Отчёт к занятию 7студентки 202 группы Рудневой Василисы.
A- и B- формы ДНК.
1. С помощью программы fiber пакета 3DNA постройте A- и B-форму дуплекса ДНК,
последовательность одной из нитей которого — 4 раза повторенная последовательность "gatc".
Структуру дуплекса в А-форме сохраните в файле gatc-a.pdb, а структуру дуплекса в В-форме
сохраните в файле gatc-b.pdb.
A- форма:
fiber -a gatc-a.pdb
Fiber data in directory: /usr/share/x3dna/FIBER/
Structure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)
Input your base sequence with only A,C,G & T:
1. From a data file (complete sequence)
2. From keyboard (enter only the repeating sequence)
Your choice (1 or 2, Dft: 2): 2
Repeating unit (Dft: polyA): gatc
Repeating unit: GATC
Number of repeats (Dft: 10): 4
B- форма:
fiber -b gatc-b.pdb
Fiber data in directory: /usr/share/x3dna/FIBER/
Structure #4; Twist: 36.0 (degrees); Rise: 3.375 (Angstrom)
Input your base sequence with only A,C,G & T:
1. From a data file (complete sequence)
2. From keyboard (enter only the repeating sequence)
Your choice (1 or 2, Dft: 2): 2
Repeating unit (Dft: polyA): gatc
Repeating unit: GATC
Number of repeats (Dft: 10): 4
2. Откройте полученные файлы в RasMol. Скопируйте в отчет следующую таблицу. Изучите структуры
и заполните два столбца таблицы.
A-форма:
Шаг спирали – 28.03
C16A.P – G5A.P
Ширина большой бороздки -- 7.98
G9A.P -- A180.P
Ширина малой бороздки -- 16.97
C8A.P -- C28B.P
B-форма:
Шаг спирали - 33.75
C16A.P - A6A.P
Ширина большой бороздки -- 17.21
A18B.P - C12A.P
Ширина малой бороздки - 11.69
T7A.P - A30B.P
dna12:
Шаг спирали - 30.57
G12A.P - G2A.P
Ширина большой бороздки - 17.12
A18B.P - G4A.P
Ширина малой бороздки - 11.13
C11A.P - A18B.P
из файла dna12.out:
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
1 CG/CG
2 GC/GC
3 CG/cG
4 GA/Tc
5 AA/TT
6 AT/AT
7 TT/AA
8 Tc/GA
9 cG/CG
10 GC/GC
11 CG/CG
Xp
-2.20
-2.01
-1.99
-2.73
-3.46
-4.00
-3.62
-2.98
-2.44
-2.19
-2.31
Yp
Zp
XpH
YpH
ZpH
8.87 -0.16 -2.64
8.81
1.01
B
9.18 -0.50 -0.82
9.02 -1.78
B
9.13 -0.09 -2.59
8.77
2.54
B
8.81 -0.50 -2.56
8.79 -0.73
B
8.88 -0.30 -5.15
8.82
1.05
B
8.96 -0.33 -4.71
8.93 -0.83
B
8.82 -0.46 -3.67
8.83 -0.10
B
8.73 -0.18 -2.41
8.66 -1.13
B
8.97
0.13 -1.16
8.95
0.57
B
8.73
0.40 -0.51
8.57 -1.69
B
8.97 -0.67 -1.36
8.90 -1.29
B
Form
Structure classification:
This is a right-handed nucleic acid structure
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 CG/CG
--------2 GC/GC
--------3 CG/cG
13.4
--17.9
--4 GA/Tc
11.7
11.6
17.8
17.8
5 AA/TT
10.2
10.1
17.1
17.0
6 AT/AT
9.4
9.4
16.1
15.6
7 TT/AA
9.5
9.5
17.4
17.4
8 Tc/GA
10.4
18.5
18.5
9 cG/CG
11.1
--17.6
--10 GC/GC
--------11 CG/CG
--------*******************************************************
Из gatc-a.out:
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
