Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

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

Table 2b:

Structures for which the helical axis is best described by a straight line.
Sigma2 of the straight line is only slightly smaller (< 0.2) than for the next best model(s). The structures are listed by the goodness of fit sigma2(straight line) (s(2)).

Number of structures: 136

PDB
NDB
 IMB Jena
Image Library
bp
 molecule
type
method
model
s(2)
r
a/a1
a2
o
l1
l2
l3
1axp
------
E   |    H   |    B
10
nuc
NMR
straight line
0.004
        
      circular line
0.006
4260
       
      single-kink line
0.007
  
1
   
6
3
  
               
1dns
adh014
E   |    H   |    B
8
nuc
diff
straight line
0.008
        
      circular line
0.016
533000000
       
      single-kink line
0.018
  
3
   
2
6
  
               
1g80
------
E   |    H   |    B
8
nuc
NMR
straight line
0.014
        
      circular line
0.028
1350
       
      single-kink line
0.048
  
3
   
1
7
  
               
189d
adh058
E   |    H   |    B
8
nuc
diff
straight line
0.026
        
      circular line
0.052
3450000
       
      single-kink line
0.086
  
2
   
3
5
  
               
1d82
adh041
E   |    H   |    B
8
nuc
diff
straight line
0.031
        
      circular line
0.063
4900000
       
      single-kink line
0.099
  
4
   
2
6
  
               
1rrr
------
E   |    H   |    B
10
nuc
NMR
straight line
0.031
        
      circular line
0.038
439
       
      single-kink line
0.040
  
6
   
2
8
  
               
1d26
adhp36
E   |    H   |    B
8
nuc
diff
straight line
0.034
        
      circular line
0.068
2790000
       
      single-kink line
0.117
  
2
   
2
5
  
               
274d
gdjb29
E   |    H   |    B
10
nuc
diff
straight line
0.034
        
      circular line
0.051
4700000
       
      single-kink line
0.056
  
2
   
7
2
  
               
295d
adh033
E   |    H   |    B
8
nuc
diff
straight line
0.034
        
      circular line
0.055
347
       
      single-kink line
0.098
  
2
   
3
4
  
               
375d
gdj059
E   |    H   |    B
10
nuc
diff
straight line
0.037
        
      circular line
0.050
848
       
      single-kink line
0.062
  
1
   
4
5
  
               
169d
------
E   |    H   |    B
10
nuc
NMR
straight line
0.044
        
      single-kink line
0.045
  
88
   
9
1
  
      circular line
0.064
883
       
               
476d
bd0018
E   |    H   |    B
10
nuc
diff
straight line
0.046
        
      circular line
0.059
618
       
      single-kink line
0.061
  
3
   
3
6
  
               
1ehv
bd0032
E   |    H   |    B
10
nuc
diff
straight line
0.048
        
      circular line
0.050
413
       
      single-kink line
0.066
  
3
   
3
7
  
               
345d
adhb100
E   |    H   |    B
8
nuc
diff
straight line
0.049
        
      circular line
0.097
3350000
       
      single-kink line
0.168
  
3
   
6
2
  
               
307d
bdj081
E   |    H   |    B
10
nuc
diff
straight line
0.050
        
      single-kink line
0.057
  
3
   
3
6
  
      circular line
0.061
508
       
               
338d
adhb92
E   |    H   |    B
8
nuc
diff
straight line
0.051
        
      circular line
0.102
2790000
       
      single-kink line
0.180
  
3
   
6
2
  
               
341d
adhb95
E   |    H   |    B
8
nuc
diff
straight line
0.051
        
      circular line
0.103
2990000
       
      single-kink line
0.171
  
4
   
6
2
  
               
118d
adh047
E   |    H   |    B
8
nuc
diff
straight line
0.052
        
      circular line
0.105
1950000
       
      single-kink line
0.113
  
4
   
4
3
  
               
1but
------
E   |    H   |    B
