IMB Jena Image Library of Biological Macromolecules
(Last update: November 15, 2004)

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Comprehensive Bending Classification of Nucleic Acid Double Helix
Structures

Bending classification of helical axis - Single-kink line 
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Table 2: 

Structures with 13 or more base 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    bp molecule method   helical  s(2)     r  a/a1 a2   o  l1 l2 l3
                  type           axis shape

1gu5 ------   15 prot-nuc diff  single-kink 0.080        14          10  5
                                double-kink 0.128         2  13   53 10  0  5
                                circular    0.197   135

1hjc pd0205   15 prot-nuc diff  single-kink 0.198        11           4 11
                                double-kink 0.286        98  89 -176  5  1  9
                                circular    0.305   228

1osl ------   18 prot-nuc NMR   single-kink 0.012         3          10  8
                                circular    0.013   725
                                double-kink 0.016         2   4  142 10  0  8
                                straight    0.060

1tf3 ------   15 prot-nuc NMR   single-kink 0.177        12           6  9
                                double-kink 0.249        15   5  142  6  1  6
                                circular    0.274   124

2pua pdr040   16 prot-nuc diff  single-kink 0.561        42           8  8
                                double-kink 0.586       109  73 -159  8  1  7

2pub pdr041   16 prot-nuc diff  single-kink 0.455        47           8  8
                                double-kink 0.555        17  41  -78  8  0  8

2puc pdr042   16 prot-nuc diff  single-kink 0.442        46           8  8
                                double-kink 0.510        39  53 -116  8  0  8

2pud pdr046   16 prot-nuc diff  single-kink 0.470        46           8  8
                                double-kink 0.548        23  29  -54  8  0  8

2puf pdr044   16 prot-nuc diff  single-kink 0.483        43           8  8
                                double-kink 0.557        23  26  -53  8  0  8

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Abbreviations

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PDB         Protein Data Bank
NDB         Nucleic Acid Database
bp          base pair number
diff        diffraction
model       theoretical model
NMR         nuclear magnetic resonance spectroscopy
prot        protein
nuc         nucleic acid
prot-nuc    protein-nucleic acid complex
carb        carbohydrate
plane       plane

s(2)        goodness of fit
r           radius of curvature (circular line)
a           kink angle (single-kink line)
a1, a2      kink angles (double-kink line)
o           twist angle (double-kink line)
l1, l2, l3  lenght of segments 1, 2, and 3 measured in bp
            (double-kink model)