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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
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3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
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1. The list of the parameters given below correspond to the 5' to 3'
direction
of strand I and 3' to 5' direction of strand II.
2. All angular parameters, except for the phase angle of sugar pseudo-
rotation, are measured in degrees in the range of [-180, +180], and all
displacements are measured in Angstrom units.
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File name: 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
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Structure classification:
This is a right-handed nucleic acid structure
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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
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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 --- --- --- ---
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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
-
Hi,
Thanks for using 3DNA. The number of local helical parameters should be ONE less than the number of base-pairs.
Note that helical parameters refer to a double helix region, and the smallest helix fragment is a dinucleotide step, which is one less than the number of bps. In 3DNA, the helical parameters for each dinucleotide step are defined symmetrically such that they are exactly the same for the two bps.
Hope this clarifies the issue a little bit.
Xiang-Jun
PS. Please make use the file attachment facility -- it is a much better choice than enclosing a long file with your post.
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University