Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

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

Table 2c:

Structures for which the helical axis is best described by a double-kink line.
Sigma2 of a double-kink line is only slightly smaller (< 0.2) than for the next best model(s). The structures are listed by the number of base pairs (bp).

Number of structures: 92

PDB 
NDB 
IMB Jena
Image Library
bp
molecule
type
method
model
s(2)
r
a/a1
a2
a1+a2
o
l1
l2
l3
1b69
------
E   |    H   |    B
13
prot-nuc
NMR
double-kink line
0.509
  
11
27
38
77
3
6
4
      single-kink line
0.553
  
28
   
9
4
 
                
1efs
------
E   |    H   |    B
13
nuc
NMR
double-kink line
0.042
  
8
4
12
113
4
4
5
      single-kink line
0.061
  
7
   
4
9
 
      circular line
0.073
249
       
      straight line
0.143
        
                
1j1v
pd0371
E   |    H   |    B
13
prot-nuc
diff
double-kink line
0.226
  
14
15
29
53
3
5
5
      circular line
0.277
72
       
      single-kink line
0.346
 
18
   
7
6
 
                
1j59
pd0299
E   |    H   |    B
13
prot-nuc
diff
double-kink line
0.372
  
15
32
47
33
5
4
4
      circular line
0.494
38
       
      single-kink line
0.494
 
38
   
8
5
 
                
1nk5
pd0378
E   |    H   |    B
13
prot-nuc
diff
double-kink line
0.270
  
18
14
32
-137
4
2
7
      circular line
0.379
130
       
      single-kink line
0.428
 
10
   
5
8
 
                
1nkb
pd0383
E   |    H   |    B
13
prot-nuc
diff
double-kink line
0.228
  
28
15
43
102
6
4
3
      single-kink line
0.312
  
27
   
6
7
 
                
1qln
ph0002
E   |    H   |    B
13
prot-nuc
diff
double-kink line
0.310
  
13
12
25
84
4
6
3
      circular line
0.317
99
       
      single-kink line
0.405
 
13
   
6
7
 
                
6gat
------
E   |    H   |    B
13
prot-nuc
NMR
double-kink line
0.058
  
10
13
23
-33
5
3
5
      circular line
0.102
76
       
      single-kink line
0.116
 
19
   
7
6
 
                
1ahd
------
E   |    H   |    B
14
prot-nuc
NMR
double-kink line
0.412
  
25
12
37
-76
5
3
6
      single-kink line
0.461
  
29
   
6
8
 
      circular line
0.580
51
       
                
1bwg
------
E   |    H   |    B
14
nuc
NMR
double-kink line
0.155
  
15
8
23
-147
4
6
4
      single-kink line
0.197
  
14
   
3
11
 
                
1cqt
pd0092
E   |    H   |    B
14
prot-nuc
diff
double-kink line
0.533
  
12
25
37
-92
4
5
4
      single-kink line
0.707
  
23
   
9
5
 
                
1ecr
pdte01
E   |    H   |    B
14
prot-nuc
diff
double-kink line
0.243
  
22
13
35
-92
5
6
3
      single-kink line
0.346
  
22
   
5
9
 
                
1j46
------
E   |    H   |    B
14
prot-nuc
NMR
double-kink line
0.278
  
13
34
47
4
4
5
5
      single-kink line
0.291
  
40
   
8
6
 
      circular line
0.335
38
       
                
1jey
pd0220
E   |    H   |    B
14
prot-nuc
diff
double-kink line
0.155
  
13
13
26
96
7
4
3
      single-kink line
0.236
  
14
   
7
7
 
      circular line
0.286
103
       
                
1k8j
------
E   |    H   |    B
14
nuc
NMR
double-kink line
0.174
  
11
12
23
147
2
9
3
      single-kink line
0.210
  
10
   
11
2
 
      straight line
0.233
        
      circular line
0.274
733
       
                
1k9h
------
E   |    H   |    B
14
nuc
NMR
double-kink line
0.086
  
12
15
27
-51
4
4
6
      single-kink line
0.165
  
20
   
7
7
 
      circular line
0.177
62
       
                
1mdy
pdt016
E   |    H   |    B
14
prot-nuc
diff
double-kink line
0.266
  
16
16
32
110
6
2
6
      single-kink line
0.310
  
18
   
7
7
 
      circular line
0.421
84
       
                
9ant
pd0007
E   |    H   |    B
14
prot-nuc
diff
double-kink line
0.220
  
22
13
35
-106
6
2
6
      single-kink line
0.327
  
21
   
6
8
 
                
1cf7
pd0045
E   |    H   |    B
15
prot-nuc
diff
double-kink line
0.239
  
7
10
17
-91
4
4
6
      single-kink line
0.261
  
10
   
9
6
 
      circular line
0.276
158
       
                
1drg
pd0113
E   |    H   |    B
15
prot-nuc
diff
double-kink line
0.272
  
18
16
34
-48
7
3
5
      single-kink line
0.287
  
28
   
8
7
 
                
1dsz
pd0115
E   |    H   |    B
