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 - Other -------------------------------------------------------------------------- Structures with a complex helical axis. Here duplexes are compiled for which the curvilinear helical axes show the largest deviations from any of the models used for fitting. For these structures the best models have a goodness-of-fit value larger 2. Except for the superhelical structures (1aoi, 1eqz, 1f66, 1id3, 1kx5, 1m19) most of them can nevertheless roughly be classified as straight line (1fja) or double-kink structures (1bpz, 1fjl, 1ihf, 2irf, 4crx, 5crx). This is explained in more detail below. In the extent of bending classification these structures are included as separate tables in the no bending, slight, moderate and strong bending categories. -------------------------------------------------------------------------- Number of structures: 33 PDB NDB bp molecule method helical s(2) r a/a1 a2 o l1 l2 l3 type axes shape 1aoi pd0001 146 prot-nuc diff 1eqz pd0137 146 prot-nuc diff 1f66 pd0171 146 prot-nuc diff 1id3 pd0209 146 prot-nuc diff 1kx3 pd0285 146 prot-nuc diff 1kx4 pd0286 146 prot-nuc diff 1m1a pd0330 146 prot-nuc diff 1m18 pd0328 146 prot-nuc diff 1m19 pd0329 146 prot-nuc diff 1kx5 pd0287 147 prot-nuc diff 1bpz pde0124 16 prot-nuc diff plane 0.939 double-kink 2.241 64 32 10 6 3 7 single-kink 2.447 87 7 9 circular 5.123 20.0 straight 53.310 1dfu pr0018 15 prot-nuc diff plane 1.120 double-kink 3.516 62 31 -180 4 5 6 single-kink 4.874 53 3 12 straight 6.190 circular 7.363 192.0 1fja ------ 6 prot-nuc NMR plane 0.014 circular 0.000 0.0 double-kink 0.000 0 0 0 0 0 0 single-kink 0.000 0 0 0 straight 4.685 1fjl pde025 41 prot-nuc diff plane 1.654 double-kink 2.521 31 31 141 19 3 19 single-kink 3.436 20 20 20 circular 5.906 220.0 straight 15.036 1ihf pdt040 34 prot-nuc diff plane 5.055 double-kink 3.423 92 82 -21 12 10 12 circular 7.937 25.0 single-kink 26.266 135 17 17 straight 227.064 1j9h ar0034 9 nuc diff plane 1.364 double-kink 0.000 0 0 0 0 0 0 circular 3.280 12.0 single-kink 5.649 73 4 5 straight 11.666 1j9n ------ 6 prot-nuc NMR plane 0.054 circular 0.000 0.0 double-kink 0.000 0 0 0 0 0 0 single-kink 0.000 0 0 0 straight 5.903 1ju1 ------ 23 nuc NMR plane 0.876 double-kink 3.481 32 32 -21 5 15 3 single-kink 3.841 35 5 18 straight 5.979 circular 6.683 904000000.0 1k71 bd0056 11 nuc diff plane 0.403 double-kink 0.000 0 0 0 0 0 0 straight 3.107 circular 4.349 376000000.0 single-kink 4.776 25 9 2 1kd3 ar0036 10 nuc diff plane 0.783 double-kink 0.000 0 0 0 0 0 0 straight 2.147 circular 3.220 35800000.0 single-kink 3.527 22 2 8 1kd4 ar0037 10 nuc diff plane 1.173 double-kink 0.000 0 0 0 0 0 0 straight 3.100 circular 4.009 60.0 single-kink 4.666 18 4 5 1kd5 ar0038 10 nuc diff plane 0.906 double-kink 0.000 0 0 0 0 0 0 straight 2.315 circular 3.056 98.0 single-kink 3.650 13 4 5 1luh ------ 8 nuc NMR plane 0.961 double-kink 0.000 0 0 0 0 0 0 circular 2.835 18.0 single-kink 5.099 57 4 4 straight 13.663 1n1k ------ 6 nuc NMR plane 0.015 circular 0.000 0.0 double-kink 0.000 0 0 0 0 0 0 single-kink 0.000 0 0 0 straight 2.866 1n35 pr0087 6 prot-nuc diff plane 0.223 circular 0.000 0.0 double-kink 0.000 0 0 0 0 0 0 single-kink 0.000 0 0 0 straight 5.631 1n96 ------ 8 nuc NMR plane 0.689 double-kink 0.000 0 0 0 0 0 0 circular 34.159 9.0 straight 38.968 single-kink 46.914 104 7 1 1nyd ------ 9 nuc NMR plane 0.393 double-kink 0.000 0 0 0 0 0 0 circular 2.264 3.0 straight 3.605 single-kink 3.731 127 4 5 1nzb pd0392 36 prot-nuc diff plane 3.849 double-kink 4.446 24 78 -103 10 10 16 single-kink 7.703 76 20 16 circular 14.795 48.0 straight 119.028 1nzm ------ 7 nuc NMR plane 1.044 double-kink 0.000 0 0 0 0 0 0 single-kink 0.000 0 0 0 straight 5.708 circular 10.657 3.0 2d47 adl025 12 nuc diff plane 1.727 double-kink 0.000 0 0 0 0 0 0 single-kink 3.186 53 5 7 circular 3.220 21.0 straight 10.450 2irf pd0076 36 prot-nuc diff plane 2.495 double-kink 3.961 20 14 142 9 8 18 single-kink 5.153 9 20 15 circular 5.279 418.0 straight 6.562 4crx pd0047 34 prot-nuc diff plane 2.230 double-kink 3.227 24 82 -126 8 11 15 single-kink 5.724 77 19 15 circular 14.052 46.0 straight 108.358 5crx pd0048 32 prot-nuc diff plane 1.810 double-kink 2.926 29 83 -127 6 12 14 single-kink 5.088 78 18 14 circular 11.985 43.0 straight 100.087 -------------------------------------------------------------------------- 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 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)