Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

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

Table 1d:

Structures for which the helical axis is best described by a double-kink line.
Sigma2 of a double-kink line is significantly smaller (> 0.2) than for the next best model(s). The structures are listed by the goodness of fit sigma2(double-kink line) (s(2)).

Number of structures: 119

PDB 
NDB 
IMB Jena
Image Library
bp
molecule
type
method
s(2)
a/a1
a2
a1+a2
o
l1
l2
l3
1a35
pde0143
E   |    H   |    B
22
prot-nuc
diff
0.061
11
9
20
157
6
7
9
1glu
pdrc01
E   |    H   |    B
18
prot-nuc
diff
0.078
13
12
25
119
5
4
8
1a31
pde0142
E   |    H   |    B
22
prot-nuc
diff
0.096
9
8
17
172
6
7
9
1mjo
pd0246
E   |    H   |    B
18
prot-nuc
diff
0.112
19
17
36
-69
5
8
5
1dfm
pd0101
E   |    H   |    B
14
prot-nuc
diff
0.113
13
13
26
-122
5
4
5
1k9l
------
E   |    H   |    B
14
nuc
NMR
0.122
16
16
32
94
4
6
4
1mj2
pd0173
E   |    H   |    B
18
prot-nuc
diff
0.124
20
15
35
-69
5
8
5
1d2i
pd0153
E   |    H   |    B
14
prot-nuc
diff
0.129
13
16
29
-130
5
4
5
1hcq
pdrc03
E   |    H   |    B
17
prot-nuc
diff
0.133
13
15
28
132
6
6
5
405d
ar0002
E   |    H   |    B
16
nuc
diff
0.134
20
18
38
177
5
6
5
1mjq
pd0248
E   |    H   |    B
18
prot-nuc
diff
0.134
19
21
40
-42
5
8
5
1kfo
ar0039
E   |    H   |    B
18
nuc
diff
0.135
29
29
58
165
6
6
6
1dgc
pdt007
E   |    H   |    B
18
prot-nuc
diff
0.138
20
20
40
112
7
4
7
1je8
pd0219
E   |    H   |    B
20
prot-nuc
diff
0.138
32
31
63
-71
6
8
6
1egw
pd0121
E   |    H   |    B
16
prot-nuc
diff
0.139
16
16
32
-104
5
6
5
1rcs
------
E   |    H   |    B
20
prot-nuc
NMR
0.148
20
29
49
-32
6
8
6
3hdd
pd0016
E   |    H   |    B
20
prot-nuc
diff
0.151
10
15
25
-173
7
7
6
2cgp
pdt049
E   |    H   |    B
26
prot-nuc
diff
0.153
37
37
74
-44
8
10
8
1cma
pdr008
E   |    H   |    B
18
prot-nuc
diff
0.154
20
21
41
-78
6
7
5
1bdz
------
E   |    H   |    B
14
nuc
NMR
0.157
22
22
44
-55
4
6
4
1nh2
pd0369
E   |    H   |    B
16
prot-nuc
diff
0.161
25
38
63
70
6
4
6
1mdm
pd0338
E   |    H   |    B
25
prot-nuc
diff
0.162
13
16
29
-152
8
4
13
2or1
pdr004
E   |    H   |    B
19
prot-nuc
diff
0.176
21
18
39
-48
6
8
5
1ubd
pdt038
E   |    H   |    B
20
prot-nuc
diff
0.179
16
10
26
176
7
7
6
1d5y
pd0078
E   |    H   |    B
20
prot-nuc
diff
0.185
10
10
20
-119
6
8
6
1kbd
------
E   |    H   |    B
16
prot
NMR
0.186
10
17
27
107
5
5
6
1per
pdr015
E   |    H   |    B
19
prot-nuc
diff
0.188
22
19
41
-58
6
8
5
2drp
pdt011
E   |    H   |    B
18
prot-nuc
diff
0.191
24
14
38
-125
8
5
5
1lb2
pd0306
E   |    H   |    B
20
prot-nuc
diff
0.191
19
31
50
-32
11
4
5
1b3t
pd0024
E   |    H   |    B
18
prot-nuc
diff
0.196
25
24
49
-109
7
4
7
1ytf
pdt036
E   |    H   |    B
16
prot-nuc
diff
0.204
22
40
62
59
6
4
6
1l1m
------
E   |    H   |    B
23
prot-nuc
NMR
0.217
51
41
92
-119
10
2
11
1h8a
pd0290
E   |    H   |    B
25
prot-nuc
diff
0.218
15
14
29
101
10
8
7
1bn9
------
E   |    H   |    B
15
nuc
NMR
0.221
18
17
35
-99
7
4
4
1dh3
pd0102
E   |    H   |    B
20
prot-nuc
diff
0.226
17
14
31
134
8
4
8
2kbd
------
E   |    H   |    B
16
nuc
