Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

Slight bending (  0 ° < M <= 10 °)
Classification I (double kink: M = a1 + a2)
(Last update: November 15, 2004)

(There are structures with 13 or more base pairs for which a double-kink helical axis is selected as the most appropriate description by the automatic approach, but the central segment consists of 0 or 1 base pairs only. In these cases the double-kink geometrical parameters make no sense. Therefore, these structures have to be viewed as single-kink structures. They are indicated by a * in the model description).


Number of structures: 208

PDB 
NDB 
IMB Jena
Image Library
bp
molecule
type
method
model
s(2)
r
a/a1
a2
a1+a2
M
2hdc
------
E   |    H   |    B
17
prot-nuc
NMR
single-kink line*
0.070
 
2
  
2
1by4
pd0071
E   |    H   |    B
15
prot-nuc
diff
circular line
0.205
424
   
3
1osl
------
E   |    H   |    B
18
prot-nuc
NMR
single-kink line
0.012
 
3
  
3
1cgc
bdj039
E   |    H   |    B
10
nuc
diff
circular line
0.067
336
   
4
1d60
bdjb43
E   |    H   |    B
10
nuc
diff
circular line
0.039
340
   
4
1lrr
pd0315
E   |    H   |    B
12
prot-nuc
diff
circular line
0.212
294
   
4
1mse
------
E   |    H   |    B
11
prot-nuc
NMR
circular line
0.089
322
   
4
1pyi
pdt017
E   |    H   |    B
14
prot-nuc
diff
circular line
0.360
277
   
4
474d
gdjb58
E   |    H   |    B
10
nuc
diff
single-kink line
0.029
 
4
  
4
109d
gdl033
E   |    H   |    B
12
nuc
diff
circular line
0.073
263
   
5
121d
gdl014
E   |    H   |    B
12
nuc
diff
circular line
0.121
261
   
5
167d
bdj055
E   |    H   |    B
10
nuc
diff
circular line
0.068
216
   
5
196d
bdj060
E   |    H   |    B
10
nuc
diff
single-kink line
0.102
 
5
  
5
1afz
------
E   |    H   |    B
11
nuc
NMR
single-kink line
0.116
 
5
  
5
1d44
gdl011
E   |    H   |    B
12
nuc
diff
circular line
0.059
222
   
5
1dk9
------
E   |    H   |    B
9
nuc
NMR
single-kink line
0.051
 
5
  
5
1g14
------
E   |    H   |    B
12
nuc
NMR
circular line
0.049
268
   
5
1hq7
bd0047
E   |    H   |    B
12
nuc
diff
single-kink line
0.094
 
5
  
5
1imh
pd0214
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.169
 
5
  
5
1lo1
------
E   |    H   |    B
13
prot-nuc
NMR
single-kink line*
0.086
 
5
  
5
1qrh
pd0062
E   |    H   |    B
12
prot-nuc
diff
circular line
0.223
222
   
5
285d
bdlb76
E   |    H   |    B
12
nuc
diff
circular line
0.142
243
   
5
296d
gdl028
E   |    H   |    B
12
nuc
diff
circular line
0.070
219
   
5
445d
dd0006
E   |    H   |    B
12
nuc
diff
circular line
0.060
223
   
5
463d
bd0014
E   |    H   |    B
10
nuc
diff
circular line
0.052
245
   
5
468d
ar0016
E   |    H   |    B
12
nuc
diff
single-kink line
0.047
 
5
  
5
477d
bd0019
E   |    H   |    B
10
nuc
diff
circular line
0.051
227
   
5