15
prot-nuc
diff
double-kink line
0.200
  
11
7
18
-163
5
6
4
      single-kink line
0.224
  
9
   
4
10
 
      circular line
0.363
349
       
      straight line
0.399
        
                
1lq1
pd0314
E   |    H   |    B
15
prot-nuc
diff
double-kink line
0.113
  
14
15
29
-40
6
3
6
      circular line
0.129
62
       
      single-kink line
0.193
 
24
   
8
7
 
                
1lwa
------
E   |    H   |    B
15
nuc
NMR
double-kink line
0.468
  
23
20
43
60
3
9
3
      circular line
0.655
108
       
                
1pue
pdt033
E   |    H   |    B
15
prot-nuc
diff
double-kink line
0.185
  
27
12
39
-124
7
4
4
      single-kink line
0.303
  
24
   
7
8
 
                
2lef
------
E   |    H   |    B
15
prot-nuc
NMR
double-kink line
0.407
  
37
30
67
-28
5
4
6
      circular line
0.590
26
       
                
1g4d
------
E   |    H   |    B
16
prot-nuc
NMR
double-kink line
0.117
  
14
10
24
98
4
4
8
      circular line
0.275
141
       
                
1lei
pd0310
E   |    H   |    B
16
prot-nuc
diff
double-kink line
0.144
  
17
14
31
-14
5
5
6
      circular line
0.196
64
       
      single-kink line
0.295
 
25
   
7
9
 
                
1ma7
pd0337
E   |    H   |    B
16
prot-nuc
diff
double-kink line
0.289
  
20
18
38
30
7
3
6
      single-kink line
0.316
  
34
   
8
8
 
                
1n4l
pd0359
E   |    H   |    B
16
prot-nuc
diff
double-kink line
0.043
  
12
10
22
-87
5
7
4
      circular line
0.226
161
       
      single-kink line
0.229
 
12
   
5
11
 
                
1saa
------
E   |    H   |    B
16
nuc
NMR
double-kink line
0.113
  
15
14
29
-48
6
5
5
      circular line
0.145
84
       
                
1zme
pdt044
E   |    H   |    B
16
prot-nuc
diff
double-kink line
0.408
  
26
21
47
-38
7
3
6
      single-kink line
0.479
  
42
   
8
8
 
      circular line
0.534
38
       
                
2gat
------
E   |    H   |    B
16
prot-nuc
NMR
double-kink line
0.097
  
16
8
24
83
3
9
4
      single-kink line
0.248
  
12
   
4
12
 
      circular line
0.272
248
       
                
3gat
------
E   |    H   |    B
16
prot-nuc
NMR
double-kink line
0.130
  
12
16
28
90
2
12
2
      straight line
0.282
        
                
2crx
pd0103
E   |    H   |    B
17
prot-nuc
diff
double-kink line
0.334
  
26
12
38
-30
8
4
5
      single-kink line
0.371
  
33
   
9
8
 
      circular line
0.499
51
       
                
2stw
------
E   |    H   |    B
17
prot-nuc
NMR
double-kink line
0.266
  
28
10
38
-68
7
7
2
      single-kink line
0.282
  
29
   
7
10
 
                
3crx
pd0104
E   |    H   |    B
17
prot-nuc
diff
double-kink line
0.317
  
17
20
37
-11
7
3
7
      single-kink line
0.387
  
34
   
8
9
 
                
1ign
pdt035
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.259
  
22
9
31
86
9
3
6
      single-kink line
0.315
  
23
   
9
9
 
                
1j5o
pd0316
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.807
  
31
18
49
25
5
6
7
      circular line
0.904
52
       
                
1k3w
pd0253
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.218
  
19
30
49
2
5
4
9
      single-kink line
0.328
  
42
   
8
10
 
                
1kb2
pd0268
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.252
  
9
7
16
-159
7
2
8
      single-kink line
0.258
  
3
   
7
11
 
      circular line
0.267
724
       
      straight line
0.275
        
                
1kb4
pd0269
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.209
  
9
10
19
170
7
5
5
      straight line
0.406
        
                
1kb6
pd0270
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.227
  
8
10
18
-162
7
5
6
      single-kink line
0.367
  
5
   
13
4
 
      straight line
0.376
        
                
1ksx
pd0282
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.111
  
12
12
24
76
3
12
3
      circular line
0.229
370
       
      single-kink line
0.239
 
13
   
3
15
 
                
1lat
pdt030
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.289
  
9
7
16
-173
7
4
7
      single-kink line
0.317
  
5
   
5
13
 
      straight line
0.336
        
      circular line
0.363
968
       
                
1mm8
pd0340
