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 1a: Structures for which the helical axis is best described by a double-kink line. Sigma2 of a double-kink line is significantly smaller (>0.2) than for the next best model(s). The structures are listed by sum of the kink angles a1 and a2. Number of structures: 119 PDB NDB bp molecule method helical s(2) r a/a1 a2 a1+a2 o l1 l2 l3 Type axes shape 1f5t pd0170 41 prot-nuc diff 1.251 7 9 16 66 12 15 13 1a31 pde0142 22 prot-nuc diff 0.096 9 8 17 172 6 7 9 1a35 pde0143 22 prot-nuc diff 0.061 11 9 20 157 6 7 9 1d5y pd0078 20 prot-nuc diff 0.185 10 10 20 -119 6 8 6 1io4 pd0198 25 prot-nuc diff 0.277 13 7 20 100 8 8 9 1wai ------ 25 prot-nuc model 1.153 15 8 23 -115 5 7 12 1glu pdrc01 18 prot-nuc diff 0.078 13 12 25 119 5 4 8 3hdd pd0016 20 prot-nuc diff 0.151 10 15 25 -173 7 7 6 1dfm pd0101 14 prot-nuc diff 0.113 13 13 26 -122 5 4 5 1hdd pdt004 20 prot-nuc diff 0.247 10 16 26 168 8 7 5 1ubd pdt038 20 prot-nuc diff 0.179 16 10 26 176 7 7 6 1h6f pd0311 22 prot-nuc diff 0.366 13 14 27 -103 4 14 4 1h89 pd0289 25 prot-nuc diff 0.294 17 10 27 102 8 9 8 1kbd ------ 16 prot NMR 0.186 10 17 27 107 5 5 6 1bvo ------ 15 prot-nuc diff 0.240 14 14 28 -126 5 5 5 1hcq pdrc03 17 prot-nuc diff 0.133 13 15 28 132 6 6 5 1d2i pd0153 14 prot-nuc diff 0.129 13 16 29 -130 5 4 5 1h8a pd0290 25 prot-nuc diff 0.218 15 14 29 101 10 8 7 1mdm pd0338 25 prot-nuc diff 0.162 13 16 29 -152 8 4 13 1xbr pdt045 24 prot-nuc diff 1.028 20 10 30 167 5 6 12 1dh3 pd0102 20 prot-nuc diff 0.226 17 14 31 134 8 4 8 1tro pdr009 37 prot-nuc diff 0.717 15 16 31 -84 9 20 8 1a6y pd0008 20 prot-nuc diff 0.368 19 13 32 -166 9 4 7 1egw pd0121 16 prot-nuc diff 0.139 16 16 32 -104 5 6 5 1k9l ------ 14 nuc NMR 0.122 16 16 32 94 4 6 4 1dmu pd0108 17 prot-nuc diff 0.304 18 15 33 82 7 4 6 1hw2 pd0199 18 prot-nuc diff 0.246 20 13 33 -148 8 4 6 1bn9 ------ 15 nuc NMR 0.221 18 17 35 -99 7 4 4 1mj2 pd0173 18 prot-nuc diff 0.124 20 15 35 -69 5 8 5 1lmb pdr010 19 prot-nuc diff 0.388 18 18 36 -16 4 11 4 1mjo pd0246 18 prot-nuc diff 0.112 19 17 36 -69 5 8 5 1h88 pd0288 25 prot-nuc diff 0.341 24 13 37 161 8 10 7 1lli pdr016 19 prot-nuc diff 0.413 18 19 37 -3 4 11 4 1ddn pd0004 32 prot-nuc diff 1.259 19 19 38 23 5 19 8 2drp pdt011 18 prot-nuc diff 0.191 24 14 38 -125 8 5 5 405d ar0002 16 nuc