8
nuc
NMR
straight line
0.055
        
      circular line
0.056
184
       
      single-kink line
0.062
  
8
   
2
6
  
               
187d
adh056
E   |    H   |    B
8
nuc
diff
straight line
0.057
        
      circular line
0.061
200
       
      single-kink line
0.124
  
4
   
5
3
  
               
340d
adhb94
E   |    H   |    B
8
nuc
diff
straight line
0.058
        
      circular line
0.116
4840000
       
      single-kink line
0.201
  
3
   
6
2
  
               
8icn
pde075
E   |    H   |    B
7
prot-nuc
diff
straight line
0.059
        
      circular line
0.084
166
       
               
1zqk
pde037
E   |    H   |    B
7
prot-nuc
diff
straight line
0.060
        
      circular line
0.180
114000000
       
               
1o3z
ar0046
E   |    H   |    B
7
nuc
diff
straight line
0.067
        
      circular line
0.154
143
       
               
8drh
------
E   |    H   |    B
8
nuc
NMR
straight line
0.067
        
      circular line
0.108
226
       
      single-kink line
0.171
  
5
   
6
2
  
               
8ich
pde069
E   |    H   |    B
7
prot-nuc
diff
straight line
0.068
        
      circular line
0.118
173
       
               
8ics
pde080
E   |    H   |    B
7
prot-nuc
diff
straight line
0.069
        
      circular line
0.134
198
       
               
252d
bdj069
E   |    H   |    B
10
nuc
diff
straight line
0.070
        
      circular line
0.094
640
       
      single-kink line
0.101
  
3
   
6
3
  
               
1k2z
dd0046
E   |    H   |    B
8
nuc
diff
straight line
0.071
        
      circular line
0.119
353
       
      single-kink line
0.204
  
4
   
2
6
  
               
2d94
adh026
E   |    H   |    B
8
nuc
diff
straight line
0.074
        
      circular line
0.148
3750000
       
      single-kink line
0.197
  
4
   
4
3
  
               
250d
bdh071
E   |    H   |    B
8
nuc
diff
straight line
0.079
        
      circular line
0.144
497
       
      single-kink line
0.236
  
4
   
5
2
  
               
1h38
------
E   |    H   |    B
8
prot-nuc
diff
straight line
0.080
        
      circular line
0.148
351
       
      single-kink line
0.267
  
3
   
4
4
  
               
339d
adhb93
E   |    H   |    B
8
nuc
diff
straight line
0.080
        
      circular line
0.160
2680000
       
      single-kink line
0.262
  
5
   
2
6
  
               
382d
adj0109
E   |    H   |    B
10
nuc
diff
straight line
0.080
        
      circular line
0.094
250
       
      single-kink line
0.109
  
6
   
2
7
  
               
1k4s
pd0255
E   |    H   |    B
10
prot-nuc
diff
straight line
0.081
        
      circular line
0.103
464
       
      single-kink line
0.153
  
2
   
3
7
  
               
342d
adhb96
E   |    H   |    B
8
nuc
diff
straight line
0.082
        
      circular line
0.163
2850000
       
      single-kink line
0.251
  
5
   
2
6
  
               
346d
adhb101
E   |    H   |    B
8
nuc
diff
straight line
0.084
        
      circular line
0.169
2680000
       
      single-kink line
0.263
  
5
   
6
2
  
               
8icz
pde087
E   |    H   |    B
7
prot-nuc
diff
straight line
0.086
        
      circular line
0.157
167
       
               
8icv
pde083
E   |    H   |    B
7
prot-nuc
diff
straight line
0.096
        
      circular line
0.167
140
       
               
1mwg
------
E   |    H   |    B
8
nuc
NMR
straight line
0.097
        
      circular line
0.193
2310
       
               
1lai
------
E   |    H   |    B
13
nuc
NMR
straight line
0.101
        
      double-kink line
0.107
  
6
10
173
3
8
2
      single-kink line
0.122
  
5
   
2
11
  
      circular line
0.130