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.261
  
31
16
47
-2
6
3
9
      single-kink line
0.310
  
44
   
7
11
 
                
1muh
pd0347
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.212
  
29
19
48
0
6
3
9
      single-kink line
0.253
  
45
   
7
11
 
                
1mur
pd0349
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.218
  
19
30
49
2
5
4
9
      single-kink line
0.328
  
42
   
8
10
 
                
1mus
pd0350
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.209
  
29
18
47
5
6
3
9
      single-kink line
0.261
  
44
   
7
11
 
                
1nkp
pd0386
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.176
  
11
14
25
-161
4
6
8
      single-kink line
0.277
  
11
   
11
7
 
                
1nlw
pd0387
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.153
  
9
6
15
-1
4
6
8
      circular line
0.170
183
       
      single-kink line
0.185
 
10
   
7
11
 
                
1qar
------
E   |    H   |    B
18
prot-nuc
model
double-kink line
0.144
  
18
15
33
-54
6
6
6
      circular line
0.334
77
       
                
2dgc
pdt029
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.099
  
12
12
24
78
6
6
6
      circular line
0.277
120
       
                
2nll
pdr021
E   |    H   |    B
18
prot-nuc
diff
double-kink line
0.394
  
9
9
18
-97
5
6
6
      circular line
0.440
212
       
      single-kink line
0.530
 
8
   
10
8
 
                
1puf
pd0455
E   |    H   |    B
19
prot-nuc
diff
double-kink line
0.191
  
11
12
23
140
10
4
5
      single-kink line
0.345
  
8
   
9
10
 
                
2hap
pd0090
E   |    H   |    B
19
prot-nuc
diff
double-kink line
0.406
  
25
10
35
125
7
8
4
      single-kink line
0.506
  
24
   
7
12
 
                
3cro
pdr001
E   |    H   |    B
19
prot-nuc
diff
double-kink line
0.145
  
18
18
36
-20
6
8
5
      circular line
0.271
83
       
                
1a73
pd0002
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.238
  
33
30
63
-18
9
2
9
      single-kink line
0.274
  
61
   
10
10
 
                
1a74
pde140
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.237
  
33
31
64
-27
9
2
9
      single-kink line
0.302
  
61
   
10
10
 
                
1apl
pdt005
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.193
  
10
9
19
-94
5
6
9
      circular line
0.368
195
       
      single-kink line
0.392
 
10
   
10
10
 
                
1awc
pdt048
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.214
  
13
8
21
121
9
3
7
      single-kink line
0.301
  
11
   
8
11
 
      circular line
0.401
195
       
                
1cyq
pd0096
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.291
  
35
31
66
-30
9
2
9
      single-kink line
0.366
  
62
   
10
10
 
                
1cz0
pd0097
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.259
  
34
31
65
-23
9
2
9
      single-kink line
0.303
  
62
   
10
10
 
                
1du0
pd0114
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.185
  
11
10
21
124
8
7
5
      single-kink line
0.367
  
10
   
7
13
 
                
1ga5
pd0191
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.377
  
11
11
22
-154
8
5
7
      single-kink line
0.554
  
10
   
5
15
 
                
1hlz
pd0193
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.385
  
13
9
22
-164
8
6
6
      single-kink line
0.459
  
13
   
5
15
 
                
1i3j
pd0200
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.145
  
9
16
25
173
6
4
10
      single-kink line
0.217
  
11
   
11
9
 
                
1ipp
pde0144
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.311
  
62
12
74
-117
10
7
3
      single-kink line
0.318
  
62
   
10
10
 
                
1n5y
pd0365
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.228
  
20
11
31
-31
6
6
8
      single-kink line
0.353
  
25
   
8
12
 
                
1n6q
pd0364
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.229
  
20
8
28
-34
8
5
7
      single-kink line
0.301
  
24
   
9
11
 
      circular line
0.352
80
       
                
1nwq
pd0395
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.318
  
15
12
27
-117
10
5
5
      single-kink line
