Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

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

Table 5a - Page 1:

Structures with an automatically assigned single-kink helical axis.
All structures included in this Table have 12 or less base pairs.
Sigma2 of a single-kink line is only slightly smaller (< 0.2) than for the next best model(s). For small kink angles it is not possible to differentiate manually between single-kink or double-kink helical axes.
The structures are listed by the kink angle alpha (a).

page 2 | page 3

Number of structures: 59 (this pages) / 179 (total)

PDB 
NDB 
 IMB Jena
Image Library
bp
 molecule
type
method
model
s(2)
r
a/a1
a2
o
l1
l2
l3
474d
gdjb58
E   |    H   |    B
 10
nuc
diff
single-kink line
0.029
  
4
   
4
6
  
      
circular line
0.036
283
       
      straight line
0.054
        
               
196d
bdj060
E   |    H   |    B
 10
nuc
diff
single-kink line
0.102
  
5
   
4
5
  
      
circular line
0.112
219
       
      straight line
0.130
        
               
1afz
------
E   |    H   |    B
 11
nuc
NMR
single-kink line
0.116
  
5
   
5
6
  
      
circular line
0.124
239
       
      straight line
0.143
        
               
1dk9
------
E   |    H   |    B
 9
nuc
NMR
single-kink line
0.051
  
5
   
3
5
  
      
circular line
0.056
221
       
      straight line
0.059
        
               
1hq7
bd0047
E   |    H   |    B
 12
nuc
diff
single-kink line
0.094
  
5
   
5
7
  
      
circular line
0.104
253
       
      straight line
0.152
        
               
468d
ar0016
E   |    H   |    B
 12
nuc
diff
single-kink line
0.047
  
5
   
8
4
  
      
circular line
0.055
251
       
      straight line
0.060
        
               
1dn9
bdl007
E   |    H   |    B
 12
nuc
diff
single-kink line
0.085
  
6
   
3
9
  
      straight line
0.101
        
      
circular line
0.107
511
       
               
2ezf
------
E   |    H   |    B
 12
prot-nuc
NMR
single-kink line
0.072
  
6
   
8
4
  
      
circular line
0.074
276
       
      straight line
0.179
        
               
469d
ar0015
E   |    H   |    B
 12
nuc
diff
single-kink line
0.043
  
6
   
8
4
  
      
circular line
0.055
177
       
      straight line
0.079
        
               
470d
ar0017
E   |    H   |    B
 12
nuc
diff
single-kink line
0.097
  
6
   
5
6
  
      
circular line
0.106
166
       
      straight line
0.128
        
               
101d
gdlb31
E   |    H   |    B
 12
nuc
diff
single-kink line
0.061
  
7
   
7
5
  
      
circular line
0.071
178
       
      straight line
0.224
        
               
1nk0
pd0376
E   |    H   |    B
 11
prot-nuc
diff
single-kink line
0.059
  
7
   
5
6
  
      
circular line
0.069
175
       
      straight line
0.157
        
               
1qms
------
E   |    H   |    B
 12
nuc
NMR
single-kink line
0.018
  
7
   
7
5
  
      
circular line
0.026
181
       
      straight line
0.132
        
               
408d
bdd003
E   |    H   |    B
 10
nuc
diff
single-kink line
0.188
  
7
   
5
5
  
      
circular line
0.208
156
       
      straight line
0.261
        
               
102d
gdl032
E   |    H   |    B
 12
nuc
diff
single-kink line
0.053
  
8
   
4
8
  
      
circular line
0.073
175
       
      straight line
0.234
        
               
1a1g
pdt056
E   |    H   |    B
 10
prot-nuc
diff
single-kink line
0.111
  
8
   
6
4
  
      
circular line
0.112
132
       
      straight line