NMR
0.231
30
48
78
95
6
4
6
1l3l
pd0298
E   |    H   |    B
20
prot-nuc
diff
0.236
19
28
47
-80
7
6
7
1hlv
pd0192
E   |    H   |    B
21
prot-nuc
diff
0.237
16
35
51
33
8
7
6
1bvo
------
E   |    H   |    B
15
prot-nuc
diff
0.240
14
14
28
-126
5
5
5
1ckt
pd0051
E   |    H   |    B
16
prot-nuc
diff
0.240
24
38
62
53
6
3
7
1hw2
pd0199
E   |    H   |    B
18
prot-nuc
diff
0.246
20
13
33
-148
8
4
6
1hdd
pdt004
E   |    H   |    B
20
prot-nuc
diff
0.247
10
16
26
168
8
7
5
1rpe
pdr011
E   |    H   |    B
19
prot-nuc
diff
0.250
22
20
42
-58
6
8
5
1io4
pd0198
E   |    H   |    B
25
prot-nuc
diff
0.277
13
7
20
100
8
8
9
1h0m
------
E   |    H   |    B
18
prot-nuc
diff
0.279
26
13
39
-64
6
6
6
1hwt
pd0089
E   |    H   |    B
20
prot-nuc
diff
0.286
26
17
43
-165
7
8
5
1cit
pd0046
E   |    H   |    B
16
prot-nuc
diff
0.287
24
19
43
129
5
6
5
1akh
pdr049
E   |    H   |    B
19
prot-nuc
diff
0.289
20
38
58
-51
6
6
7
1h89
pd0289
E   |    H   |    B
25
prot-nuc
diff
0.294
17
10
27
102
8
9
8
1b72
pd0075
E   |    H   |    B
19
prot-nuc
diff
0.295
18
22
40
-177
10
4
5
4kbd
------
E   |    H   |    B
16
nuc
NMR
0.298
21
34
55
103
5
5
6
2ram
pdr051
E   |    H   |    B
20
prot-nuc
diff
0.303
20
20
40
166
10
6
4
1dmu
pd0108
E   |    H   |    B
17
prot-nuc
diff
0.304
18
15
33
82
7
4
6
1o3t
pd0401
E   |    H   |    B
13
prot-nuc
diff
0.306
36
12
48
51
3
4
6
1qn4
pd0154
E   |    H   |    B
14
prot-nuc
diff
0.307
41
32
73
48
5
4
5
1yrn
pdt028
E   |    H   |    B
18
prot-nuc
diff
0.339
29
33
62
-68
7
6
5
1oct
pdt019
E   |    H   |    B
14
prot-nuc
diff
0.340
18
27
45
-63
5
5
4
1h88
pd0288
E   |    H   |    B
25
prot-nuc
diff
0.341
24
13
37
161
8
10
7
2dnj
pde006
E   |    H   |    B
14
prot-nuc
diff
0.351
20
20
40
154
5
4
5
1h6f
pd0311
E   |    H   |    B
22
prot-nuc
diff
0.366
13
14
27
-103
4
14
4
1dp7
pd0111
E   |    H   |    B
16
prot-nuc
diff
0.366
24
24
48
122
5
6
5
1le8
pd0308
E   |    H   |    B
19
prot-nuc
diff
0.366
30
31
61
-51
6
6
7
1a6y
pd0008
E   |    H   |    B
20
prot-nuc
diff
0.368
19
13
32
-166
9
4
7
1qne
pd0163
E   |    H   |    B
14
prot-nuc
diff
0.376
49
37
86
54
5
4
5
1au7
pdr034
E   |    H   |    B
24
prot-nuc
diff
0.377
22
21
43
147
4
14
6
1ysa
pdt002
E   |    H   |    B
16
prot-nuc
diff
0.385
16
33
49
-176
6
5
5
1lmb
pdr010
E   |    H   |    B
19
prot-nuc
diff
0.388
18
18
36
-16
4
11
4
1cgp
pdr006
E   |    H   |    B
30
prot-nuc
diff
0.389
48
44
92
-36
9
11
10
1tc3
pde0128
E   |    H   |    B
19
prot-nuc
diff
0.407
34
32
66
54
4
8
7
1lli
pdr016
E   |    H   |    B
19
prot-nuc
diff
0.413
18
19
37
-3
4
11
4
1bl0
pdr056
E   |    H   |    B
22
prot-nuc
diff
0.428
29
27
56
-73
8
6
8
2hmi
pd0005
E   |    H   |    B
18
prot-nuc
diff
0.432
24
17
41
44
5
5
8
1nk3
------
E   |    H   |    B
14
prot-nuc
NMR
0.446
28
19
47
162
3
4
7
2rve
pde002
E   |    H   |    B
16
prot-nuc
diff
0.454
43
40
83
126
6
3
7
1efa
pd0118
E   |    H   |    B
17
prot-nuc
diff
0.465
40
20
60
67
7
6
4
1owg
pd0407
E   |    H   |    B
20
prot-nuc
diff
0.468
28
67
95
46
8
4
8
1fok
pde0127
E   |    H   |    B
19
prot-nuc
diff
0.483
28
28
56
-125
4
10
5
433d
ar0008
E   |    H   |    B
