Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

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

Table 3.

Structures with 13 or more base pairs for which a double-kink helical axis is selected as the most appropriate description, but the central segment consists of 0 or 1 base pairs. In these cases the double-kink geometrical parameters make no sense. Therefore, these structures have to be viewed as single-kink structures. These duplexes are classified as double-kink structures by the automatic approach. However, they have central segments consisting of 0 or 1 base pairs. According to our definition structures of this type are classified as single-kink structures. In this case the difference in the goodness-of fit values between the best and the next best models is not used as a classification criterion. Because of the small number of structures different listings are not given. These structures are indicated by a * in the classification by extent of bending.

Number of structures: 21

PDB
NDB
 IMB Jena
Image Library
bp
 molecule
type
method
model
s(2)
r
a/a1
a2
a1+a2
o
l1
l2
l3
1bdh
pdr028
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.458
  
25
31
56
-89
8
0
8
      single-kink line
0.532
  
39
    
8
8
  
                
1bdi
pdr029
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.432
  
28
28
56
-85
8
0
8
      single-kink line
0.598
  
41
    
8
8
  
                
1jfs
pd0223
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.457
  
63
47
110
-132
8
0
8
      single-kink line
0.484
  
42
    
8
8
  
                
1jft
pd0224
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.548
  
110
73
183
-158
8
1
7
      single-kink line
0.557
  
43
    
8
8
  
                
1jh9
pd0226
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.275
  
35
26
61
-80
8
0
8
      single-kink line
0.369
  
46
    
8
8
  
                
1lo1
------
E   |    H   |    B
13
prot-nuc
NMR
 double-kink lines
0.074
  
10
12
22
161
5
1
6
      single-kink line
0.086
  
5
    
8
5
  
      circular arc
0.102
305
        
      straight line
0.156
         
                
1qp0
pd0057
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.532
  
27
29
56
-89
8
0
8
      single-kink line
0.644
  
39
    
8
8
  
                
1qp4
pd0058
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.518
  
106
79
185
-154
8
1
7
      single-kink line
0.660
  
38
    
8
8
  
                
1qp7
pd0059
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.431
  
80
105
185
-154
7
1
8
      single-kink line
0.613
  
37
    
8
8
  
                
1qpz
pd0056
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.539
  
44
35
79
-114
8
0
8
      single-kink line
0.554
  
41
    
8
8
  
                
1qqa
pd0060
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.474
  
107
77
184
-156
8
1
7
      single-kink line
0.551
  
39
    
8
8
  
                
1qqb
pd0061
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.474
  
107
77
184
-156
8
1
7
      single-kink line
0.551
  
39
    
8
8
  
                
1vpw
pdt063
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.432
  
25
39
64
-104
8
0
8
      single-kink line
0.489
  
39
    
8
8
  
                
1zay
pd0109
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.343
  
39
34
73
-104
8
0
8
      single-kink line
0.429
  
43
    
8
8
  
                
2hdc
------
E   |    H   |    B
17
prot-nuc
NMR
 double-kink lines
0.041
  
91
91
182
-179
11
1
5
      single-kink line
0.070
  
2
    
8
8
  
      circular arc
0.075
1010
        
      straight line
0.083
         
                
2pue
pdr043
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.444
  
29
32
61
-94
8
0
8
      single-kink line
0.474
  
41
    
8
8
  
                
2pug
pdr045
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.497
  
74
109
183
-158
7
1
8
      single-kink line
0.542
  
42
    
8
8
  
                
1cjg
------
E   |    H   |    B
22
prot-nuc
NMR
 double-kink lines
0.294
  
88
100
188
-144
10
1
11
      single-kink line
1.309
  
38
    
11
11
  
                
1exi
pd0145
E   |    H   |    B
21
prot-nuc
diff
 double-kink lines
0.285
  
93
92
185
-147
10
1
10
      single-kink line
0.533
  
33
    
10
10
  
                
1pnr
pdr020
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.443
  
79
107
186
-149
7
1
8
      single-kink line
0.801
  
42
    
8
8
  
                
1wet
pdr030
E   |    H   |    B
16
prot-nuc
diff
 double-kink lines
0.323
  
80
106
186
-149
7
1
8
      single-kink line
0.712
  
40
    
8
8
  

Abbreviations