Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

Bending classification of helical axis - Single-kink line
(Last update: November 15, 2004)

Table 4c :

Structures with an automatically assigned single-kink helical axis that are in fact, however, in almost all cases double-kink structures.
Sigma2 of a single-kink line is significantly smaller (> 0.2) than for the next best model(s). All structures of this Table have 12 or less base pairs. Therefore, fitting a double-kink helical axis is not possible. Visual inspection shows that almost all of these structures have in fact a double-kink helical axis even though, especially for small kink angles, a non-ambigious manual classification is impossible.
The structures are listed by goodness-of-fit sigma2(single-kink line) (s(2)).

Number of structures: 54

PDB 
NDB 
IMB Jena
Image Library
bp
molecule
type
method
s(2)
a
l1
l2
1bsu
pde0145
E   |    H   |    B
10
prot-nuc
diff
0.050
50
5
5
1d8x
bd0024
E   |    H   |    B
10
nuc
diff
0.116
36
5
5
410d
ah0002
E   |    H   |    B
10
nuc
diff
0.133
29
4
6
1bss
pde0139
E   |    H   |    B
10
prot-nuc
diff
0.145
43
5
5
1eo3
pd0129
E   |    H   |    B
9
prot-nuc
diff
0.184
58
4
5
1b94
pd0037
E   |    H   |    B
10
prot-nuc
diff
0.190
53
5
5
1dnt
ah0008
E   |    H   |    B
10
nuc
diff
0.190
32
3
7
1az0
pde139
E   |    H   |    B
10
prot-nuc
diff
0.195
43
5
5
1bua
pde0146
E   |    H   |    B
10
prot-nuc
diff
0.207
43
5
5
1d88
ahj044
E   |    H   |    B
10
nuc
diff
0.207
29
3
7
1b96
pd0039
E   |    H   |    B
10
prot-nuc
diff
0.211
53
5
5
1rvb
pde015
E   |    H   |    B
10
prot-nuc
diff
0.217
46
5
5
1eop
pd0133
E   |    H   |    B
10
prot-nuc
diff
0.218
44
5
5
1eoo
pd0132
E   |    H   |    B
12
prot-nuc
diff
0.235
57
6
6
1qtm
pd0067
E   |    H   |    B
12
prot-nuc
diff
0.235
19
4
8
1eon
pd0131
E   |    H   |    B
10
prot-nuc
diff
0.238
50
5
5
1qsy
pd0065
E   |    H   |    B
12
prot-nuc
diff
0.238
20
4
8
3ktq
pd0032
E   |    H   |    B
12
prot-nuc
diff
0.265
24
4
8
1b97
pd0040
E   |    H   |    B
10
prot-nuc
diff
0.272
54
5
5
2ktq
pd0030
E   |    H   |    B
12
prot-nuc
diff
0.276
20
4
8
4ktq
pd0033
E   |    H   |    B
12
prot-nuc
diff
0.276
20
4
8
1rva
pde014
E   |    H   |    B
10
prot-nuc
diff
0.280
44
5
5
1rvc
pde016
E   |    H   |    B
10
prot-nuc
diff
0.288
45
5
5
1b95
pd0038
E   |    H   |    B
10
prot-nuc
diff
0.307
50
5
5
1rv5
pd0013
E   |    H   |    B
10
prot-nuc
diff
0.308
38
5
5
1bgb
pd0010
E   |    H   |    B
10
prot-nuc
diff
0.340
52
5
5
1eo4
pd0130
E   |    H   |    B
9
prot-nuc
diff
0.342
51
4
5
1jb8
ah0019
E   |    H   |    B
10
nuc
diff
0.346
38
4
6
1azq
pdr048
E   |    H   |    B
8
prot-nuc
diff
0.364
46
3
5
207d
------
E   |    H   |    B
10
nuc
NMR
0.388
35
5
5
1g4q
ah0012
E   |    H   |    B
10
nuc
diff
0.446
37
5
5
1svc
pdt022
E   |    H   |    B
10
prot-nuc
diff
0.452
28
6
4
1cfl
------
E   |    H   |    B
10
nuc
NMR
0.455
37
6
4
2pvi
pd0011
E   |    H   |    B
12
prot-nuc
diff
0.460
19
6
6
4rve
pde003
E   |    H   |    B
10
prot-nuc
diff
0.503
57
5
5
1cw0
pd0100
E   |    H   |    B
12
prot-nuc
diff
0.508
47
7
5
1ca6
pd0120
E   |    H   |    B
8
prot-nuc
diff
0.510
34
3
5
1f0o
pd0149
E   |    H   |    B
11
prot-nuc
diff
0.530
26
5
6
1n8c
------
E   |    H   |    B
11
nuc
NMR
0.611
22
4
7
1kc6
pd0272
E   |    H   |    B
12
prot-nuc
diff
0.619
37
6
6
1hx4
------
E   |    H   |    B
11
nuc
NMR
0.650
29
4
7
1tau
pde024
E   |    H   |    B
8
prot-nuc
diff
0.788
27
3
5
103d
------
E   |    H   |    B
12
nuc
NMR
0.848
25
6
6
1a84
------
E   |    H   |    B
12
nuc
NMR
0.852
78
6
6
1iha
ah0018
E   |    H   |    B
8
nuc
diff
0.993
49
4
4
1idw
ah0017
E   |    H   |    B
8
nuc
diff
1.023
50
4
4
1pvi
pde017
E   |    H   |    B
12
prot-nuc
diff
1.034
23
6
6
1icg
ah0015
E   |    H   |    B
8
nuc
diff
1.101
47
4
4
399d
adl047
E   |    H   |    B
12
nuc
diff
1.203
51
6
6
1id9
ah0016
E   |    H   |    B
8
nuc
diff
1.296
47
4
4
1qbp
ar0025
E   |    H   |    B
14
nuc
diff
1.303
30
6
7
422d
ar0007
E   |    H   |    B
8
nuc
diff
1.338
53
4
4
1oh8
------
E   |    H   |    B
10
prot-nuc
diff
1.397
63
7
3
255d
arl037
E   |    H   |    B
12
nuc
diff
1.398
35
6
6

Abbreviations