14
nuc
diff
0.488
31
30
61
176
7
2
4
2bop
pdv001
E   |    H   |    B
16
prot-nuc
diff
0.505
26
26
52
-82
6
4
6
1jfi
pd0221
E   |    H   |    B
17
prot-nuc
diff
0.508
41
39
80
68
7
4
6
1jj4
pd0227
E   |    H   |    B
16
prot-nuc
diff
0.518
32
33
65
-99
6
4
6
1c7u
------
E   |    H   |    B
20
prot-nuc
NMR
0.524
27
27
54
118
5
10
5
1run
pdr024
E   |    H   |    B
30
prot-nuc
diff
0.527
48
42
90
-34
10
10
10
1cdw
pdt034
E   |    H   |    B
16
prot-nuc
diff
0.533
56
48
104
55
6
5
5
1ngm
pd0368
E   |    H   |    B
19
prot-nuc
diff
0.573
57
38
95
62
5
4
10
1ouz
pd0405
E   |    H   |    B
20
prot-nuc
diff
0.574
25
67
92
42
8
4
8
1owf
pd0406
E   |    H   |    B
20
prot-nuc
diff
0.579
24
65
89
40
8
4
8
1gdt
pde0115
E   |    H   |    B
34
prot-nuc
diff
0.588
44
31
75
94
15
4
15
1iaw
pd0207
E   |    H   |    B
16
prot-nuc
diff
0.590
52
21
73
124
8
3
5
1ir5
------
E   |    H   |    B
17
nuc
NMR
0.598
35
21
56
144
3
5
9
1exj
pd0146
E   |    H   |    B
21
prot-nuc
diff
0.605
16
41
57
-175
5
5
11
1ais
pdr031
E   |    H   |    B
17
prot-nuc
diff
0.617
49
29
78
82
7
6
4
1nk2
------
E   |    H   |    B
16
prot-nuc
NMR
0.646
32
27
59
134
9
3
4
1ewq
pd0142
E   |    H   |    B
21
prot-nuc
diff
0.660
27
40
67
-47
11
2
8
1lfu
------
E   |    H   |    B
14
prot-nuc
NMR
0.662
24
16
40
178
5
5
4
1ouq
pd0404
E   |    H   |    B
21
prot-nuc
diff
0.663
35
28
63
36
5
6
10
1d3u
pd0070
E   |    H   |    B
23
prot-nuc
diff
0.683
58
44
102
71
11
5
7
1tro
pdr009
E   |    H   |    B
37
prot-nuc
diff
0.717
15
16
31
-84
9
20
8
2stt
------
E   |    H   |    B
17
prot-nuc
NMR
0.722
17
37
54
94
4
4
9
1ic8
pd0208
E   |    H   |    B
21
prot-nuc
diff
0.737
18
48
66
151
13
4
4
1co0
------
E   |    H   |    B
20
prot-nuc
NMR
0.772
16
38
54
153
7
6
7
1jwl
pd0250
E   |    H   |    B
14
prot-nuc
diff
0.786
40
31
71
-147
6
4
4
1gt0
------
E   |    H   |    B
23
prot-nuc
diff
0.821
55
17
72
-78
5
11
7
1c9b
pd0112
E   |    H   |    B
17
prot-nuc
diff
0.914
43
44
87
45
6
5
6
1n14
------
E   |    H   |    B
13
nuc
NMR
0.990
37
38
75
160
4
5
4
1xbr
pdt045
E   |    H   |    B
24
prot-nuc
diff
1.028
20
10
30
167
5
6
12
1trr
pdr013
E   |    H   |    B
32
prot-nuc
diff
1.070
19
20
39
-109
11
9
12
1rpd
------
E   |    H   |    B
42
prot-nuc
model
1.081
24
27
51
14
9
21
12
1wai
------
E   |    H   |    B
25
prot-nuc
model
1.153
15
8
23
-115
5
7
12
1lws
pd0319
E   |    H   |    B
34
prot-nuc
diff
1.163
56
17
73
-72
12
9
13
1ruo
pdr025
E   |    H   |    B
30
prot-nuc
diff
1.164
46
47
93
-39
10
10
10
1f5t
pd0170
E   |    H   |    B
41
prot-nuc
diff
1.251
7
9
16
66
12
15
13
1ddn
pd0004
E   |    H   |    B
32
prot-nuc
diff
1.259
19
19
38
23
5
19
8
2gli
pdt008
E   |    H   |    B
20
prot-nuc
diff
1.264
31
41
72
136
8
3
9
1c0w
pd0069
E   |    H   |    B
21
prot-nuc
diff
1.309
30
28
58
169
9
3
9
1lwt
pd0320
E   |    H   |    B
36
prot-nuc
diff
1.483
52
19
71
-49
11
10
15
1mnm
pdr036
E   |    H   |    B
25
prot-nuc
diff
1.552
40
24
64
-59
10
4
11
1an4
pdt027
E   |    H   |    B
20
prot-nuc
diff
1.782
25
23
48
168
6
6
8
1k6o
pd0258
E   |    H   |    B
23
prot-nuc
diff
1.853
21
57
78
-160
4
10
9

Abbreviations