54.3
54.3
10.7
8.9
9.8
2 A-T
54.3
54.3
10.7
8.9
9.9
3 T-A
54.3
54.3
10.7
8.9
9.9
4 C-G
54.3
54.3
10.7
8.9
9.8
5 G-C
54.3
54.3
10.7
8.9
9.8
6 A-T
54.3
54.3
10.7
8.9
9.9
7 T-A
54.3
54.3
10.7
8.9
9.9
8 C-G
54.3
54.3
10.7
8.9
9.8
9 G-C
54.3
54.3
10.7
8.9
9.8
10 A-T
54.3
54.3
10.7
8.9
9.9
11 T-A
54.3
54.3
10.7
8.9
9.9
12 C-G
54.3
54.3
10.7
8.9
9.8
13 G-C
54.3
54.3
10.7
8.9
9.8
14 A-T
54.3
54.3
10.7
8.9
9.9
15 T-A
54.3
54.3
10.7
8.9
9.9
16 C-G
54.3
54.3
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 -0.92
8.36
2.48 -4.98
6.90
5.33
A
2 AT/AT -0.90
8.36
2.48 -5.18
6.85
5.40
A
3 TC/GA -0.92
8.36
2.48 -4.98
6.90
5.33
A
4 CG/CG -0.95
8.36
2.48 -5.69
6.70
5.58
A
5 GA/TC -0.92
8.36
2.48 -4.98
6.90
5.33
A
6 AT/AT -0.90
8.36
2.48 -5.18
6.85
5.40
A
7 TC/GA -0.92
8.36
2.48 -4.98
6.90
5.33
A
8 CG/CG -0.95
8.36
2.48 -5.69
6.70
5.58
A
9 GA/TC -0.92
8.36
2.48 -4.98
6.90
5.33
A
10 AT/AT -0.90
8.36
2.48 -5.18
6.85
5.40
A
11 TC/GA -0.92
8.36
2.48 -4.98
6.90
5.33
A
12 CG/CG -0.95
8.36
2.48 -5.69
6.70
5.58
A
13 GA/TC -0.92
8.36
2.48 -4.98
6.90
5.33
A
14 AT/AT -0.90
8.36
2.48 -5.18
6.85
5.40
A
15 TC/GA -0.92
8.36
2.48 -4.98
6.90
5.33
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.
1 GA/TC
2 AT/AT
3 TC/GA
4 CG/CG
Minor Groove
P-P
Refined
--------18.5
--18.5
16.7
Major Groove
P-P
Refined
--------15.2
--15.2
11.1
5 GA/TC
18.5
16.7
15.2
11.1
6 AT/AT
18.5
16.7
15.2
11.1
7 TC/GA
18.5
16.7
15.2
11.1
8 CG/CG
18.5
16.7
15.2
11.1
9 GA/TC
18.5
16.7
15.2
11.1
10 AT/AT
18.5
16.7
15.2
11.1
11 TC/GA
18.5
16.7
15.2
11.1
12 CG/CG
18.5
16.7
15.2
11.1
13 GA/TC
18.5
--15.2
--14 AT/AT
--------15 TC/GA
--------****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 2.55(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 -38.220
Average and standard deviation of helix radius:
P: 8.59(0.00), O4': 9.09(0.00), C1': 8.50(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
6.87
20.58
32.70
2.55
2 A-T
6.87
20.58
32.70
2.55
3 T-A
6.87
20.58
32.70
2.55
4 C-G
6.87
20.58
32.70
2.55
5 G-C
6.87
20.58
32.70
2.55
6 A-T
6.87
20.58
32.70
2.55
7 T-A
6.87
20.58
32.69
2.55
8 C-G
6.87
20.58
32.70
2.55
9 G-C
6.87
20.58
32.70
2.55
10 A-T
6.87
20.58
32.71
2.55
11 T-A
6.87
20.58
32.70
2.55
12 C-G
6.87
20.58
32.70
2.55
13 G-C
6.87
20.58
32.70
2.55
14 A-T
6.87
20.58
32.70
2.55
15 T-A
6.87
20.58
32.70
2.55
16 C-G
6.87
20.58
----****************************************************************************
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
1G
2A
3T
4C
5G
6A
7T
8C
9G
10 A
11 T
12 C
13 G
14 A
15 T
16 C
alpha
---51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
beta
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
gamma delta epsilon zeta
chi
41.7