3280
       
               
4bna
bdlb04
E   |    H   |    B
12
nuc
diff
straight line
0.103
        
      single-kink line
0.118
  
5
   
2
9
  
      circular line
0.127
830
       
               
1jtl
dd0042
E   |    H   |    B
8
nuc
diff
straight line
0.104
        
      circular line
0.128
182
       
      single-kink line
0.221
  
6
   
3
5
  
               
9ica
pde091
E   |    H   |    B
7
prot-nuc
diff
straight line
0.105
        
      circular line
0.145
130
       
               
337d
adhb91
E   |    H   |    B
8
nuc
diff
straight line
0.107
        
      circular line
0.214
6720000
       
               
3orc
pd0022
E   |    H   |    B
8
prot-nuc
diff
straight line
0.108
        
      circular line
0.126
171
       
      single-kink line
0.192
  
5
   
4
4
  
               
1d19
------
E   |    H   |    B
8
nuc
NMR
straight line
0.109
        
      circular line
0.200
335
       
      single-kink line
0.303
  
5
   
2
5
  
               
9icj
pde099
E   |    H   |    B
7
prot-nuc
diff
straight line
0.109
        
      circular line
0.116
111
       
               
9icy
pde0114
E   |    H   |    B
7
prot-nuc
diff
straight line
0.109
        
      circular line
0.118
111
       
               
8icj
pde071
E   |    H   |    B
7
prot-nuc
diff
straight line
0.110
        
      circular line
0.172
127
       
               
8icp
pde077
E   |    H   |    B
7
prot-nuc
diff
straight line
0.113
        
      circular line
0.214
141
       
               
1nxr
------
E   |    H   |    B
8
nuc
NMR
straight line
0.121
        
      circular line
0.174
127
       
      single-kink line
0.291
  
9
   
2
6
  
               
1rrd
------
E   |    H   |    B
10
nuc
NMR
straight line
0.126
        
      single-kink line
0.153
  
7
   
2
7
  
      circular line
0.156
272
       
               
1gm5
pd0267
E   |    H   |    B
9
prot-nuc
diff
straight line
0.127
        
      circular line
0.192
353
       
      single-kink line
0.245
  
5
   
3
6
  
               
8ice
pde066
E   |    H   |    B
7
prot-nuc
diff
straight line
0.128
        
      circular line
0.235
128
       
               
8icm
pde074
E   |    H   |    B
7
prot-nuc
diff
straight line
0.128
        
      circular line
0.150
107
       
               
8icr
pde079
E   |    H   |    B
7
prot-nuc
diff
straight line
0.128
        
      circular line
0.176
108
       
               
1da3
bdjb48
E   |    H   |    B
10
nuc
diff
straight line
0.129
        
      circular line
0.145
289
       
      single-kink line
0.179
  
4
   
6
4
  
               
1huz
pd0197
E   |    H   |    B
8
prot-nuc
diff
straight line
0.129
        
      circular line
0.167
158
       
               
1zqp
pde042
E   |    H   |    B
7
prot-nuc
diff
straight line
0.129
        
      circular line
0.250
139
       
               
9dna
adh008
E   |    H   |    B
8
nuc
diff
straight line
0.129
        
      circular line
0.131
121
       
      single-kink line
0.244
  
6
   
4
4
  
               
8icu
pde082
E   |    H   |    B
7
prot-nuc
diff
straight line
0.137
        
      circular line
0.178
106
       
               
1qps
pd0055
E   |    H   |    B
12
prot-nuc
diff
straight line
0.143
        
      circular line
0.191
152000000
       
      single-kink line
0.223
  
3
   
2
10
  
               
8ico
pde076
E   |    H   |    B
7
prot-nuc
diff
straight line
0.145
        
      circular line
0.167
100
       
               
1lc4
dr0007
E   |    H   |    B
8
nuc
diff
straight line
0.158
        
      circular line
0.262
152
       
               
1cw9
bd0021
E   |    H   |    B
10
nuc
diff
straight line
0.159
        