0.208
        
               
1bw7
------
E   |    H   |    B
 12
nuc
NMR
single-kink line
0.214
  
8
   
4
8
  
      
circular line
0.257
207
       
      straight line
0.271
        
               
1cvx
dd0020
E   |    H   |    B
 10
nuc
diff
single-kink line
0.150
  
8
   
4
6
  
      
circular line
0.169
136
       
      straight line
0.272
        
               
1d20
------
E   |    H   |    B
 10
nuc
NMR
single-kink line
0.098
  
8
   
7
3
  
      
circular line
0.109
188
       
      straight line
0.139
        
               
1d57
bdj037
E   |    H   |    B
 10
nuc
diff
single-kink line
0.197
  
8
   
5
5
  
      
circular line
0.204
129
       
      straight line
0.307
        
               
1eel
dd0025
E   |    H   |    B
 12
nuc
diff
single-kink line
0.107
  
8
   
3
8
  
      
circular line
0.142
226
       
      straight line
0.213
        
               
1jk2
pd0231
E   |    H   |    B
 10
prot-nuc
diff
single-kink line
0.110
  
8
   
5
5
  
      
circular line
0.113
134
       
      straight line
0.212
        
               
1qv8
dd0060
E   |    H   |    B
 12
nuc
diff
single-kink line
0.067
  
8
   
5
7
  
      
circular line
0.071
162
       
      straight line
0.257
        
               
444d
dd0005
E   |    H   |    B
 12
nuc
diff
single-kink line
0.044
  
8
   
4
8
  
      
circular line
0.058
184
       
      straight line
0.209
        
               
471d
ar0018
E   |    H   |    B
 12
nuc
diff
single-kink line
0.121
  
8
   
7
5
  
      
circular line
0.152
146
       
      straight line
0.183
        
               
128d
gdlb19
E   |    H   |    B
 12
nuc
diff
single-kink line
0.097
  
9
   
5
7
  
      
circular line
0.167
168
       
               
129d
gdl021
E   |    H   |    B
 12
nuc
diff
single-kink line
0.097
  
9
   
5
7
  
      
circular line
0.104
151
       
               
166d
gdl027
E   |    H   |    B
 12
nuc
diff
single-kink line
0.060
  
9
   
4
8
  
      
circular line
0.095
162
       
               
1d30
gdl008
E   |    H   |    B
 12
nuc
diff
single-kink line
0.056
  
9
   
4
8
  
      
circular line
0.104
189
       
      straight line
0.240
        
               
1d56
bdj036
E   |    H   |    B
 10
nuc
diff
single-kink line
0.191
  
9
   
5
5
  
      
circular line
0.192
117
       
      straight line
0.335
        
               
1l3u
pd0302
E   |    H   |    B
 11
prot-nuc
diff
single-kink line
0.166
  
9
   
4
7
  
      
circular line
0.179
138
       
      straight line
0.300
        
               
1ndn
bdl032
E   |    H   |    B
 12
nuc
diff
single-kink line
0.212
  
9
   
4
8
  
      
circular line
0.278
216
       
      straight line
0.321
        
               
1njw
pd0372
E   |    H   |    B
 11
prot-nuc
diff
single-kink line
0.101
  
9
   
5
6
  
      
circular line
0.117
131
       
      straight line
0.276
        
               
1t7p
pde0135
E   |    H   |    B
 11
prot-nuc
diff
single-kink line
0.248
  
9
   
4
7
  
      
circular line
0.268
142
       
      straight line
0.358
        
               
1vkx
pdr033
E   |    H   |    B
 11
prot-nuc
diff
single-kink line
0.113
  
9
   
7
4
  
      
circular line
0.175
172
       
      straight line
0.253
        
               
1zaa
pdt006
E   |    H   |    B
 10
prot-nuc
diff
single-kink line
0.208
  
9
   
5
4
  
      
circular line
0.211
121
       
      straight line
0.309
        
               
268d
gdlb42