79.0 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.0 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.0 -147.8 -75.0 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.7 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1
----- -157.2
Strand II
base
alpha
beta gamma delta epsilon zeta
chi
1C
-51.7 174.8
41.7
79.0
----- -157.2
2T
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
3A
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
4G
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
5C
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
6T
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
7A
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
8G
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
9C
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
10 T
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
11 A
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
12 G
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
13 C
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
14 T
-51.7 174.8
41.7
79.1 -147.8 -75.1 -157.2
15 A
-51.7 174.8
41.7
79.0 -147.8 -75.1 -157.2
16 G
--174.8
41.7
79.1 -147.7 -75.1 -157.2
****************************************************************************
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
1G
2A
3T
4C
5G
6A
7T
8C
9G
v0
8.2
8.2
8.2
8.2
8.2
8.2
8.2
8.3
8.2
v1
-33.5
-33.5
-33.5
-33.6
-33.5
-33.5
-33.5
-33.6
-33.6
v2
44.0
44.0
44.1
44.1
44.1
44.0
44.1
44.0
44.1
v3
-40.1
-40.1
-40.2
-40.2
-40.1
-40.1
-40.1
-40.1
-40.2
v4
20.5
20.6
20.6
20.6
20.6
20.5
20.5
20.5
20.6
tm
44.5
44.5
44.5
44.5
44.5
44.4
44.5
44.5
44.5
P
7.9
8.0
8.0
7.9
7.9
7.9
7.9
7.9
7.9
Puckering
C3'-endo
C3'-endo
C3'-endo
C3'-endo
C3'-endo
C3'-endo
C3'-endo
C3'-endo
C3'-endo
10 A
11 T
12 C
13 G
14 A
15 T
16 C
8.3
8.3
8.2
8.3
8.2
8.3
8.2
-33.6
-33.6
-33.5
-33.6
-33.5
-33.6
-33.6
44.1
44.1
44.1
44.1
44.0
44.1
44.1
-40.2
-40.2
-40.1
-40.2
-40.1
-40.1
-40.2
20.5
20.5
20.5
20.6
20.6
20.5
20.5
44.5
44.5
44.5
44.5
44.5
44.5
44.5
7.9
7.9
7.9
7.9
8.0
7.9
7.9
C3'-endo
C3'-endo
C3'-endo
C3'-endo
C3'-endo
C3'-endo
C3'-endo
Strand II
base
v0
v1
v2
v3
v4
tm
P
Puckering
1C
8.2 -33.5
44.0 -40.1
20.5
44.5
7.9
C3'-endo
2T
8.3 -33.6
44.1 -40.2
20.6
44.5
7.9
C3'-endo
3A
8.2 -33.6
44.1 -40.2
20.6
44.5
8.0
C3'-endo
4G
8.2 -33.6
44.1 -40.2
20.6
44.5
7.9
C3'-endo
5C
8.3 -33.6
44.1 -40.2
20.5
44.5
7.9
C3'-endo
6T
8.2 -33.6
44.1 -40.1
20.5
44.5
7.9
C3'-endo
7A
8.2 -33.5
44.1 -40.2
20.6
44.5
8.0
C3'-endo
8G
8.2 -33.5
44.0 -40.1
20.6
44.5
8.0
C3'-endo
9C
8.2 -33.5
44.1 -40.2
20.6
44.5
8.0
C3'-endo
10 T
8.2 -33.5
44.1 -40.2
20.6
44.5
8.0
C3'-endo
11 A
8.2 -33.6
44.1 -40.2
20.6
44.5
8.0
C3'-endo
12 G
8.2 -33.5
44.1 -40.2
20.6
44.5
8.0
C3'-endo
13 C
8.2 -33.6
44.1 -40.2
20.6
44.5
7.9
C3'-endo
14 T
8.2 -33.6
44.1 -40.2
20.6
44.5
8.0
C3'-endo
