Банк EMBL
| | A-форма | B-форма | Файл dna13.pdb |
| Тип спирали (правая или левая) |
правая | правая | правая |
| Шаг спирали (Å) |
28,03 | 33,75 | 24,085 |
| Число оснований на виток |
12 | 11 | 12(виток не полный) |
| Ширина большой бороздки |
9,63 (G21B.P-G5A.P) | 20.584 (A6A.P-A22B.P) | 8.12 |
| Ширина малой бороздки |
18,49 (A22B.P-T15A.P) | 13.199 (C16A.P-A22B.P) | 16.24 |
используя команду "find_pair -t dna13.pdb stdout | analyze", получили
данные о торсионных углах моего куска днк.
Strand I
base alpha beta gamma delta epsilon zeta chi
1 c --- --- 90.1 80.0 -144.1 -76.9 -167.2
2 g -66.8 178.7 52.1 81.8 -151.9 -68.3 -161.3
3 c -79.4 -175.5 52.4 83.1 -150.4 -79.0 -158.1
4 g -60.6 167.9 49.4 79.3 -148.4 -83.5 -169.2
5 a -47.0 171.8 41.7 77.9 -153.9 -81.6 -161.1
6 a -43.0 174.0 40.2 86.4 -160.1 -66.1 -160.1
7 u -75.2 -180.0 53.0 82.0 -153.5 -77.8 -164.6
8 u -70.6 173.4 51.7 79.3 -148.8 -72.8 -161.1
9 c -62.6 172.0 54.9 82.6 -148.7 -81.9 -166.0
10 g -62.6 169.2 50.4 78.0 -147.4 -80.1 -165.5
11 c -50.6 171.8 44.8 81.7 -170.0 -67.1 -154.8
12 g -175.0 -168.0 149.5 77.1 --- --- -172.1
Strand II
base alpha beta gamma delta epsilon zeta chi
1 g -54.6 157.1 65.3 73.2 --- --- -161.3
2 c -62.2 157.6 61.0 79.1 -133.8 -86.7 -168.9
3 g -63.5 178.2 43.1 83.8 -144.1 -82.7 -164.4
4 c -56.1 172.1 51.2 78.4 -157.2 -76.8 -165.1
5 u -63.8 -171.0 45.8 81.3 -161.0 -71.1 -158.5
6 u -63.7 179.4 45.4 82.6 -160.2 -60.8 -148.7
7 a -51.6 179.2 44.2 79.1 -150.1 -75.1 -152.2
8 a -72.2 -173.3 46.2 80.4 -150.4 -70.8 -161.5
9 g -62.6 173.6 53.2 83.0 -161.3 -73.5 -163.3
10 c -71.5 177.7 55.5 80.2 -149.1 -73.2 -157.8
11 g -66.5 174.9 48.1 82.6 -151.1 -78.2 -162.6
12 c --- --- 58.2 84.4 -143.5 -80.8 -167.2
для А-формы:find_pair -t gatc-a.pdb stdout | analyze
Strand I
base alpha beta gamma delta epsilon zeta chi
1 G --- 174.8 41.7 79.0 -147.8 -75.1 -157.2
2 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
3 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
4 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
5 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
6 A -51.7 174.8 41.7 79.0 -147.8 -75.1 -157.2
7 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
8 C -51.7 174.8 41.7 79.0 -147.8 -75.0 -157.2
9 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
10 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
11 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
12 C -51.7 174.8 41.7 79.1 -147.7 -75.1 -157.2
13 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
14 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
15 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
16 C -51.7 174.8 41.7 79.1 --- --- -157.2
Strand II
base alpha beta gamma delta epsilon zeta chi
1 C -51.7 174.8 41.7 79.0 --- --- -157.2
2 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
3 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
4 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
5 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
6 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
7 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
8 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
9 C -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
для B-формы:find_pair -t gatc-b.pdb stdout | analyze
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
Стопочные модели ДНК
команда:pdb2img -bcu dna13.pdb dna13.ps
команда:rotate_mol -b dna13.pdb dna13_bpmi.pdb
команда:pdb2img -bcu gatc-a.pdb gatc-a.ps
команда:rotate_mol -b gatc-a.pdb gatc-a_bpmi.pdb
команда:pdb2img -bcu gatc-b.pdb gatc-b.ps
команда:rotate_mol -b gatc-b.pdb gatc-b_bpmi.pdb
©Дёмин Олег