0.455
  
13
   
9
11
 
      circular line
0.460
149
       
                
1qp9
pd0148
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.400
  
22
10
32
98
8
8
4
      single-kink line
0.464
  
22
   
8
12
 
                
2hdd
pdt043
E   |    H   |    B
20
prot-nuc
diff
double-kink line
0.138
  
7
13
20
148
8
7
5
      single-kink line
0.316
  
10
   
15
5
 
                
1f4k
pd0167
E   |    H   |    B
21
prot-nuc
diff
double-kink line
0.124
  
11
11
22
-2
4
12
5
      circular line
0.135
200
       
      single-kink line
0.291
 
10
   
12
9
 
                
1ksy
pd0283
E   |    H   |    B
21
prot-nuc
diff
double-kink line
0.151
  
7
7
14
-175
9
3
9
      straight line
0.197
        
      single-kink line
0.212
 
2
   
16
5
 
      circular line
0.223
275000000
       
                
1p47
pd0424
E   |    H   |    B
21
prot-nuc
diff
double-kink line
0.286
  
7
12
19
-156
6
7
8
      single-kink line
0.340
  
10
   
15
6
 
                
1par
pdr012
E   |    H   |    B
21
prot-nuc
diff
double-kink line
0.489
  
22
11
33
-30
8
6
7
      circular line
0.504
78
       
      single-kink line
0.585
 
27
   
10
11
 
                
1rep
pd0107
E   |    H   |    B
21
prot-nuc
diff
double-kink line
0.276
  
9
18
27
26
5
6
10
      single-kink line
0.312
  
22
   
10
11
 
      circular line
0.313
96
       
                
1rtd
pd0023
E   |    H   |    B
21
prot-nuc
diff
double-kink line
0.160
  
15
11
26
30
7
7
7
      circular line
0.184
107
       
                
1a36
pde0141
E   |    H   |    B
22
prot-nuc
diff
double-kink line
0.096
  
5
7
12
148
3
13
6
      single-kink line
0.100
  
7
   
17
5
 
      circular line
0.184
667
       
      straight line
0.263
        
                
1an2
pdt023
E   |    H   |    B
22
prot-nuc
diff
double-kink line
0.332
  
9
8
17
170
7
3
12
      straight line
0.371
        
      single-kink line
0.385
 
2
   
11
11
 
      circular line
0.401
1820
       
                
1ej9
pd0125
E   |    H   |    B
22
prot-nuc
diff
double-kink line
0.067
  
7
6
13
-166
7
6
9
      straight line
0.229
        
      circular line
0.230
1370
       
      single-kink line
0.238
 
3
   
6
16
 
                
1hf0
pd0274
E   |    H   |    B
22
prot-nuc
diff
double-kink line
0.417
  
6
17
23
-58
6
12
3
      circular line
0.449
329
       
      single-kink line
0.555
 
8
   
7
15
 
                
1juw
------
E   |    H   |    B
22
prot-nuc
model
double-kink line
0.096
  
5
7
12
148
3
13
6
      single-kink line
0.100
  
7
   
17
5
 
      circular line
0.184
667
       
      straight line
0.263
        
                
1lpq
pd0313
E   |    H   |    B
22
prot-nuc
diff
double-kink line
0.041
  
2
4
6
-137
12
5
4
      single-kink line
0.043
  
3
   
18
4
 
      straight line
0.053
        
      circular line
0.060
43500000
       
                
1g9y
pd0189
E   |    H   |    B
24
prot-nuc
diff
double-kink line
0.702
  
28
22
50
-21
7
10
7
      circular line
0.706
74
       
                
1mey
pdtb41
E   |    H   |    B
24
prot-nuc
diff
double-kink line
0.720
  
11
17
28
-61
7
7
10
      circular line
0.859
113
       
                
6pax
pd0050
E   |    H   |    B
24
prot-nuc
diff
double-kink line
0.211
  
20
5
25
-129
10
3
10
      single-kink line
0.226
  
18
   
10
14
 
                
1k78
pd0259
E   |    H   |    B
25
prot-nuc
diff
double-kink line
0.252
  
10
10
20
-137
10
3
12
      circular line
0.387
348
       
      single-kink line
0.414
 
7
   
13
12
 
                
1jt0
pd0249
E   |    H   |    B
28
prot-nuc
diff
double-kink line
0.777
  
12
13
25
-46
4
20
4
      circular line
0.832
511
       
                
1tf6
pdt065
E   |    H   |    B
30
prot-nuc
diff
double-kink line
1.040
  
12
12
24
4
17
5
7
      single-kink line
1.040
  
21
   
19
11
 
                
1gfx
------
E   |    H   |    B
43
prot-nuc
model
double-kink line
1.718
  
20
21
41
-10
13
15
15
      circular line
1.814
143
       
                
1j5g
------
E   |    H   |    B
43
prot-nuc
model
double-kink line
1.713
  
20
21
41
-10
13
15
15
      circular line
1.809
143
       
                

Abbreviations