15 A
8.3 -33.5
44.1 -40.1
20.5
44.5
7.9
C3'-endo
16 G
8.3 -33.6
44.1 -40.1
20.5
44.5
7.9
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/A
5.5
5.4
1 C/T
5.5
5.4
2 A/T
5.5
5.4
2 T/A
5.5
5.4
3 T/C
5.5
5.4
3 A/G
5.5
5.4
4 C/G
5.5
5.4
4 G/C
5.5
5.4
5 G/A
5.5
5.4
5 C/T
5.5
5.4
6 A/T
5.5
5.4
6 T/A
5.5
5.4
7 T/C
5.5
5.4
7 A/G
5.5
5.4
8 C/G
5.5
5.4
8 G/C
5.5
5.4
9 G/A
5.5
5.4
9 C/T
5.5
5.4
10 A/T
5.5
5.4
10 T/A
5.5
5.4
11 T/C
5.5
5.4
11 A/G
5.5
5.4
12 C/G
5.5
5.4
12 G/C
5.5
5.4
13 G/A
5.5
5.4
13 C/T
5.5
5.4
14 A/T
5.5
5.4
14 T/A
5.5
5.4
15 T/C
5.5
5.4
15 A/G
5.5
5.4
****************************************************************************
Helix radius (radial displacement of P, O4', and C1' atoms in local helix
frame of each dimer)
step
1 GA/TC
2 AT/AT
3 TC/GA
4 CG/CG
5 GA/TC
6 AT/AT
7 TC/GA
P
8.6
8.6
8.4
8.8
8.6
8.6
8.4
Strand I
O4'
9.0
9.1
8.9
9.4
9.0
9.1
8.9
C1'
8.4
8.5
8.3
8.9
8.4
8.5
8.3
P
8.4
8.6
8.6
8.8
8.4
8.6
8.6
Strand II
O4'
8.9
9.1
9.0
9.4
8.9
9.1
9.0
C1'
8.3
8.5
8.4
8.9
8.3
8.5
8.4
8 CG/CG
8.8
9.4
8.9
8.8
9.4
9 GA/TC
8.6
9.0
8.4
8.4
8.9
10 AT/AT
8.6
9.1
8.5
8.6
9.1
11 TC/GA
8.4
8.9
8.3
8.6
9.0
12 CG/CG
8.8
9.4
8.9
8.8
9.4
13 GA/TC
8.6
9.0
8.4
8.4
8.9
14 AT/AT
8.6
9.1
8.5
8.6
9.1
15 TC/GA
8.4
8.9
8.3
8.6
9.0
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
bp
1 GA/TC
2 AT/AT
3 TC/GA
4 CG/CG
5 GA/TC
6 AT/AT
7 TC/GA
8 CG/CG
9 GA/TC
10 AT/AT
11 TC/GA
12 CG/CG
13 GA/TC
14 AT/AT
15 TC/GA
Px
0.19
0.01
0.11
0.20
-0.23
-0.01
-0.23
0.21
0.11
0.01
0.19
-0.47
0.08
0.00
-0.02
Py
-0.14
-0.01
-0.21
0.45
-0.05
-0.00
0.05
-0.45
0.21
0.01
0.14
0.14
-0.22
-0.01
-0.23
Pz
-1.27
-3.82
-6.38
-8.92
-11.46
-14.01
-16.57
-19.11
-21.65
-24.21
-26.76
-29.30
-31.84
-34.40
-36.95
Hx
-0.00
-0.00
-0.01
0.02
-0.01
-0.00
0.01
-0.02
0.01
0.00
0.00
0.01
-0.01
-0.00
-0.01
Hy
-0.01
-0.00
-0.00
-0.01
0.01
0.00
0.01
-0.01
-0.00
-0.00
-0.01
0.02
-0.01
-0.00
0.00
8.9
8.3
8.5
8.4
8.9
8.3
8.5
8.4
Hz
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
Из gatc-b.out:
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'
1 G-C
54.2
54.2
10.7
2 A-T
54.2
54.2
10.7
3 T-A
54.1
54.2
10.7
4 C-G
54.2
54.1
10.7
5 G-C
54.2
54.2
10.7
6 A-T
54.2
54.2
10.7
7 T-A
54.2
54.2
10.7
8 C-G
54.1
54.2
10.7
9 G-C
54.2
54.1
10.7
10 A-T
54.2
54.2
10.7
11 T-A
54.2
54.2
10.7
12 C-G
54.2
54.2
10.7
13 G-C
54.1
54.2
10.7
14 A-T
54.2
54.1
10.7
15 T-A
54.2
54.2
10.7
16 C-G
54.2
54.2
10.7
RN9-YN1
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
8.9
RC8-YC6
9.8
9.9
9.9
9.8
9.8
9.9
9.9
9.8
9.8
9.9
9.9
9.8
9.8
9.9
9.9
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
1G
2A
3T
4C
5G
6A
7T
8C
9G
10 A
11 T
12 C
13 G
14 A
15 T
16 C
alpha
---29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
beta
136.4
136.3
136.3
136.4
136.3
136.4
136.3
136.3
136.4