1agh
------
E   |    H   |    B
11
nuc
NMR
circular line
0.025
187
   
6
1bc7
pd0027
E   |    H   |    B
11
prot-nuc
diff
circular line
0.159
188
   
6
1bjd
------
E   |    H   |    B
12
nuc
NMR
circular line
0.024
184
   
6
1cvy
dd0021
E   |    H   |    B
10
nuc
diff
circular line
0.136
188
   
6
1d43
gdl010
E   |    H   |    B
12
nuc
diff
circular line
0.067
213
   
6
1dn9
bdl007
E   |    H   |    B
12
nuc
diff
single-kink line
0.085
 
6
  
6
1dvl
dd0024
E   |    H   |    B
10
nuc
diff
circular line
0.126
191
   
6
1fkz
------
E   |    H   |    B
11
nuc
NMR
circular line
0.021
179
   
6
1fq2
bd0041
E   |    H   |    B
12
nuc
diff
circular line
0.079
181
   
6
1ikk
bd0051
E   |    H   |    B
10
nuc
diff
circular line
0.097
197
   
6
1jgr
bd0054
E   |    H   |    B
12
nuc
diff
circular line
0.071
183
   
6
1jk1
pd0230
E   |    H   |    B
10
prot-nuc
diff
circular line
0.137
200
   
6
1lpq
pd0313
E   |    H   |    B
22
prot-nuc
diff
double-kink line
0.041
 
2
4
6
6
1odh
------
E   |    H   |    B
13
prot-nuc
diff
circular line
0.153
213
   
6
1pyj
------
E   |    H   |    B
11
nuc
NMR
circular line
0.071
178
   
6
1rvi
------
E   |    H   |    B
12
nuc
NMR
circular line
0.107
199
   
6
265d
bdlb72
E   |    H   |    B
12
nuc
diff
circular line
0.042
204
   
6
269d
gdlb43
E   |    H   |    B
12
nuc
diff
circular line
0.041
207
   
6
286d
bdjb77
E   |    H   |    B
10
nuc
diff
circular line
0.091
192
   
6
2ezf
------
E   |    H   |    B
12
prot-nuc
NMR
single-kink line
0.072
 
6
  
6
328d
gdl053
E   |    H   |    B
12
nuc
diff
circular line
0.059
177
   
6
355d
bdl084
E   |    H   |    B
12
nuc
diff
circular line
0.082
177
   
6
3bna
bdlb03
E   |    H   |    B
12
nuc
diff
circular line
0.098
189
   
6
469d
ar0015
E   |    H   |    B
12
nuc
diff
single-kink line
0.043
 
6
  
6
470d
ar0017
E   |    H   |    B
12
nuc
diff
single-kink line
0.097
 
6
  
6
101d
gdlb31
E   |    H   |    B
12
nuc
diff
single-kink line
0.061
 
7
  
7
1a1k
pdt058
E   |    H   |    B
10
prot-nuc
diff
circular line
0.083
164
   
7
1cs2
------
E   |    H   |    B
12
nuc
NMR
circular line
0.110
153
   
7
1d65
bdl038
E   |    H   |    B
12
nuc
diff
circular line
0.057
172
   
7
1d68
------
E   |    H   |    B
10
nuc
NMR
circular line
0.140
173
   
7
1dou
bd0029
E   |    H   |    B
12
nuc
diff
circular line
0.071
162
   
7
1fiu
pd0177
E   |    H   |    B
10
prot-nuc
diff
circular line
0.326
151
   
7
1fky
------
E   |    H   |    B
11
nuc
NMR
circular line
0.021
151
   
7
1fos
pdt014
E   |    H   |    B
19
prot-nuc
diff
single-kink line
0.130
 
7
  
7
1g2d
pd0186
E   |    H   |    B
15
prot-nuc
diff
circular line
0.161
149
   
7
1g2f
pd0187
E   |    H   |    B
15
prot-nuc
diff
circular line
0.150
154
   
7
1g3x
dd0037
E   |    H   |    B
