2 38.0 -35.1 23.2 -0.7 37.3 160.5 C2'-endo
6 T 5.3 -27.3 36.4 -32.9 19.0 36.9 9.8 C3'-endo
7 T -38.0 17.2 8.9 -33.4 45.4 44.5 78.4 O4'-endo
8 T -26.7 26.3 -15.8 0.9 15.8 27.2 125.6 C1'-exo
9 T -37.3 15.7 11.2 -36.4 45.7 45.3 75.7 O4'-endo
10 T -48.0 43.5 -23.2 -6.1 34.5 48.8 118.4 C1'-exo
****************************************************************************
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 A/A --- 5.2 1 T/T 6.6 5.4
2 A/A 6.5 5.5 2 T/T 6.8 4.6
3 A/A 7.1 4.7 3 T/T 6.8 4.8
4 A/A 6.7 5.1 4 T/T 6.9 5.4
5 A/A 6.8 5.6 5 T/T 6.3 5.2
6 A/A 6.8 5.0 6 T/T 6.6 5.1
7 A/A 7.0 5.3 7 T/T 7.1 5.0
8 A/A 6.8 4.7 8 T/T 6.6 5.3
9 A/A 7.0 4.9 9 T/T --- 4.3
****************************************************************************
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 AA/TT 8.7 5.8 4.8 11.8 9.3 8.5
2 AA/TT 11.2 8.3 7.7 8.0 4.5 4.1
3 AA/TT 10.0 6.5 6.0 10.5 7.3 6.8
4 AA/TT 11.0 7.7 7.1 9.8 7.3 6.7
5 AA/TT 10.7 8.1 7.2 8.3 6.8 6.1
6 AA/TT 9.8 6.5 5.9 10.1 7.2 6.4
7 AA/TT 8.9 6.4 5.9 9.8 6.5 5.9
8 AA/TT 8.0 5.2 4.7 10.5 7.6 6.8
9 AA/TT 11.1 7.8 7.3 9.0 5.6 5.0
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
bp Px Py Pz Hx Hy Hz
1 AA/TT 37.21 33.71 22.97 -0.36 -0.84 0.40
2 AA/TT 32.37 34.19 25.48 -0.73 -0.67 0.15
3 AA/TT 31.56 29.91 26.67 -0.66 -0.75 0.10
4 AA/TT 29.69 26.78 26.12 -0.63 -0.77 0.13
5 AA/TT 26.83 24.25 26.33 -0.75 -0.62 0.23
6 AA/TT 24.13 22.67 27.05 -0.52 -0.84 0.15
7 AA/TT 22.46 19.77 27.11 -0.48 -0.86 0.18
8 AA/TT 20.06 17.65 26.39 -0.56 -0.83 -0.03
9 AA/TT 18.51 14.63 28.82 -0.49 -0.86 -0.12
I wonder why that the number of helical parameters printed out of
'analyze' is one less than the number of base-pairs. Is there a reason why
or I am missing something fundamental?
Appended below is the a.out file.
Thanks,
kp
****************************************************************************
****************************************************************************
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: test.pdb
Date and time: Mon Aug 20 17:11:05 2007
Number of base-pairs: 10
Number of atoms: 3390
****************************************************************************
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)
Strand I Strand II Helix
1 (0.063) A:...1_:[..A]A-----T[..T]:..20_:A (0.051) |
2 (0.071) A:...2_:[..A]A-----T[..T]:..19_:A (0.042) |
3 (0.066) A:...3_:[..A]A-----T[..T]:..18_:A (0.046) |
4 (0.080) A:...4_:[..A]A-----T[..T]:..17_:A (0.074) |
5 (0.055) A:...5_:[..A]A-----T[..T]:..16_:A (0.040) |
6 (0.067) A:...6_:[..A]A-----T[..T]:..15_:A (0.041) |
7 (0.042) A:...7_:[..A]A-----T[..T]:..14_:A (0.059) |
8 (0.070) A:...8_:[..A]A-----T[..T]:..13_:A (0.064) |
9 (0.046) A:...9_:[..A]A-----T[..T]:..12_:A (0.061) |
10 (0.061) A:..10_:[..A]A-----T[..T]:..11_:A (0.076) |
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 A-----T [2] N6 - O4 2.90 N1 - N3 2.98