136.3
136.4
136.3
136.3
136.4
136.3
136.4
gamma delta epsilon zeta
chi
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.3 -140.8 -160.5 -97.9
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.3 -140.8 -160.5 -97.9
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4
-----98.0
Strand II
base
alpha
beta
1C
-29.9 136.4
2T
-29.9 136.3
3A
-29.9 136.4
gamma delta epsilon zeta
chi
31.1 143.4
-----98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
4G
-29.9 136.3
31.1 143.3 -140.8 -160.5 -98.0
5C
-29.9 136.3
31.2 143.3 -140.8 -160.5 -98.0
6T
-29.9 136.4
31.1 143.4 -140.8 -160.5 -98.0
7A
-29.9 136.3
31.2 143.3 -140.8 -160.5 -98.0
8G
-29.9 136.4
31.1 143.4 -140.8 -160.5 -98.0
9C
-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
1G
2A
3T
4C
5G
6A
7T
8C
9G
10 A
11 T
12 C
13 G
14 A
15 T
16 C
v0
-33.0
-33.0
-33.0
-33.0
-33.1
-33.0
-33.0
-33.0
-33.0
-33.1
-33.0
-33.0
-33.0
-33.0
-33.1
-33.0
v1
44.7
44.7
44.7
44.7
44.8
44.7
44.7
44.7
44.7
44.8
44.7
44.7
44.7
44.7
44.8
44.7
v2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
v3
23.1
23.1
23.1
23.0
23.1
23.1
23.1
23.1
23.0
23.1
23.1
23.1
23.1
23.0
23.1
23.1
v4
5.9
5.9
5.9
6.0
5.9
5.9
5.9
5.9
6.0
5.9
5.9
5.9
5.9
6.0
5.9
5.9
tm
44.8
44.7
44.8
44.8
44.8
44.8
44.7
44.8
44.8
44.8
44.8
44.7
44.8
44.8
44.8
44.8
P
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
Puckering
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
Strand II
base
1C
2T
3A
4G
5C
6T
7A
8G
9C
10 T
11 A
12 G
13 C
v0
-33.0
-33.1
-33.0
-33.0
-33.0
-33.0
-33.1
-33.0
-33.0
-33.0
-33.0
-33.1
-33.0
v1
44.7
44.8
44.7
44.7
44.7
44.7
44.8
44.7
44.7
44.7
44.7
44.8
44.7
v2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
-40.2
v3
23.1
23.1
23.0
23.1
23.1
23.1
23.1
23.0
23.1
23.1
23.1
23.1
23.0
v4
5.9
5.9
6.0
5.9
5.9
5.9
5.9
6.0
5.9
5.9
5.9
5.9
6.0
tm
44.8
44.8
44.8
44.8
44.7
44.8
44.8
44.8
44.8
44.7
44.8
44.8
44.8
P
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
153.9
Puckering
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
C2'-endo
14 T
-33.0
44.7 -40.2
23.1
5.9
44.8 153.9
15 A
-33.0
44.7 -40.2
23.1
5.9
44.7 153.9
16 G
-33.0
44.7 -40.2
23.1
5.9
44.8 153.9
****************************************************************************
Same strand P--P and C1'--C1' virtual bond distances
C2'-endo
C2'-endo
C2'-endo
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
1 GA/TC
2 AT/AT
3 TC/GA
4 CG/CG
5 GA/TC
6 AT/AT
7 TC/GA
8 CG/CG
9 GA/TC
10 AT/AT
Px
0.04
-0.02
0.05
0.05
-0.07
0.03
-0.07
0.00
0.07
-0.03
Py
-0.07
0.02
-0.06
0.07
0.03
-0.01
0.01
-0.09
0.01
-0.01
Pz
-1.68
-5.06
-8.44
-11.81
-15.18
-18.56
-21.94
-25.31
-28.68
-32.06
Hx
-0.00
0.00
-0.00
0.00
-0.00
-0.00
0.00
-0.00
0.00
-0.00
Hy
-0.00
0.00
0.00
-0.00
0.00
-0.00
0.00
0.00
-0.00
0.00
Hz