      circular line
0.180
279
       
      single-kink line
0.221
  
4
   
4
5
  
               
8icc
pde065
E   |    H   |    B
7
prot-nuc
diff
straight line
0.161
        
      circular line
0.240
104
       
               
425d
bd0003
E   |    H   |    B
12
nuc
diff
straight line
0.162
        
      single-kink line
0.177
  
9
   
10
2
  
      circular line
0.188
624
       
               
1d02
pd0151
E   |    H   |    B
10
prot-nuc
diff
straight line
0.163
        
      circular line
0.239
936
       
      single-kink line
0.289
  
2
   
4
5
  
               
1eri
pde001
E   |    H   |    B
12
prot-nuc
diff
straight line
0.163
        
      circular line
0.217
232000000
       
      single-kink line
0.260
  
1
   
12
0
  
               
1zql
pde038
E   |    H   |    B
7
prot-nuc
diff
straight line
0.163
        
      circular line
0.214
99
       
               
1bhm
pde020
E   |    H   |    B
10
prot-nuc
diff
straight line
0.164
        
      circular line
0.214
381
       
      single-kink line
0.248
  
4
   
4
5
  
               
8icq
pde078
E   |    H   |    B
7
prot-nuc
diff
straight line
0.164
        
      circular line
0.188
94
       
               
3dnb
bdj008
E   |    H   |    B
10
nuc
diff
straight line
0.168
        
      circular line
0.252
360000000
       
      single-kink line
0.289
  
90
   
9
1
  
               
1gau
------
E   |    H   |    B
8
prot-nuc
NMR
straight line
0.169
        
      circular line
0.214
141
       
      single-kink line
0.264
  
8
   
3
5
  
               
8icy
pde086
E   |    H   |    B
7
prot-nuc
diff
straight line
0.172
        
      circular line
0.240
96
       
               
8icw
pde084
E   |    H   |    B
7
prot-nuc
diff
straight line
0.174
        
      circular line
0.235
96
       
               
1zqi
pde035
E   |    H   |    B
7
prot-nuc
diff
straight line
0.181
        
      circular line
0.325
111
       
               
424d
bd0002
E   |    H   |    B
12
nuc
diff
straight line
0.181
        
      circular line
0.195
394
       
      single-kink line
0.200
  
5
   
8
4
  
               
1ene
bd0036
E   |    H   |    B
10
nuc
diff
straight line
0.186
        
      single-kink line
0.268
  
11
   
8
2
  
      circular line
0.279
5560000
       
               
1enn
bd0037
E   |    H   |    B
8
nuc
diff
straight line
0.186
        
      circular line
0.301
193
       
               
157d
arl048
E   |    H   |    B
12
nuc
diff
straight line
0.187
        
      circular line
0.194
230
       
      single-kink line
0.194
  
7
   
3
8
  
               
1lej
------
E   |    H   |    B
13
nuc
NMR
straight line
0.191
        
      single-kink line
0.203
  
8
   
10
2
  
      double-kink line
0.213
  
90
104
-173
10
1
2
      circular line
0.222
569
       
               
423d
bd0001
E   |    H   |    B
12
nuc
diff
straight line
0.191
        
      circular line
0.215
414
       
      single-kink line
0.294
  
2
   
3
8
  
               
1zqf
pde032
E   |    H   |    B
7
prot-nuc
diff
straight line
0.197
        
      circular line
0.373
110
       
               
8icb
pde064
E   |    H   |    B
7
prot-nuc
diff
straight line
0.198
        
      circular line
0.335
99
       
               
1dsd
------
E   |    H   |    B
8
prot-nuc
NMR
straight line
0.200
        
      circular line
0.219
140
       
               
472d
ar0022
E   |    H   |    B
8
nuc
diff
straight line
0.205
        
      circular line
0.258
79
       
      single-kink line
0.345
  
10
   
3
5
  
               
1en9
bd0035
E   |    H   |    B
10
nuc
diff
straight line
0.206
        
      single-kink line
