IMB Jena Image Library of Biological Macromolecules (Last update: November 15, 2004) -------------------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures Bending classification of helical axis - Single-kink line -------------------------------------------------------------------------- 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 bp molecule method helical s(2) r a/a1 a2 a1+a2 o l1 l2 l3 type axes shape 1bdh pdr028 16 prot-nuc diff double-kink 0.458 25 31 56 -89 8 0 8 single-kink 0.532 39 8 8 1bdi pdr029 16 prot-nuc diff double-kink 0.432 28 28 56 -85 8 0 8 single-kink 0.598 41 8 8 1jfs pd0223 16 prot-nuc diff double-kink 0.457 63 47 110 -132 8 0 8 single-kink 0.484 42 8 8 1jft pd0224 16 prot-nuc diff double-kink 0.548 110 73 183 -158 8 1 7 single-kink 0.557 43 8 8 1jh9 pd0226 16 prot-nuc diff double-kink 0.275 35 26 61 -80 8 0 8 single-kink 0.369 46 8 8 1lo1 ------ 13 prot-nuc NMR double-kink 0.074 10 12 22 161 5 1 6 single-kink 0.086 5 8 5 circular 0.102 305 straight 0.156 1qp0 pd0057 16 prot-nuc diff double-kink 0.532 27 29 56 -89 8 0 8 single-kink 0.644 39 8 8 1qp4 pd0058 16 prot-nuc diff double-kink 0.518 106 79 185 -154 8 1 7 single-kink 0.660 38 8 8 1qp7 pd0059 16 prot-nuc diff double-kink 0.431 80 105 185 -154 7 1 8 single-kink 0.613 37 8 8 1qpz pd0056 16 prot-nuc diff double-kink 0.539 44 35 79 -114 8 0 8 single-kink 0.554 41 8 8 1qqa pd0060 16 prot-nuc diff double-kink 0.474 107 77 184 -156 8 1 7 single-kink 0.551 39 8 8 1qqb pd0061 16 prot-nuc diff double-kink 0.474 107 77 184 -156 8 1 7 single-kink 0.551 39 8 8 1vpw pdt063 16 prot-nuc diff double-kink 0.432 25 39 64 -104 8 0 8 single-kink 0.489 39 8 8 1zay pd0109 16 prot-nuc diff double-kink 0.343 39 34 73 -104 8 0 8 single-kink 0.429 43 8 8 2hdc ------ 17 prot-nuc NMR double-kink 0.041 91 91 182 -179 11 1 5 single-kink 0.070 2 8 8 circular 0.075 1010 straight 0.083 2pue pdr043 16 prot-nuc diff double-kink 0.444 29 32 61 -94 8 0 8 single-kink 0.474 41 8 8 2pug pdr045 16 prot-nuc diff double-kink 0.497 74 109 183 -158 7 1 8 single-kink 0.542 42 8 8 1cjg ------ 22 prot-nuc NMR double-kink 0.294 88 100 188 -144 10 1 11 single-kink 1.309 38 11 11 1exi pd0145 21 prot-nuc diff double-kink 0.285 93 92 185 -147 10 1 10 single-kink 0.533 33 10 10 1pnr pdr020 16 prot-nuc diff double-kink 0.443 79 107 186 -149 7 1 8 single-kink 0.801 42 8 8 1wet pdr030 16 prot-nuc diff double-kink 0.323 80 106 186 -149 7 1 8 single-kink 0.712 40 8 8 -------------------------------------------------------------------------- Abbreviations -------------------------------------------------------------------------- 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)