12
prot-nuc
diff
circular line
0.182
166
   
7
1ilc
bd0052
E   |    H   |    B
12
nuc
diff
circular line
0.127
152
   
7
1j8l
bd0053
E   |    H   |    B
12
nuc
diff
circular line
0.073
153
   
7
1jnm
pd0241
E   |    H   |    B
20
prot-nuc
diff
single-kink line
0.203
 
7
  
7
1mnn
pd0341
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.182
 
7
  
7
1naj
------
E   |    H   |    B
12
nuc
NMR
circular line
0.019
163
   
7
1nk0
pd0376
E   |    H   |    B
11
prot-nuc
diff
single-kink line
0.059
 
7
  
7
1qms
------
E   |    H   |    B
12
nuc
NMR
single-kink line
0.018
 
7
  
7
263d
gdl039
E   |    H   |    B
12
nuc
diff
circular line
0.068
155
   
7
266d
bdlb73
E   |    H   |    B
12
nuc
diff
circular line
0.042
174
   
7
298d
gdl044
E   |    H   |    B
12
nuc
diff
circular line
0.150
174
   
7
2d25
bdjb27
E   |    H   |    B
10
nuc
diff
circular line
0.346
150
   
7
2dau
------
E   |    H   |    B
12
nuc
NMR
circular line
0.186
169
   
7
408d
bdd003
E   |    H   |    B
10
nuc
diff
single-kink line
0.188
 
7
  
7
428d
bd0005
E   |    H   |    B
12
nuc
diff
circular line
0.074
166
   
7
447d
dd0007
E   |    H   |    B
12
nuc
diff
circular line
0.073
151
   
7
457d
bd0010
E   |    H   |    B
12
nuc
diff
circular line
0.054
162
   
7
102d
gdl032
E   |    H   |    B
12
nuc
diff
single-kink line
0.053
 
8
  
8
1a1g
pdt056
E   |    H   |    B
10
prot-nuc
diff
single-kink line
0.111
 
8
  
8
1a1h
pdt057
E   |    H   |    B
10
prot-nuc
diff
circular line
0.182
147
   
8
1am9
pdt062
E   |    H   |    B
38
prot-nuc
diff
circular line
0.626
141
   
8
1bc8
pd0020
E   |    H   |    B
9
prot-nuc
diff
circular line
0.094
131
   
8
1bw7
------
E   |    H   |    B
12
nuc
NMR
single-kink line
0.214
 
8
  
8
1cvx
dd0020
E   |    H   |    B
10
nuc
diff
single-kink line
0.150
 
8
  
8
1d20
------
E   |    H   |    B
10
nuc
NMR
single-kink line
0.098
 
8
  
8
1d23
bdj025
E   |    H   |    B
10
nuc
diff
circular line
0.296
138
   
8
1d27
bdlb26
E   |    H   |    B
12
nuc
diff
circular line
0.036
141
   
8
1d57
bdj037
E   |    H   |    B
10
nuc
diff
single-kink line
0.197
 
8
  
8
1d63
gdl016
E   |    H   |    B
12
nuc
diff
circular line
0.100
136
   
8
1d64
gdl015
E   |    H   |    B
12
nuc
diff
circular line
0.073
129
   
8
1d77
bdlb40
E   |    H   |    B
12
nuc
diff
circular line
0.140
140
   
8
1d86
gdl018
E   |    H   |    B
12
nuc
diff
circular line
0.080
137
   
8
1dl4
------
E   |    H   |    B
11
nuc
NMR
circular line
0.189
139
   
8
1edr
bd0031
E   |    H   |    B
12
nuc
diff
circular line
0.050
132
   
8
1eel
dd0025
E   |    H   |    B
12
nuc
diff
single-kink line
0.107
 
8
  
8
1ftd
dd0036
E   |    H   |    B
12
nuc
diff
circular line
0.073
128
   
8
1fzx
------
E   |    H   |    B
12
nuc
NMR
circular line
0.020
140
   