2 A-----T [2] N6 - O4 3.26 N1 - N3 3.07
3 A-----T [2] N6 - O4 3.09 N1 - N3 3.02
4 A-----T [2] N6 - O4 3.14 N1 - N3 2.94
5 A-----T [2] N6 - O4 3.03 N1 - N3 3.02
6 A-----T [2] N6 - O4 2.81 N1 - N3 2.95
7 A-----T [2] N6 - O4 2.75 N1 - N3 3.05
8 A-----T [2] N6 - O4 2.96 N1 - N3 2.89
9 A-----T [2] N6 - O4 3.54 N1 - N3 2.84
10 A-----T [2] N6 - O4 2.88 N1 - N3 3.06
****************************************************************************
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 AA/TT 4.74( 3.05) 0.00( 0.00) 0.00( 0.00) 5.23( 0.01) 9.96( 3.06)
2 AA/TT 0.39( 0.00) 0.00( 0.00) 0.00( 0.00) 8.19( 2.68) 8.58( 2.68)
3 AA/TT 3.24( 2.18) 0.00( 0.00) 0.00( 0.00) 4.08( 0.02) 7.31( 2.20)
4 AA/TT 2.56( 2.03) 0.00( 0.00) 0.00( 0.00) 3.14( 0.00) 5.69( 2.03)
5 AA/TT 2.08( 0.86) 0.00( 0.00) 0.00( 0.00) 7.48( 1.76) 9.56( 2.61)
6 AA/TT 4.10( 3.17) 0.00( 0.00) 0.00( 0.00) 3.60( 0.00) 7.70( 3.17)
7 AA/TT 2.63( 1.82) 0.00( 0.00) 0.00( 0.00) 4.59( 0.14) 7.22( 1.96)
8 AA/TT 3.96( 2.47) 0.00( 0.00) 0.00( 0.00) 4.46( 0.00) 8.43( 2.47)
9 AA/TT 1.82( 0.64) 0.00( 0.00) 0.00( 0.00) 7.77( 1.86) 9.59( 2.50)
****************************************************************************
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 A-T 37.60 35.96 24.86 -0.75 -0.59 0.30
2 A-T 35.23 34.08 25.15 -0.67 -0.74 0.07
3 A-T 32.07 31.79 27.06 -0.65 -0.75 0.14
4 A-T 29.66 29.31 26.84 -0.67 -0.73 0.14
5 A-T 27.08 26.55 26.22 -0.67 -0.74 0.11
6 A-T 24.53 24.26 26.06 -0.62 -0.76 0.20
7 A-T 23.12 21.15 26.43 -0.63 -0.76 0.13
8 A-T 21.78 18.24 27.04 -0.59 -0.81 0.03
9 A-T 19.56 16.18 27.53 -0.61 -0.79 -0.01
10 A-T 18.52 12.87 27.38 -0.64 -0.76 -0.09
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 A-T -0.10 -0.27 -0.81 12.69 -25.71 7.98
2 A-T -0.20 0.22 0.47 24.48 -9.98 7.73
3 A-T 0.38 0.10 0.38 1.16 -16.25 1.81
4 A-T 0.21 0.13 0.18 -4.00 -16.93 5.81
5 A-T 0.21 0.14 -0.25 -18.33 -3.53 -2.54
6 A-T 0.50 0.03 -0.08 -9.36 -12.22 -4.65
7 A-T 0.10 -0.02 -0.06 2.81 -2.71 -10.65
8 A-T -0.06 -0.05 -0.12 12.01 -14.90 -0.77
9 A-T 0.06 0.11 0.80 15.69 -27.91 15.23
10 A-T 0.11 0.09 0.64 14.73 -14.33 -8.04
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.12 0.05 0.12 5.19 -14.45 1.19
s.d. 0.21 0.14 0.48 13.11 8.16 8.06
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 AA/TT 0.34 -0.17 3.02 -11.74 11.19 32.23
2 AA/TT -1.71 -0.22 3.98 -3.17 -3.15 40.48
3 AA/TT 0.23 -0.68 3.39 0.81 -1.24 32.38
4 AA/TT -0.10 -1.08 3.67 1.81 0.00 34.47
5 AA/TT -0.75 -0.30 3.33 -2.83 5.37 33.25
6 AA/TT 0.19 -0.89 3.31 1.29 -3.94 28.47
7 AA/TT 0.24 -0.78 3.16 2.91 -6.07 35.57
8 AA/TT 0.70 0.04 2.99 -2.95 -0.16 41.95
9 AA/TT -1.27 -0.18 3.22 -5.25 1.58 29.06
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.24 -0.48 3.34 -2.12 0.40 34.21
s.d. 0.82 0.39 0.32 4.55 5.23 4.59
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 AA/TT -1.72 -2.05 2.56 18.74 19.67 35.99
2 AA/TT 0.12 2.02 4.11 -4.54 4.57 40.71