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
-1.00
11 TC/GA
12 CG/CG
13 GA/TC
14 AT/AT
15 TC/GA
0.07
-0.05
-0.05
0.02
-0.04
0.03
0.07
-0.06
0.02
-0.07
-35.44
-38.81
-42.18
-45.56
-48.94
-0.00
0.00
-0.00
0.00
-0.00
-0.00
0.00
-0.00
-0.00
0.00
-1.00
-1.00
-1.00
-1.00
-1.00
4.Проведите анализ всех трёх структур ДНК, используя программы find_pair и analyze. В отчете
приведите результаты сравнения значений конформационно важных торсионых углов (α, β, γ, δ, ε, ζ,
χ).
(*) Какая информация, выданная программой analyze, показалась Вам интересной (кратко напишите
об этом в отчете)?
find_pair
===========================================================================
NAME
find_pair - locate base-pairs and helical regions
SYNOPSIS
find_pair [OPTION] PDBFILE OUTFILE
DESCRIPTION
locate base-pairs and helical regions given a PDB data file. Its
output can be directly fed into analyze, cehs and Lavery's Curves
program.
-s, -1 treat the whole structure as a continuous single helix.
Useful for get all backbone torsion angles
-c
get Curves input for a duplex
-d
generate a separate output file for each helical region
-p
find all base-pairs and higher base associations
-t
read also HETATM records [recommended]
-z
more detailed base-pairing information in the output
-h
this help message (any non-recognized options will do)
INPUT
PDB data file
One-letter options can be in either case, any order and combined
EXAMPLES
find_pair -t sample.pdb sample.inp
find_pair -pt sample.pdb allbp_list
find_pair -c sample.pdb sample_curves.inp
OUTPUT
base-pair listing for input to analyze, cehs and Curves
bestpairs.pdb, hel_regions.pdb, col_chains.scr, col_helices.scr
allpairs.pdb, multiplets.pdb, mulbp.inp
SEE ALSO
analyze, cehs, anyhelix, ex_str, stack2img
AUTHOR
Written by Xiang-Jun Lu at Wilma K. Olson Laboratory at Rutgers
Check URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/
Report bugs to <xiangjun@rutchem.rutgers.edu>
===========================================================================
find_pair -t gatc-a.pdb stdout | analyze
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
...... /usr/share/x3dna/BASEPARS/ ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
Time used: 0.03 seconds
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
...... /usr/share/x3dna/BASEPARS/ ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: raster3d.par ......
Time used: 0.04 seconds
find_pair -t gatc-b.pdb stdout | analyze
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
...... /usr/share/x3dna/BASEPARS/ ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
Time used: 0.02 seconds
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
...... /usr/share/x3dna/BASEPARS/ ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: raster3d.par ......
