Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

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

Table 1a :

Structures for which the helical axis is best described by a single-kink line.
Sigma2 of a single-kink line is only slightly smaller (< 0.2) than for the next best model(s). All structures have 13 or more base pairs and, therefore, an unambigious classification as single-kink structure is possible, in principle, even though the goodness-of-fit difference to the next-best model is small.
The structures are listed by kink angle alpha (a).

Number of structures: 30

PDB 
NDB 
IMB Jena
Image Library
bp
molecule
type
method
model
s(2)
r
a/a1
a2
o
l1
l2
l3
1imh
pd0214
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.169
 
5.0
  
5
7
 
      
circular line
0.188
320.0
      
      double-kink line
0.194
 
10.0
7.0
-140.0
4
3
6
      line
0.209
       
               
1fos
pdt014
E   |    H   |    B
19
prot-nuc
diff
single-kink line
0.130
 
7.0
  
11
8
 
      double-kink line
0.143
 
8.0
7.0
149.0
2
8
9
      
circular line
0.149
301.0
      
               
1jnm
pd0241
E   |    H   |    B
20
prot-nuc
diff
single-kink line
0.203
 
7.0
  
17
3
 
      
circular line
0.221
924.0
      
      line
0.227
       
      double-kink line
0.233
 
4.0
6.0
8.0
3
14
3
               
1mnn
pd0341
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.182
 
7.0
  
9
4
 
      double-kink line
0.210
 
8.0
8.0
-164.0
2
6
4
      
circular line
0.215
343.0
      
      line
0.222
       
               
1mhd
pd0243
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.123
 
9.0
  
10
3
 
      double-kink line
0.130
 
6.0
10.0
-143.0
3
7
3
      line
0.221
       
      
circular line
0.284
780000000.0
      
               
3kbd
------
E   |    H   |    B
16
nuc
NMR
single-kink line
0.161
 
11.0
  
5
11
 
      double-kink line
0.191
 
11.0
3.0
109.0
5
4
6
      
circular line
0.229
191.0
      
               
1gtw
------
E   |    H   |    B
15
prot-nuc
diff
single-kink line
0.199
 
12.0
  
10
5
 
      double-kink line
0.212
 
8.0
16.0
164.0
5
4
6
      
circular line
0.341
158.0
      
               
1ig9
pd0212
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.106
 
12.0
  
4
9
 
      double-kink line
0.110
 
13.0
6.0
151.0
5
4
4
      
circular line
0.216
148.0
      
               
1a0a
pdt046
E   |    H   |    B
17
prot-nuc
diff
single-kink line
0.370
 
13.0
  
12
4
 
      double-kink line
0.421
 
28.0
12.0
34.0
1
11
4
      
circular line
0.540
223.0
      
               
1gu4
------
E   |    H   |    B
15
prot-nuc
diff
single-kink line
0.153
 
13.0
  
10
5
 
      double-kink line
0.196
 
5.0
16.0
155.0
6
3
5
      
circular line
0.301
147.0
      
               
1a02
pdt050
E   |    H   |    B
18
prot-nuc
diff
single-kink line
0.101
 
15.0
  
11
7
 
      double-kink line
0.126
 
14.0
4.0
65.0
11
2
4
      
circular line
0.288
132.0
      
               
1b8i
pd0042
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.173
 
18.0
  
7
6
 
      
circular line
0.205
74.0
      
      double-kink line
0.299
 
5.0
16.0
34.0
3
5
5
               
1ig7
pd0211
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.185
 
18.0
  
8
5
 
      double-kink line
0.187
 
12.0
18.0
-18.0
7
4
2
      
circular line
0.190
74.0
      
               
1pdn
pdr018
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.280
 
18.0
  
5
8
 
      double-kink line
0.344
 
21.0
8.0
-153.0
5
4
3
               
4gat
------
E   |    H   |    B
13
prot-nuc
NMR
single-kink line
0.108
 
18.0
  
7
6
 
      double-kink line
0.118
 
11.0
12.0
-39.0
6
3
4
      
circular line
0.185
80.0
      
               
1h9t
pd0232
E   |    H   |    B
19
prot-nuc
diff
single-kink line
0.369
 
20.0
  
10
9
 
      double-kink line
0.377
 
22.0
15.0
-117.0
9
2
8
               
1kqq
------
E   |    H   |    B
15
prot-nuc
NMR
single-kink line
0.248
 
22.0
  
7
8
 
      double-kink line
0.263
 
21.0
9.0
70.0
7
6
2
      
circular line
0.283
77.0
      
               
1tsr
pdr022
E   |    H   |    B
20
prot-nuc
diff
single-kink line
0.287
 
22.0
  
4
16
 
      double-kink line
0.309
 
21.0
3.0
22.0
4
10
5
               
1tup
pdr027
E   |    H   |    B
20
prot-nuc
diff
single-kink line
0.282
 
22.0
  
4
16
 
      double-kink line
0.301
 
21.0
4.0
23.0
4
10
5
               
141d
------
E   |    H   |    B
13
nuc
NMR
single-kink line
0.070
 
23.0
  
6
7
 
      
circular line
0.073
50.0
      
      double-kink line
0.085
 
13.0
13.0
-7.0
5
3
5
               
1rna
arn035
E   |    H   |    B
14
nuc
diff
single-kink line
0.080
 
23.0
  
8
6
 
      double-kink line
0.108
 
5.0
21.0
-14.0
4
4
6
      
circular line
0.162
50.0
      
               
5gat
------
E   |    H   |    B
13
prot-nuc
NMR
single-kink line
0.173
 
23.0
  
7
6
 
      double-kink line
0.186
 
10.0
18.0
-56.0
6
2
5
      
circular line
0.262
63.0
      
               
1f44
pd0166
E   |    H   |    B
15
prot-nuc
diff
single-kink line
0.276
 
27.0
  
8
7
 
      double-kink line
0.277
 
13.0
21.0
-55.0
6
3
6
      
circular line
0.470
55.0
      
               
1skn
pdt064
E   |    H   |    B
13
prot-nuc
diff
single-kink line
0.196
 
27.0
  
7
6
 
      double-kink line
0.272
 
10.0
20.0
-5.0
6
2
5
      
circular line
0.281
49.0
      
               
1kbu
pd0271
E   |    H   |    B
16
prot-nuc
diff
single-kink line
0.352
 
33.0
  
8
8
 
      double-kink line
0.407
 
17.0
19.0
32.0
7
3
6
               
1lbg
pdr026
E   |    H   |    B
16
prot-nuc
diff
single-kink line
0.666
 
44.0
  
8
8
 
      double-kink line
0.834
 
43.0
8.0
83.0
8
4
4
               
1j5n
------
E   |    H   |    B
15
prot-nuc
NMR
single-kink line
0.419
 
48.0
  
10
5
 
      double-kink line
0.455
 
7.0
51.0
146.0
5
5
5
               
1hbx
pd0233
E   |    H   |    B
25
prot-nuc
diff
single-kink line
1.881
 
57.0
  
16
9
 
      double-kink line
1.920
 
9.0
59.0
-146.0
6
10
9
               
1e3m
pd0201
E   |    H   |    B
17
prot-nuc
diff
single-kink line
1.164
 
70.0
  
8
9
 
      double-kink line
1.206
 
25.0
51.0
20.0
6
2
9
               
1ng9
pd0367
E   |    H   |    B
17
prot-nuc
diff
single-kink line
1.020
 
71.0
  
7
10
 
      double-kink line
1.105
 
30.0
46.0
21.0
6
2
9
               

Abbreviations