3 AA/TT -0.99 -0.27 3.42 -2.23 -1.44 32.41
4 AA/TT -1.82 0.48 3.66 0.00 -3.05 34.52
5 AA/TT -1.41 0.82 3.29 9.30 4.90 33.78
6 AA/TT -0.89 -0.09 3.41 -7.95 -2.61 28.77
7 AA/TT -0.41 0.02 3.25 -9.82 -4.71 36.18
8 AA/TT 0.06 -1.25 2.94 -0.22 4.11 42.05
9 AA/TT -0.69 1.35 3.38 3.12 10.35 29.56
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.86 0.12 3.33 0.71 3.53 34.88
s.d. 0.71 1.25 0.43 8.86 7.78 4.49
****************************************************************************
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 A-T 57.8 59.3 10.2 8.6 9.7
2 A-T 58.6 61.9 10.3 8.8 10.0
3 A-T 57.6 53.6 10.7 9.1 10.1
4 A-T 63.2 55.8 10.5 9.0 10.2
5 A-T 57.6 52.5 10.8 9.1 10.0
6 A-T 58.3 49.0 10.9 9.1 10.0
7 A-T 53.8 51.2 10.9 9.1 9.9
8 A-T 56.9 57.4 10.5 8.9 9.9
9 A-T 58.6 63.4 10.0 8.6 10.0
10 A-T 50.0 52.6 11.1 9.2 10.0
****************************************************************************
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 AA/TT -4.31 8.40 -0.82 -5.70 8.18 2.19 B
2 AA/TT -3.79 8.82 -0.03 -3.61 8.79 -0.71 B
3 AA/TT -3.80 9.11 -0.42 -4.74 9.09 -0.76 B
4 AA/TT -3.41 9.03 -0.04 -5.11 9.03 -0.05 B
5 AA/TT -2.16 9.02 0.77 -3.60 8.79 2.18
6 AA/TT -2.18 9.46 0.84 -3.02 9.48 -0.44
7 AA/TT -2.57 8.91 0.46 -3.01 8.87 -0.97 B
8 AA/TT -3.16 8.75 0.08 -3.04 8.75 0.05 B
9 AA/TT -4.05 8.81 -1.27 -4.72 8.87 -0.76 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 AA/TT --- --- --- ---
2 AA/TT --- --- --- ---
3 AA/TT 10.8 --- 18.9 ---
4 AA/TT 11.3 11.1 18.2 18.1
5 AA/TT 12.9 12.9 21.3 21.1
6 AA/TT 13.2 13.2 20.6 20.6
7 AA/TT 10.7 --- 21.3 ---
8 AA/TT --- --- --- ---
9 AA/TT --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.36(0.50)
Helix: -0.630 -0.763 0.142
HETATM 9998 XS X X 999 36.556 36.152 24.444
HETATM 9999 XE X X 999 17.508 13.084 28.739
Average and standard deviation of helix radius:
P: 9.85(0.67), O4': 6.92(0.71), C1': 6.32(0.68)
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 A-T 3.82 2.16 33.56 3.82
2 A-T 3.13 4.54 36.57 2.73
3 A-T 4.33 -2.32 32.44 2.92
4 A-T 3.94 -3.48 35.36 3.18
5 A-T 3.55 -2.90 31.94 4.13
6 A-T 4.04 -5.26 30.09 3.63
7 A-T 3.07 -0.86 36.64 3.15
8 A-T 3.15 -4.43 40.17 3.09
9 A-T 3.06 -14.65 30.16 3.57
10 A-T 3.22 -11.90 --- ---
****************************************************************************
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 A --- --- 48.5 136.9 -134.9 -69.1 -131.4
2 A -99.1 178.1 44.1 140.5 -89.8 161.2 -77.4
3 A -96.7 141.7 65.9 119.1 172.4 -71.1 -116.3
4 A -74.6 174.2 57.2 111.9 -170.8 -103.0 -129.0
5 A -43.3 165.4 37.6 116.9 -160.9 -103.2 -146.8
6 A -83.6 165.2 74.7 110.0 -166.9 -91.9 -128.2
7 A -51.8 170.9 50.5 135.7 171.7 -118.8 -116.0
8 A -56.5 -178.8 61.3 139.0 172.7 -94.9 -102.0
9 A -46.4 -178.9 60.1 145.5 -167.4 -73.4 -91.9
10 A -94.0 169.0 44.6 126.5 --- --- -84.2
Strand II
base alpha beta gamma delta epsilon zeta chi