diff 0.134 20 18 38 177 5 6 5 1h0m ------ 18 prot-nuc diff 0.279 26 13 39 -64 6 6 6 1trr pdr013 32 prot-nuc diff 1.070 19 20 39 -109 11 9 12 2or1 pdr004 19 prot-nuc diff 0.176 21 18 39 -48 6 8 5 1b72 pd0075 19 prot-nuc diff 0.295 18 22 40 -177 10 4 5 1dgc pdt007 18 prot-nuc diff 0.138 20 20 40 112 7 4 7 1lfu ------ 14 prot-nuc NMR 0.662 24 16 40 178 5 5 4 1mjq pd0248 18 prot-nuc diff 0.134 19 21 40 -42 5 8 5 2dnj pde006 14 prot-nuc diff 0.351 20 20 40 154 5 4 5 2ram pdr051 20 prot-nuc diff 0.303 20 20 40 166 10 6 4 1cma pdr008 18 prot-nuc diff 0.154 20 21 41 -78 6 7 5 1per pdr015 19 prot-nuc diff 0.188 22 19 41 -58 6 8 5 2hmi pd0005 18 prot-nuc diff 0.432 24 17 41 44 5 5 8 1rpe pdr011 19 prot-nuc diff 0.250 22 20 42 -58 6 8 5 1au7 pdr034 24 prot-nuc diff 0.377 22 21 43 147 4 14 6 1cit pd0046 16 prot-nuc diff 0.287 24 19 43 129 5 6 5 1hwt pd0089 20 prot-nuc diff 0.286 26 17 43 -165 7 8 5 1bdz ------ 14 nuc NMR 0.157 22 22 44 -55 4 6 4 1oct pdt019 14 prot-nuc diff 0.340 18 27 45 -63 5 5 4 1l3l pd0298 20 prot-nuc diff 0.236 19 28 47 -80 7 6 7 1nk3 ------ 14 prot-nuc NMR 0.446 28 19 47 162 3 4 7 1an4 pdt027 20 prot-nuc diff 1.782 25 23 48 168 6 6 8 1dp7 pd0111 16 prot-nuc diff 0.366 24 24 48 122 5 6 5 1o3t pd0401 13 prot-nuc diff 0.306 36 12 48 51 3 4 6 1b3t pd0024 18 prot-nuc diff 0.196 25 24 49 -109 7 4 7 1rcs ------ 20 prot-nuc NMR 0.148 20 29 49 -32 6 8 6 1ysa pdt002 16 prot-nuc diff 0.385 16 33 49 -176 6 5 5 1lb2 pd0306 20 prot-nuc diff 0.191 19 31 50 -32 11 4 5 1hlv pd0192 21 prot-nuc diff 0.237 16 35 51 33 8 7 6 1rpd ------ 42 prot-nuc model 1.081 24 27 51 14 9 21 12 2bop pdv001 16 prot-nuc diff 0.505 26 26 52 -82 6 4 6 1c7u ------ 20 prot-nuc NMR 0.524 27 27 54 118 5 10 5 1co0 ------ 20 prot-nuc NMR 0.772 16 38 54 153 7 6 7 2stt ------ 17 prot-nuc NMR 0.722 17 37 54 94 4 4 9 4kbd ------ 16 nuc NMR 0.298 21 34 55 103 5 5 6 1bl0 pdr056 22 prot-nuc diff 0.428 29 27 56 -73 8 6 8 1fok pde0127 19 prot-nuc diff 0.483 28 28 56 -125 4 10 5 1ir5 ------ 17 nuc NMR 0.598 35 21 56 144 3 5 9 1exj pd0146 21 prot-nuc diff 0.605 16 41 57 -175 5 5 11 1akh pdr049 19 prot-nuc diff 0.289 20 38 58 -51 6 6 7 1c0w pd0069 21 prot-nuc diff 1.309 30 28 58 169 9 3 9 1kfo ar0039 18 nuc diff 0.135 29 29 58 165 6 6 6 1nk2 ------ 16 prot-nuc NMR 0.646 32 27 59 134 9 3 4 1efa pd0118 17 prot-nuc diff 