8
1g3v
bd0042
E   |    H   |    B
8
nuc
diff
circular line
0.090
128
   
8
1gip
------
E   |    H   |    B
12
nuc
NMR
circular line
0.139
131
   
8
1jgg
pdt031
E   |    H   |    B
10
prot-nuc
diff
circular line
0.276
131
   
8
1jk2
pd0231
E   |    H   |    B
10
prot-nuc
diff
single-kink line
0.110
 
8
  
8
1k4t
pd0256
E   |    H   |    B
10
prot-nuc
diff
circular line
0.041
128
   
8
1kkw
------
E   |    H   |    B
10
nuc
NMR
circular line
0.232
142
   
8
1lex
gdl037
E   |    H   |    B
12
nuc
diff
circular line
0.094
129
   
8
1nk8
pd0381
E   |    H   |    B
11
prot-nuc
diff
circular line
0.115
143
   
8
1prp
gdl023
E   |    H   |    B
12
nuc
diff
circular line
0.073
131
   
8
1qc1
bd0015
E   |    H   |    B
10
nuc
diff
circular line
0.058
133
   
8
1qv4
dd0059
E   |    H   |    B
12
nuc
diff
circular line
0.066
132
   
8
1qv8
dd0060
E   |    H   |    B
12
nuc
diff
single-kink line
0.067
 
8
  
8
1vzk
------
E   |    H   |    B
12
nuc
diff
circular line
0.080
132
   
8
249d
bdl070
E   |    H   |    B
11
nuc
diff
circular line
0.168
147
   
8
259d
arh074
E   |    H   |    B
8
nuc
diff
circular line
0.016
135
   
8
264d
gdl026
E   |    H   |    B
12
nuc
diff
circular line
0.075
134
   
8
267d
gdlb41
E   |    H   |    B
12
nuc
diff
circular line
0.087
133
   
8
270d
bdlb74
E   |    H   |    B
12
nuc
diff
circular line
0.046
147
   
8
2bdp
pde0131
E   |    H   |    B
9
prot-nuc
diff
circular line
0.064
133
   
8
2ezd
------
E   |    H   |    B
12
prot-nuc
NMR
circular line
0.038
128
   
8
2eze
------
E   |    H   |    B
12
prot-nuc
NMR
circular line
0.048
137
   
8
363d
adls105
E   |    H   |    B
12
nuc
diff
circular line
0.183
134
   
8
407d
bdd002
E   |    H   |    B
10
nuc
diff
circular line
0.171
134
   
8
432d
dd0002
E   |    H   |    B
8
nuc
diff
circular line
0.116
140
   
8
444d
dd0005
E   |    H   |    B
12
nuc
diff
single-kink line
0.044
 
8
  
8
471d
ar0018
E   |    H   |    B
12
nuc
diff
single-kink line
0.121
 
8
  
8
113d
bdl009
E   |    H   |    B
12
nuc
diff
circular line
0.032
125
   
9
124d
------
E   |    H   |    B
8
nuc
NMR
circular line
0.043
119
   
9
128d
gdlb19
E   |    H   |    B
12
nuc
diff
single-kink line
0.097
 
9
  
9
129d
gdl021
E   |    H   |    B
12
nuc
diff
single-kink line
0.097
 
9
  
9
166d
gdl027
E   |    H   |    B
12
nuc
diff
single-kink line
0.060
 
9
  
9
1bdn
bdl015
E   |    H   |    B
12
nuc
diff
circular line
0.108
127
   
9
1d30
gdl008
E   |    H   |    B
12
nuc
diff
single-kink line
0.056
 
9
  
9
1d49
bdj031
E   |    H   |    B
10
nuc
diff
circular line
0.188
127
   
9
1d56
bdj036
E   |    H   |    B
10
nuc
diff
single-kink line
0.191
 
9
  
9
1fyl
pd0183
E   |    H   |    B
12
prot-nuc
diff
circular line
0.021
114
   
9
1g75
bd0043
E   |    H   |    B
12