1 T -56.3 158.2 78.8 122.3 --- --- -120.7
2 T -64.9 163.6 55.0 96.0 179.2 -96.0 -141.3
3 T -61.9 -178.2 44.6 136.2 -176.5 -91.2 -106.9
4 T -65.7 -170.7 49.8 132.5 173.9 -90.3 -112.1
5 T -61.5 170.1 78.6 140.0 176.4 -98.7 -115.6
6 T -83.7 170.9 61.7 76.9 -169.8 -69.0 -142.4
7 T -80.0 174.1 55.4 89.4 167.9 -67.0 -146.1
8 T -66.5 176.6 69.7 120.7 -175.6 -89.6 -128.2
9 T -74.9 161.6 69.3 86.5 177.1 -93.0 -146.5
10 T --- --- 60.1 112.7 -179.3 -86.7 -121.1
****************************************************************************
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 A -27.0 31.5 -22.9 8.4 10.9 30.3 139.2 C1'-exo
2 A -34.1 43.4 -37.2 17.9 10.8 43.7 148.4 C2'-endo
3 A -25.4 36.7 -34.2 18.8 4.6 37.6 155.5 C2'-endo
4 A -41.8 39.4 -19.0 -5.4 29.0 42.1 116.8 C1'-exo
5 A -35.6 29.5 -13.0 -7.7 29.8 35.8 111.2 C1'-exo
6 A -27.3 31.5 -21.0 6.7 12.9 29.8 134.9 C1'-exo
7 A -35.5 43.1 -31.5 11.3 15.4 41.4 139.5 C1'-exo
8 A -6.9 21.3 -24.8 24.4 -11.1 24.9 185.4 C3'-exo
9 A -11.1 28.7 -31.7 28.7 -12.3 31.7 180.7 C3'-exo
10 A -35.3 35.5 -21.4 -0.1 23.2 37.3 125.0 C1'-exo
Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 T -31.2 31.9 -21.5 3.7 17.2 32.9 130.9 C1'-exo
2 T -40.2 22.2 2.2 -24.3 39.0 40.9 86.9 O4'-endo
3 T -29.2 43.8 -38.6 22.7 4.1 42.5 155.4 C2'-endo
4 T -10.0 23.5 -26.4 20.9 -7.3 26.4 176.3 C2'-endo
5 T -24.2 38.0 -35.1 23.2 -0.7 37.3 160.5 C2'-endo
6 T 5.3 -27.3 36.4 -32.9 19.0 36.9 9.8 C3'-endo
7 T -38.0 17.2 8.9 -33.4 45.4 44.5 78.4 O4'-endo
8 T -26.7 26.3 -15.8 0.9 15.8 27.2 125.6 C1'-exo
9 T -37.3 15.7 11.2 -36.4 45.7 45.3 75.7 O4'-endo
10 T -48.0 43.5 -23.2 -6.1 34.5 48.8 118.4 C1'-exo
****************************************************************************
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 A/A --- 5.2 1 T/T 6.6 5.4
2 A/A 6.5 5.5 2 T/T 6.8 4.6
3 A/A 7.1 4.7 3 T/T 6.8 4.8
4 A/A 6.7 5.1 4 T/T 6.9 5.4
5 A/A 6.8 5.6 5 T/T 6.3 5.2
6 A/A 6.8 5.0 6 T/T 6.6 5.1
7 A/A 7.0 5.3 7 T/T 7.1 5.0
8 A/A 6.8 4.7 8 T/T 6.6 5.3
9 A/A 7.0 4.9 9 T/T --- 4.3
****************************************************************************
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 AA/TT 8.7 5.8 4.8 11.8 9.3 8.5
2 AA/TT 11.2 8.3 7.7 8.0 4.5 4.1
3 AA/TT 10.0 6.5 6.0 10.5 7.3 6.8
4 AA/TT 11.0 7.7 7.1 9.8 7.3 6.7
5 AA/TT 10.7 8.1 7.2 8.3 6.8 6.1
6 AA/TT 9.8 6.5 5.9 10.1 7.2 6.4
7 AA/TT 8.9 6.4 5.9 9.8 6.5 5.9
8 AA/TT 8.0 5.2 4.7 10.5 7.6 6.8
9 AA/TT 11.1 7.8 7.3 9.0 5.6 5.0
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
bp Px Py Pz Hx Hy Hz
1 AA/TT 37.21 33.71 22.97 -0.36 -0.84 0.40
2 AA/TT 32.37 34.19 25.48 -0.73 -0.67 0.15
3 AA/TT 31.56 29.91 26.67 -0.66 -0.75 0.10
4 AA/TT 29.69 26.78 26.12 -0.63 -0.77 0.13
5 AA/TT 26.83 24.25 26.33 -0.75 -0.62 0.23
6 AA/TT 24.13 22.67 27.05 -0.52 -0.84 0.15
7 AA/TT 22.46 19.77 27.11 -0.48 -0.86 0.18
8 AA/TT 20.06 17.65 26.39 -0.56 -0.83 -0.03
9 AA/TT 18.51 14.63 28.82 -0.49 -0.86 -0.12