0.298
  
4
   
4
5
  
      circular line
0.309
3220000
       
               
435d
ar0010
E   |    H   |    B
7
nuc
diff
straight line
0.206
        
      circular line
0.262
64
       
               
1aay
pdt039
E   |    H   |    B
10
prot-nuc
diff
straight line
0.209
        
      circular line
0.210
188
       
      single-kink line
0.230
  
6
   
5
4
  
               
1bd1
bdj017
E   |    H   |    B
10
nuc
diff
straight line
0.210
        
      single-kink line
0.299
  
12
   
8
2
  
      circular line
0.316
2910000
       
               
1ckq
pd0049
E   |    H   |    B
12
prot-nuc
diff
straight line
0.216
        
      circular line
0.263
593
       
      single-kink line
0.300
  
3
   
6
6
  
               
1eka
------
E   |    H   |    B
8
nuc
NMR
straight line
0.218
        
      circular line
0.373
176
       
               
183d
bdjb57
E   |    H   |    B
10
nuc
diff
straight line
0.222
        
      single-kink line
0.311
  
13
   
1
9
  
      circular line
0.333
5010000
       
               
1d62
bd0055
E   |    H   |    B
10
nuc
diff
straight line
0.223
        
      single-kink line
0.331
  
27
   
1
9
  
      circular line
0.335
4570000
       
               
8ica
pde089
E   |    H   |    B
7
prot-nuc
diff
straight line
0.224
        
      circular line
0.237
78
       
               
1zqb
pde028
E   |    H   |    B
7
prot-nuc
diff
straight line
0.236
        
      circular line
0.322
83
       
               
1hu0
pd0195
E   |    H   |    B
7
prot-nuc
diff
straight line
0.238
        
      circular line
0.435
92
       
               
1ku7
pd0284
E   |    H   |    B
10
prot-nuc
diff
straight line
0.238
        
      circular line
0.328
343
       
      single-kink line
0.349
  
10
   
8
2
  
               
1zqj
pde036
E   |    H   |    B
7
prot-nuc
diff
straight line
0.239
        
      circular line
0.298
76
       
               
209d
ddh051
E   |    H   |    B
8
nuc
diff
straight line
0.242
        
      circular line
0.272
148
       
               
1zqn
pde040
E   |    H   |    B
7
prot-nuc
diff
straight line
0.245
        
      circular line
0.399
86
       
               
1cl8
pd0054
E   |    H   |    B
12
prot-nuc
diff
straight line
0.247
        
      circular line
0.328
3180
       
      single-kink line
0.387
  
1
   
6
5
  
               
1qri
pd0063
E   |    H   |    B
12
prot-nuc
diff
straight line
0.247
        
      circular line
0.329
807000000
       
      single-kink line
0.334
  
3
   
7
4
  
               
1nfk
pdt015
E   |    H   |    B
10
prot-nuc
diff
straight line
0.255
        
      circular line
0.299
223
       
      single-kink line
0.303
  
7
   
3
7
  
               
371d
adh0105
E   |    H   |    B
8
nuc
diff
straight line
0.255
        
      circular line
0.279
79
       
      single-kink line
0.344
  
12
   
5
3
  
               
1zqt
pde046
E   |    H   |    B
7
prot-nuc
diff
straight line
0.256
        
      circular line
0.328
81
       
               
1nnj
pd0389
E   |    H   |    B
7
prot-nuc
diff
straight line
0.259
        
      circular line
0.370
79
       
               
1zqg
pde033
E   |    H   |    B
7
prot-nuc
diff
straight line
0.259
        
      circular line
0.392
83
       
               
473d
dd0016
E   |    H   |    B
8
nuc
diff
straight line
0.259
        
      circular line
0.419
155
       
               
1zqo
pde041
E   |    H   |    B
7
prot-nuc
diff
straight line
0.261
        
      circular line
0.293
75
       
               
2bam
pd0029
E   |    H   |    B
10
prot-nuc
diff
straight line
0.275
        
      circular line
0.353