E   |    H   |    B
 12
nuc
diff
single-kink line
0.067
  
9
   
5
7
  
      
circular line
0.079
141
       
               
2dbe
gdl009
E   |    H   |    B
 12
nuc
diff
single-kink line
0.061
  
9
   
4
8
  
      
circular line
0.095
187
       
      straight line
0.230
        
               
3hts
pd0073
E   |    H   |    B
 12
prot-nuc
diff
single-kink line
0.080
  
9
   
6
6
  
      
circular line
0.117
138
       
               
127d
gdl022
E   |    H   |    B
 12
nuc
diff
single-kink line
0.099
  
10
   
5
7
  
      
circular line
0.124
132
       
               
130d
gdlb20
E   |    H   |    B
 12
nuc
diff
single-kink line
0.149
  
10
   
5
6
  
      
circular line
0.210
124
       
               
1d46
gdl013
E   |    H   |    B
 12
nuc
diff
single-kink line
0.071
  
10
   
2
10
  
      straight line
0.115
        
      
circular line
0.119
462
       
               
1d85
gdlb17
E   |    H   |    B
 12
nuc
diff
single-kink line
0.126
  
10
   
6
6
  
      
circular line
0.158
128
       
               
1dnh
gdl002
E   |    H   |    B
 12
nuc
diff
single-kink line
0.108
  
10
   
5
7
  
      
circular line
0.132
130
       
               
1i47
bd0049
E   |    H   |    B
 12
nuc
diff
single-kink line
0.080
  
10
   
4
8
  
      
circular line
0.109
141
       
               
1jxl
pd0252
E   |    H   |    B
 12
prot-nuc
diff
single-kink line
0.123
  
10
   
5
7
  
      
circular line
0.133
122
       
               
1l5u
pd0304
E   |    H   |    B
 12
prot-nuc
diff
single-kink line
0.127
  
10
   
5
6
  
      
circular line
0.158
116
       
               
1le9
pd0309
E   |    H   |    B
 11
prot-nuc
diff
single-kink line
0.171
  
10
   
5
6
  
      
circular line
0.200
115
       
               
226d
------
E   |    H   |    B
 10
nuc
NMR
single-kink line
0.174
  
10
   
4
6
  
      
circular line
0.190
124
       
      straight line
0.290
        
               
227d
gdl036
E   |    H   |    B
 12
nuc
diff
single-kink line
0.035
  
10
   
4
8
  
      
circular line
0.079
163
       
               
311d
gdl052
E   |    H   |    B
 12
nuc
diff
single-kink line
0.052
  
10
   
4
8
  
      
circular line
0.102
156
       
               
365d
gdj057
E   |    H   |    B
 10
nuc
diff
single-kink line
0.088
  
10
   
5
5
  
      
circular line
0.113
109
       
               
6bna
gdlb05
E   |    H   |    B
 12
nuc
diff
single-kink line
0.063
  
10
   
6
6
  
      
circular line
0.064
127
       
               
1a66
------
E   |    H   |    B
 12
prot-nuc
NMR
single-kink line
0.118
  
11
   
3
9
  
      
circular line
0.169
181
       
      straight line
0.300
        
               
1bna
bdl001
E   |    H   |    B
 12
nuc
diff
single-kink line
0.070
  
11
   
5
7
  
      
circular line
0.076
118
       
               
1bpx
pde0126
E   |    H   |    B
 10
prot-nuc
diff
single-kink line
0.226
  
11
   
3
7
  
      
circular line
0.261
139
       
      straight line
0.298
        
               
1bpy
pde0125
E   |    H   |    B
 10
prot-nuc
diff
single-kink line
0.106
  
11
   
3
7
  
      
circular line
0.178
125
       
      straight line
0.281
        
               
1fmq
dd0034
E   |    H   |    B
 12
nuc
diff
single-kink line
0.090
  
11
   
4
8
  
      
circular line
0.147
149
       
               
1fms
dd0035
E   |    H   |    B
 12
nuc
diff
single-kink line
0.075
  
11
   
4
8
  
      
circular line
0.105
131
       
               

Abbreviations