Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

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

Table 2:

Structures with 13 or more pairs for which the helical axis is best described by a single-kink line and the alternative double-kink model has a short central segment with 0 or 1 base pairs. 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.

Number of structures: 9

PDB 
NDB 
IMB Jena
Image Library
bp
molecule
type
method
model
s(2)
r
a/a1
a2
o
l1
l2
l3
1gu5
------
E   |    H   |    B
15
prot-nuc
diff
single-kink line
0.080
 
14.0
  
10
5
 
      double-kink line
0.128
 
2.0
13.0
53.0
10
0
5
      
circular line
0.197
135.0
      
               
1hjc
pd0205
E   |    H   |    B
15
prot-nuc
diff
single-kink line
0.198
 
11.0
  
4
11
 
      double-kink line
0.286
 
98.0
89.0
-176.0
5
1
9
      
circular line
0.305
228.0
      
               
1osl
------
E   |    H   |    B
18
prot-nuc
NMR
single-kink line
0.012
 
3.0
  
10
8
 
      
circular line
0.013
725.0
      
      double-kink line
0.016
 
2.0
4.0
142.0
10
0
8
      line
0.060
       
               
1tf3
------
E   |    H   |    B
15
prot-nuc
NMR
single-kink line
0.177
 
12.0
  
6
9
 
      double-kink line
0.249
 
15.0
5.0
142.0
6
1
6
      
circular line
0.274
124.0
      
               
2pua
pdr040
E   |    H   |    B
16
prot-nuc
diff
single-kink line
0.561
 
42.0
  
8
8
 
      double-kink line
0.586
 
109.0
73.0
-159.0
8
1
7
               
2pub
pdr041
E   |    H   |    B
16
prot-nuc
diff
single-kink line
0.455
 
47.0
  
8
8
 
      double-kink line
0.555
 
17.0
41.0
-78.0
8
0
8
               
2puc
pdr042
E   |    H   |    B
16
prot-nuc
diff
single-kink line
0.442
 
46.0
  
8
8
 
      double-kink line
0.510
 
39.0
53.0
-116.0
8
0
8
               
2pud
pdr046
E   |    H   |    B
16
prot-nuc
diff
single-kink line
0.470
 
46.0
  
8
8
 
      double-kink line
0.548
 
23.0
29.0
-54.0
8
0
8
               
2puf
pdr044
E   |    H   |    B
16
prot-nuc
diff
single-kink line
0.483
 
43.0
  
8
8
 
      double-kink line
0.557
 
23.0
26.0
-53.0
8
0
8
               

Abbreviations