nuc
diff
circular line
0.065
112
   
9
1g8n
bd0044
E   |    H   |    B
12
nuc
diff
circular line
0.063
118
   
9
1gat
------
E   |    H   |    B
8
prot-nuc
NMR
circular line
0.102
117
   
9
1jj8
pd0229
E   |    H   |    B
12
prot-nuc
diff
circular line
0.141
117
   
9
1jkq
pd0236
E   |    H   |    B
12
prot-nuc
diff
circular line
0.258
116
   
9
1l3t
pd0301
E   |    H   |    B
10
prot-nuc
diff
circular line
0.209
114
   
9
1l3u
pd0302
E   |    H   |    B
11
prot-nuc
diff
single-kink line
0.166
 
9
  
9
1le5
pd0307
E   |    H   |    B
11
prot-nuc
diff
circular line
0.081
120
   
9
1ley
gdl038
E   |    H   |    B
12
nuc
diff
circular line
0.099
116
   
9
1m6f
dd0052
E   |    H   |    B
12
nuc
diff
circular line
0.084
115
   
9
1mhd
pd0243
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.123
 
9
  
9
1mq2
pd0343
E   |    H   |    B
10
prot-nuc
diff
circular line
0.160
115
   
9
1ndn
bdl032
E   |    H   |    B
12
nuc
diff
single-kink line
0.212
 
9
  
9
1njw
pd0372
E   |    H   |    B
11
prot-nuc
diff
single-kink line
0.101
 
9
  
9
1rxb
arh064
E   |    H   |    B
8
nuc
diff
circular line
0.015
126
   
9
1t7p
pde0135
E   |    H   |    B
11
prot-nuc
diff
single-kink line
0.248
 
9
  
9
1vkx
pdr033
E   |    H   |    B
11
prot-nuc
diff
single-kink line
0.113
 
9
  
9
1zaa
pdt006
E   |    H   |    B
10
prot-nuc
diff
single-kink line
0.208
 
9
  
9
202d
------
E   |    H   |    B
8
nuc
NMR
circular line
0.366
115
   
9
214d
------
E   |    H   |    B
11
nuc
NMR
circular line
0.149
116
   
9
243d
adh070
E   |    H   |    B
8
nuc
diff
circular line
0.050
113
   
9
268d
gdlb42
E   |    H   |    B
12
nuc
diff
single-kink line
0.067
 
9
  
9
287d
bdl078
E   |    H   |    B
12
nuc
diff
circular line
0.110
113
   
9
297d
bdlb82
E   |    H   |    B
12
nuc
diff
circular line
0.080
122
   
9
2dbe
gdl009
E   |    H   |    B
12
nuc
diff
single-kink line
0.061
 
9
  
9
2dnd
gdl003
E   |    H   |    B
12
nuc
diff
circular line
0.151
121
   
9
302d
gdl047
E   |    H   |    B
12
nuc
diff
circular line
0.042
127
   
9
303d
gdl048
E   |    H   |    B
12
nuc
diff
circular line
0.038
122
   
9
344d
adhb99
E   |    H   |    B
8
nuc
diff
circular line
0.072
113
   
9
3hts
pd0073
E   |    H   |    B
12
prot-nuc
diff
single-kink line
0.080
 
9
  
9
403d
bdd001
E   |    H   |    B
12
nuc
diff
circular line
0.068
123
   
9
431d
bd0006
E   |    H   |    B
8
nuc
diff
circular line
0.039
113
   
9
449d
dd0009
E   |    H   |    B
12
nuc
diff
circular line
0.059
118
   
9
456d
bd0009
E   |    H   |    B
12
nuc
diff
circular line
0.056
118
   
9
458d
bd0011
E   |    H   |    B
12
nuc
diff
circular line
0.106
117
   
9
459d
dd0014
E   |    H   |    B
12
nuc
diff
circular line
0.055
125
   
9
7bna
bdl005
E   |    H   |    B
12
nuc
diff
