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 4c: Structures with an automatically assigned single-kink helical axis that are in fact, however, in almost all cases double-kink structures. Sigma2 of a single-kink line is significantly smaller (>0.2) than for the next best model(s). All structures of this Table have 12 or less base pairs. Therefore, fitting a double-kink helical axis is not possible. Visual inspection shows that almost all of these structures have in fact a double-kink helical axis even though, especially for small kink angles, a non-ambigious manual classification is impossible. The structures are listed by the goodness of fit sigma2(single-kink line) (s(2)). Number of structures: 54 PDB NDB bp molecule method s(2) a l1 l2 type 1bsu pde0145 10 prot-nuc diff 0.050 50 5 5 1d8x bd0024 10 nuc diff 0.116 36 5 5 410d ah0002 10 nuc diff 0.133 29 4 6 1bss pde0139 10 prot-nuc diff 0.145 43 5 5 1eo3 pd0129 9 prot-nuc diff 0.184 58 4 5 1b94 pd0037 10 prot-nuc diff 0.190 53 5 5 1dnt ah0008 10 nuc diff 0.190 32 3 7 1az0 pde139 10 prot-nuc diff 0.195 43 5 5 1bua pde0146 10 prot-nuc diff 0.207 43 5 5 1d88 ahj044 10 nuc diff 0.207 29 3 7 1b96 pd0039 10 prot-nuc diff 0.211 53 5 5 1rvb pde015 10 prot-nuc diff 0.217 46 5 5 1eop pd0133 10 prot-nuc diff 0.218 44 5 5 1eoo pd0132 12 prot-nuc diff 0.235 57 6 6 1qtm pd0067 12 prot-nuc diff 0.235 19 4 8 1eon pd0131 10 prot-nuc diff 0.238 50 5 5 1qsy pd0065 12 prot-nuc diff 0.238 20 4 8 3ktq pd0032 12 prot-nuc diff 0.265 24 4 8 1b97 pd0040 10 prot-nuc diff 0.272 54 5 5 2ktq pd0030 12 prot-nuc diff 0.276 20 4 8 4ktq pd0033 12 prot-nuc diff 0.276 20 4 8 1rva pde014 10 prot-nuc diff 0.280 44 5 5 1rvc pde016 10 prot-nuc diff 0.288 45 5 5 1b95 pd0038 10 prot-nuc diff 0.307 50 5 5 1rv5 pd0013 10 prot-nuc diff 0.308 38 5 5 1bgb pd0010 10 prot-nuc diff 0.340 52 5 5 1eo4 pd0130 9 prot-nuc diff 0.342 51 4 5 1jb8 ah0019 10 nuc diff 0.346 38 4 6 1azq pdr048 8 prot-nuc diff 0.364 46 3 5 207d ------ 10 nuc NMR 0.388 35 5 5 1g4q ah0012 10 nuc diff 0.446 37 5 5 1svc pdt022 10 prot-nuc diff 0.452 28 6 4 1cfl ------ 10 nuc NMR 0.455 37 6 4 2pvi pd0011 12 prot-nuc diff 0.460 19 6 6 4rve pde003 10 prot-nuc diff 0.503 57 5 5 1cw0 pd0100 12 prot-nuc diff 0.508 47 7 5 1ca6 pd0120 8 prot-nuc diff 0.510 34 3 5 1f0o pd0149 11 prot-nuc diff 0.530 26 5 6 1n8c ------ 11 nuc NMR 0.611 22 4 7 1kc6 pd0272 12 prot-nuc diff 0.619 37 6 6 1hx4 ------ 11 nuc NMR 0.650 29 4 7 1tau pde024 8 prot-nuc diff 0.788 27 3 5 103d ------ 12 nuc NMR 0.848 25 6 6 1a84 ------ 12 nuc NMR 0.852 78 6 6 1iha ah0018 8 nuc diff 0.993 49 4 4 1idw ah0017 8 nuc diff 1.023 50 4 4 1pvi pde017 12 prot-nuc diff 1.034 23 6 6 1icg ah0015 8 nuc diff 1.101 47 4 4 399d adl047 12 nuc diff 1.203 51 6 6 1id9 ah0016 8 nuc diff 1.296 47 4 4 1qbp ar0025 14 nuc diff 1.303 30 6 7 422d ar0007 8 nuc diff 1.338 53 4 4 1oh8 ------ 10 prot-nuc diff 1.397 63 7 3 255d arl037 12 nuc diff 1.398 35 6 6 -------------------------------------------------------------------------- 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)