0.465 40 20 60 67 7 6 4 1le8 pd0308 19 prot-nuc diff 0.366 30 31 61 -51 6 6 7 433d ar0008 14 nuc diff 0.488 31 30 61 176 7 2 4 1ckt pd0051 16 prot-nuc diff 0.240 24 38 62 53 6 3 7 1yrn pdt028 18 prot-nuc diff 0.339 29 33 62 -68 7 6 5 1ytf pdt036 16 prot-nuc diff 0.204 22 40 62 59 6 4 6 1je8 pd0219 20 prot-nuc diff 0.138 32 31 63 -71 6 8 6 1nh2 pd0369 16 prot-nuc diff 0.161 25 38 63 70 6 4 6 1ouq pd0404 21 prot-nuc diff 0.663 35 28 63 36 5 6 10 1mnm pdr036 25 prot-nuc diff 1.552 40 24 64 -59 10 4 11 1jj4 pd0227 16 prot-nuc diff 0.518 32 33 65 -99 6 4 6 1ic8 pd0208 21 prot-nuc diff 0.737 18 48 66 151 13 4 4 1tc3 pde0128 19 prot-nuc diff 0.407 34 32 66 54 4 8 7 1ewq pd0142 21 prot-nuc diff 0.660 27 40 67 -47 11 2 8 1jwl pd0250 14 prot-nuc diff 0.786 40 31 71 -147 6 4 4 1lwt pd0320 36 prot-nuc diff 1.483 52 19 71 -49 11 10 15 1gt0 ------ 23 prot-nuc diff 0.821 55 17 72 -78 5 11 7 2gli pdt008 20 prot-nuc diff 1.264 31 41 72 136 8 3 9 1iaw pd0207 16 prot-nuc diff 0.590 52 21 73 124 8 3 5 1lws pd0319 34 prot-nuc diff 1.163 56 17 73 -72 12 9 13 1qn4 pd0154 14 prot-nuc diff 0.307 41 32 73 48 5 4 5 2cgp pdt049 26 prot-nuc diff 0.153 37 37 74 -44 8 10 8 1gdt pde0115 34 prot-nuc diff 0.588 44 31 75 94 15 4 15 1n14 ------ 13 nuc NMR 0.990 37 38 75 160 4 5 4 1ais pdr031 17 prot-nuc diff 0.617 49 29 78 82 7 6 4 1k6o pd0258 23 prot-nuc diff 1.853 21 57 78 -160 4 10 9 2kbd ------ 16 nuc NMR 0.231 30 48 78 95 6 4 6 1jfi pd0221 17 prot-nuc diff 0.508 41 39 80 68 7 4 6 2rve pde002 16 prot-nuc diff 0.454 43 40 83 126 6 3 7 1qne pd0163 14 prot-nuc diff 0.376 49 37 86 54 5 4 5 1c9b pd0112 17 prot-nuc diff 0.914 43 44 87 45 6 5 6 1owf pd0406 20 prot-nuc diff 0.579 24 65 89 40 8 4 8 1run pdr024 30 prot-nuc diff 0.527 48 42 90 -34 10 10 10 1cgp pdr006 30 prot-nuc diff 0.389 48 44 92 -36 9 11 10 1l1m ------ 23 prot-nuc NMR 0.217 51 41 92 -119 10 2 11 1ouz pd0405 20 prot-nuc diff 0.574 25 67 92 42 8 4 8 1ruo pdr025 30 prot-nuc diff 1.164 46 47 93 -39 10 10 10 1ngm pd0368 19 prot-nuc diff 0.573 57 38 95 62 5 4 10 1owg pd0407 20 prot-nuc diff 0.468 28 67 95 46 8 4 8 1d3u pd0070 23 prot-nuc diff 0.683 58 44 102 71 11 5 7 1cdw pdt034 16 prot-nuc diff 0.533 56 48 104 55 6 5 5 -------------------------------------------------------------------------- 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)