269
       
      single-kink line
0.457
  
4
   
4
6
  
               
1di2
pr0020
E   |    H   |    B
10
prot-nuc
diff
straight line
0.277
        
      circular line
0.362
209
       
      single-kink line
0.376
  
11
   
8
2
  
               
1d0e
pd0135
E   |    H   |    B
8
prot-nuc
diff
straight line
0.285
        
      single-kink line
0.287
  
13
   
3
5
  
      circular line
0.306
93
       
               
318d
adjb79
E   |    H   |    B
10
nuc
diff
straight line
0.289
        
      circular line
0.433
48400000
       
      single-kink line
0.461
  
10
   
8
2
  
               
1zqs
pde045
E   |    H   |    B
7
prot-nuc
diff
straight line
0.293
        
      circular line
0.385
74
       
               
1drn
------
E   |    H   |    B
9
nuc
NMR
straight line
0.302
        
      circular line
0.313
129
       
      single-kink line
0.490
  
7
   
3
6
  
               
1p78
pd0431
E   |    H   |    B
7
prot-nuc
diff
straight line
0.304
        
      circular line
0.414
70
       
               
325d
adjb86
E   |    H   |    B
10
nuc
diff
straight line
0.318
        
      circular line
0.478
15300
       
               
1p71
pd0430
E   |    H   |    B
7
prot-nuc
diff
straight line
0.325
        
      circular line
0.463
71
       
               
1zqr
pde044
E   |    H   |    B
7
prot-nuc
diff
straight line
0.335
        
      circular line
0.429
68
       
               
123d
bdjb50
E   |    H   |    B
10
nuc
diff
straight line
0.343
        
      circular line
0.394
198
       
      single-kink line
0.403
  
10
   
7
3
  
               
1zqc
pde029
E   |    H   |    B
7
prot-nuc
diff
straight line
0.344
        
      circular line
0.347
64
       
               
1mwl
dr0008
E   |    H   |    B
8
nuc
diff
straight line
0.359
        
      circular line
0.382
62
       
               
5dnb
bdj019
E   |    H   |    B
10
nuc
diff
straight line
0.359
        
      single-kink line
0.511
  
16
   
2
8
  
      circular line
0.538
1640000
       
               
122d
bdjb49
E   |    H   |    B
10
nuc
diff
straight line
0.368
        
      single-kink line
0.400
  
13
   
8
2
  
      circular line
0.418
188
       
               
108d
------
E   |    H   |    B
8
nuc
NMR
straight line
0.381
        
      circular line
0.451
140
       
      single-kink line
0.492
  
15
   
6
2
  
               
1en3
bd0033
E   |    H   |    B
10
nuc
diff
straight line
0.391
        
      single-kink line
0.558
  
16
   
8
2
  
      circular line
0.587
3250000
       
               
158d
bdj052
E   |    H   |    B
10
nuc
diff
straight line
0.394
        
      single-kink line
0.519
  
14
   
8
2
  
      circular line
0.527
269
       
               
1cqo
------
E   |    H   |    B
10
nuc
NMR
straight line
0.395
        
      circular line
0.487
197
       
      single-kink line
0.496
  
14
   
8
2
  
               
1d61
bdjb44
E   |    H   |    B
10
nuc
diff
straight line
0.418
        
      single-kink line
0.609
  
16
   
8
2
  
               
322d
adjb83
E   |    H   |    B
10
nuc
diff
straight line
0.615
        
      circular line
0.695
107
       
      single-kink line
0.769
  
12
   
3
7
  
               
1gd2
pd0180
E   |    H   |    B
12
prot-nuc
diff
straight line
0.650
        
      circular line
0.690
200
       
      single-kink line
0.727
  
11
   
3
9
  
               
1dsc
------
E   |    H   |    B
8
prot-nuc
NMR
straight line
0.749
        
      circular line
0.822
65
       
               
315d
ahh077
E   |    H   |    B
8
nuc
diff
straight line
0.836
        
      circular line
1.008
52
       
               

Abbreviations