Time used: 0.04 seconds
find_pair -t dna12.pdb stdout | analyze
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
uncommon residue +C
9 on chain A [#9] assigned to: c
uncommon residue +C 21 on chain B [#21] assigned to: c
...... /usr/share/x3dna/BASEPARS/ ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
Time used: 0.01 seconds
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
uncommon residue +C
9 on chain A [#9] assigned to: c
uncommon residue +C 21 on chain B [#21] assigned to: c
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: baselist.dat ......
uncommon residue +C
9 on chain A [#9] assigned to: c
uncommon residue +C 21 on chain B [#21] assigned to: c
missing " P " atom : residue name C, chain A, number
1
missing " P " atom : residue name C, chain B, number 13
...... /usr/share/x3dna/BASEPARS/ ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: misc_3dna.par ......
...... /usr/share/x3dna/BASEPARS/ ......
...... reading file: raster3d.par ......
Time used: 0.04 seconds
По файлу XXXX.out:
1) A-форма
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
1G
2A
3T
4C
5G
6A
7T
8C
9G
10 A
11 T
12 C
13 G
14 A
15 T
16 C
alpha
---51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
beta
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
gamma delta epsilon zeta
chi
41.7
79.0 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.0 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.0 -147.8 -75.0 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.7 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1 -147.8 -75.1 -157.2
41.7
79.1
----- -157.2
Strand II
base
1C
2T
3A
4G
5C
6T
7A
8G
9C
10 T
11 A
12 G
13 C
14 T
15 A
16 G
alpha
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
-51.7
---
beta
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
174.8
gamma
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
41.7
delta epsilon zeta
chi
79.0
----- -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.1 -147.8 -75.1 -157.2
79.0 -147.8 -75.1 -157.2
79.1 -147.7 -75.1 -157.2
2) B-форма:
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
1G
2A
3T
alpha
beta
--136.4
-29.9 136.3
-29.9 136.3
gamma delta epsilon zeta
chi
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.3 -140.8 -160.5 -97.9
4C
5G
6A
7T
8C
9G
10 A
11 T
12 C
13 G
14 A
15 T
16 C
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
136.4
136.3
136.4
136.3
136.3
136.4
136.3
136.4
136.3
136.3
136.4
136.3
136.4
31.1
31.2
31.1
31.2
31.1
31.1
31.2
31.1
31.2
31.1
31.1
31.2
31.1
143.4
143.3
143.4
143.3
143.3
143.4
143.3
143.4
143.3
143.3
143.4
143.3
143.4
-140.8
-140.8
-140.8
-140.8
-140.8
-140.8
-140.8
-140.8
-140.8
-140.8
-140.8
-140.8
---
-160.5 -98.0
-160.5 -98.0
-160.5 -98.0
-160.5 -98.0
-160.5 -97.9
-160.5 -98.0
-160.5 -98.0
-160.5 -98.0
-160.5 -98.0
-160.5 -98.0
-160.5 -98.0
-160.5 -98.0
---98.0
Strand II
base
1C
2T
3A
4G
5C
6T
7A
8G
9C
10 T
11 A
12 G
13 C
14 T
15 A
16 G
alpha
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
-29.9
---
beta
136.4
136.3
136.4
136.3
136.3
136.4
136.3
136.4
136.3
136.3
136.4
136.3
136.4
136.3
136.3
136.4
gamma delta epsilon zeta
chi
31.1 143.4
-----98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
31.1 143.3 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
31.1 143.3 -140.8 -160.5 -97.9
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