circular line
0.074
125
   
9
8bna
gdl006
E   |    H   |    B
12
nuc
diff
circular line
0.141
122
   
9
119d
bdl042
E   |    H   |    B
12
nuc
diff
circular line
0.585
101
   
10
127d
gdl022
E   |    H   |    B
12
nuc
diff
single-kink line
0.099
 
10
  
10
130d
gdlb20
E   |    H   |    B
12
nuc
diff
single-kink line
0.149
 
10
  
10
170d
------
E   |    H   |    B
12
nuc
NMR
circular line
0.639
110
   
10
1a1l
pdt061
E   |    H   |    B
10
prot-nuc
diff
circular line
0.208
105
   
10
1d29
bdl029
E   |    H   |    B
12
nuc
diff
circular line
0.065
107
   
10
1d46
gdl013
E   |    H   |    B
12
nuc
diff
single-kink line
0.071
 
10
  
10
1d85
gdlb17
E   |    H   |    B
12
nuc
diff
single-kink line
0.126
 
10
  
10
1d89
bdl047
E   |    H   |    B
12
nuc
diff
circular line
0.182
108
   
10
1d98
bdl006
E   |    H   |    B
12
nuc
diff
circular line
0.059
105
   
10
1dne
gdl004
E   |    H   |    B
12
nuc
diff
circular line
0.243
100
   
10
1dnh
gdl002
E   |    H   |    B
12
nuc
diff
single-kink line
0.108
 
10
  
10
1fym
pd0184
E   |    H   |    B
12
prot-nuc
diff
circular line
0.010
99
   
10
1g7z
------
E   |    H   |    B
8
nuc
NMR
circular line
0.126
108
   
10
1gxp
------
E   |    H   |    B
22
prot-nuc
diff
circular line
0.370
103
   
10
1hjb
pd0204
E   |    H   |    B
25
prot-nuc
diff
circular line
0.291
99
   
10
1i47
bd0049
E   |    H   |    B
12
nuc
diff
single-kink line
0.080
 
10
  
10
1iu3
pd0297
E   |    H   |    B
9
prot-nuc
diff
circular line
0.217
105
   
10
1jx4
pd0251
E   |    H   |    B
13
prot-nuc
diff
circular line
0.129
108
   
10
1jxl
pd0252
E   |    H   |    B
12
prot-nuc
diff
single-kink line
0.123
 
10
  
10
1l5u
pd0304
E   |    H   |    B
12
prot-nuc
diff
single-kink line
0.127
 
10
  
10
1le9
pd0309
E   |    H   |    B
11
prot-nuc
diff
single-kink line
0.171
 
10
  
10
1lp7
bd0057
E   |    H   |    B
12
nuc
diff
circular line
0.058
105
   
10
226d
------
E   |    H   |    B
10
nuc
NMR
single-kink line
0.174
 
10
  
10
227d
gdl036
E   |    H   |    B
12
nuc
diff
single-kink line
0.035
 
10
  
10
246d
ahh071
E   |    H   |    B
8
nuc
diff
circular line
0.069
110
   
10
271d
bdl075
E   |    H   |    B
12
nuc
diff
circular line
0.053
106
   
10
311d
gdl052
E   |    H   |    B
12
nuc
diff
single-kink line
0.052
 
10
  
10
365d
gdj057
E   |    H   |    B
10
nuc
diff
single-kink line
0.088
 
10
  
10
448d
dd0008
E   |    H   |    B
12
nuc
diff
circular line
0.060
110
   
10
6bna
gdlb05
E   |    H   |    B
12
nuc
diff
single-kink line
0.063
 
10
  
10
8icf
pde067
E   |    H   |    B
7
prot-nuc
diff
circular line
0.099
100
   
10
8ict
pde081
E   |    H   |    B
7
prot-nuc
diff
circular line
0.092
103
   
10
9ice
pde094
E   |    H   |    B
7
prot-nuc
diff
circular line
0.104
101
   
10

Abbreviations