31.1 143.3 -140.8 -160.5 -97.9
31.2 143.3 -140.8 -160.5 -98.0
31.1 143.4 -140.8 -160.5 -98.0
3) dna12
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
1C
--2G
-57.0
3C
-61.6
4G
-65.1
5A
-56.8
6A
-66.3
7T
-59.9
8T
-60.9
9c
-59.6
10 G
-65.0
beta gamma delta epsilon zeta
chi
--175.7 170.5 -165.3 -136.4 -90.9
166.8
47.1 113.5 178.5 -85.4 -121.1
173.3
58.3 107.9 -179.8 -94.8 -133.6
-175.8
59.8 147.5 171.6 -113.1 -105.4
173.9
64.4 136.7 -175.9 -99.6 -116.6
177.7
61.0 126.3 175.0 -89.4 -118.8
-179.1
55.3
95.8 173.9 -80.2 -129.6
177.2
65.1 102.6 164.3 -76.7 -126.8
179.9
49.3
99.2 -171.7 -76.9 -132.9
173.7
61.8 149.5 -115.8 159.7 -94.3
11 C
12 G
Strand II
base
1G
2C
3G
4c
5T
6T
7A
8A
9G
10 C
11 G
12 C
-65.1 147.2
-90.3 -167.3
alpha
-67.9
-92.2
-92.8
-60.3
-53.6
-61.1
-61.7
-51.6
-58.0
-53.4
-50.8
---
46.5
54.9
149.2 -173.2
100.2
---
-88.9 -111.8
--- -107.6
beta gamma delta epsilon zeta
chi
175.8
51.1
85.7
----- -132.8
150.2
42.7 123.5 -176.4 -108.4 -108.3
-162.1
49.0 155.9 -74.0 157.9 -90.1
-179.9
42.3
85.6 156.8 -49.4 -123.0
175.1
57.0 109.0 -177.6 -84.3 -127.9
169.0
67.7 100.3 -175.8 -83.3 -140.9
176.0
60.2 100.7 179.6 -78.0 -133.7
-174.6
54.4 140.4 173.6 -94.2 -107.9
-180.0
62.7 146.1 166.1 -107.1 -100.2
164.6
51.9
82.8 172.1 -79.4 -140.6
158.0
47.2 136.4 -178.0 -110.6 -110.0
--38.3 154.7 -155.9 -147.4 -94.8
3) Работа с pdb2img:
pdb2img -h
===========================================================================
NAME
pdb2img - generate a block representation image from a PDB file
SYNOPSIS
pdb2img [OPTION] [-s=factor] PDBFILE OUTFILE
DESCRIPTION
generate a block representation of base or peptide bond in PS, XFIG
or Raster3D format. The six faces of each block can also be shown in
different styles, resulting in much more revealing presentation than
an atomic model. With Raster3D input, these blocks can be combined
with other schematic representations (e.g., from MolScript)
-f
generate an XFIG file
-r
generate an input to render of Raster3D
-n
without header for Raster3D (with -r)
-p
block representation for peptide bond
-c
color image
-i
identical style for the 6 faces of each block
-u
up-down faces instead of minor/major groove faces
-m
minor groove plus identical 5 other sides
-s=factor set scale factor (to put image in the same scale)
-b
draw a boundary frame around image
-h
this help message (any non-recognized options will do)
INPUT
PDB file
One-letter options can be in either case, any order and combined
EXAMPLES
pdb2img -bcu sample.pdb sample.ps
pdb2img -fc sample.pdb sample.fig
pdb2img -rc sample.pdb stdout | render -jpeg > sample.jpg
OUTPUT
PS, XFIG or Raster3D input file
bblk_lkg.alc, pblk_lkg.alc
SEE ALSO
r3d_atom, alc2img, stack2img, blocview
AUTHOR
Written by Xiang-Jun Lu at Wilma K. Olson Laboratory at Rutgers
Check URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/
Report bugs to <xiangjun@rutchem.rutgers.edu>
===========================================================================
pdb2img -c -u dna12.pdb dna12.ps
rotate_mol -b dna12.pdb dna12_view.pdb
pdb2img -c -u dna12_view.pdb dna12_view.ps
pdb2img -c -u gatc-a.pdb gatc-a.ps
rotate_mol -b gatc-a.pdb gatc-a_view.pdb
pdb2img -c -u gatc-a_view.pdb gatc-a_view.ps
pdb2img -c -u gatc-b.pdb gatc-b.ps
rotate_mol -b gatc-b.pdb gatc-b_view.pdb
pdb2img -c -u gatc-b_view.pdb gatc-b_view.ps