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 5b : Structures with an automatically assigned single-kink helical axis. Sigma2 of a single-kink line is only slightly smaller (<0.2) than for the next best model(s). All structures included in this Table have 12 or less base pairs. For small kink angles it is not possible to differentiate manually between single-kink or double-kink helical axes. The structures are listed by the number of base pairs (bp). Number of structures: 179 PDB NDB bp molecule method helical s(2) r a/a1 a2 o l1 l2 l3 type axis shape 197d adh059 8 nuc diff single-kink 0.129 16 5 3 circular 0.160 52 straight 0.235 1au5 ------ 8 nuc NMR single-kink 0.833 56 4 4 circular 0.867 15 1azp pdr047 8 prot-nuc diff single-kink 0.632 35 2 6 circular 0.736 41 1bf4 pd0088 8 prot-nuc diff single-kink 0.785 37 2 6 straight 0.857 circular 0.945 54 1bnz pd0012 8 prot-nuc diff single-kink 1.004 35 3 5 circular 1.034 29 1c8c pd0143 8 prot-nuc diff single-kink 0.465 31 2 6 circular 0.659 42 1ca5 pd0119 8 prot-nuc diff single-kink 0.429 26 3 5 circular 0.555 35 1nk6 pd0379 8 prot-nuc diff single-kink 0.264 24 6 2 circular 0.445 60 1rxa arh063 8 nuc diff single-kink 0.229 30 4 4 circular 0.336 24 370d adh0104 8 nuc diff single-kink 0.137 13 5 3 circular 0.158 66 straight 0.231 409d ar0004 8 nuc diff single-kink 0.237 29 4 4 circular 0.336 25 421d dr0003 8 nuc diff single-kink 0.071 13 3 5 circular 0.121 75 straight 0.211 438d ar0011 8 nuc diff single-kink 0.262 21 3 5 circular 0.289 40 1c4l ------ 9 nuc NMR single-kink 0.873 45 5 4 circular 0.910 19 1dk9 ------ 9 nuc NMR single-kink 0.051 5 3 5 circular 0.056 221 straight 0.059 1hg9 ------ 9 nuc NMR single-kink 0.117 14 4 5 circular 0.136 58 1l3s pd0300 9 prot-nuc diff single-kink 0.088 13 7 2 circular 0.145 145 straight 0.171 1nk7 pd0380 9 prot-nuc diff single-kink 0.207 14 7 2 straight 0.250 circular 0.255 127 1oka ------ 9 nuc NMR single-kink 0.146 16 5 4 circular 0.147 52 1qrv pd0110 9 prot-nuc diff single-kink 0.412 48 4 5 circular 0.506 16 479d ah0005 9 nuc diff single-kink 0.521 19 5 3 circular 0.698 51 126d bdj051 10 nuc diff single-kink 0.500 21 7 3 circular 0.606 74 137d adj050 10 nuc diff single-kink 0.312 25 5 5 circular 0.348 35 138d adj051 10 nuc diff single-kink 0.240 24 5 5 circular 0.291 37 196d bdj060 10 nuc diff single-kink 0.102 5 4 5 circular 0.112 219 straight 0.130 1a1f pdt055 10 prot-nuc diff single-kink 0.252 15 7 3 circular 0.424 91 1a1g pdt056 10 prot-nuc diff single-kink 0.111 8 6 4 circular 0.112 132 straight 0.208 1a1i pdt059 10 prot-nuc diff single-kink 0.230 12 6 4 circular 0.249 92 1a1j pdt060 10 prot-nuc diff single-kink 0.170 14 6 4 circular 0.206 73 1b01 pd0091 10 prot-nuc diff single-kink 1.128 40 6 4 circular 1.182 27 1bpx pde0126 10 prot-nuc diff single-kink 0.226 11 3 7 circular 0.261 139 straight 0.298 1bpy pde0125 10 prot-nuc diff single-kink 0.106 11 3 7 circular 0.178 125 straight 0.281 1cvx dd0020 10 nuc diff single-kink 0.150 8 4 6 circular 0.169 136 straight 0.272 1d20 ------ 10 nuc NMR single-kink 0.098 8 7 3 circular 0.109 188 straight 0.139 1d56 bdj036 10 nuc diff single-kink 0.191 9 5 5 circular 0.192 117 straight 0.335 1d57 bdj037 10 nuc diff single-kink 0.197 8 5 5 circular 0.204 129 straight 0.307 1d96 ahj015 10 nuc diff single-kink 0.105 22 4 6 circular 0.300 44 1d9h ah0006 10 nuc diff single-kink 0.148 30 4 6 circular 0.306 29 1d9r bd0025 10 nuc diff single-kink 0.140 26 5 5 circular 0.339 41 1dcv bd0028 10 nuc diff single-kink 0.178 12 5 5 circular 0.210 85 1dno ah0007 10 nuc diff single-kink 0.128 19 3 7 circular 0.235 54 1drr ------ 10 nuc NMR single-kink 0.104 16 6 4 circular 0.110 60 1evp ah0011 10 nuc diff single-kink 0.368 28 5 5 circular 0.563 31 1f5e ------ 10 prot-nuc NMR single-kink 0.543 22 6 4 circular 0.625 54 1g9z pd0190 10 prot-nuc diff single-kink 0.172 20 6 4 circular 0.263 54 1h9d pd0210 10 prot-nuc diff single-kink 0.255 11 6 3 circular 0.342 126 straight 0.400 1jk2 pd0231 10 prot-nuc diff single-kink 0.110 8 5 5 circular 0.113 134 straight 0.212 1mq3 pd0344 10 prot-nuc diff single-kink 0.077 12 4 6 circular 0.127 96 1mxk ------ 10 nuc NMR single-kink 0.437 37 6 4 circular 0.555 29 1n1n ------ 10 nuc NMR single-kink 0.068 11 5 5 circular 0.087 121 1n3e pd0360 10 prot-nuc diff single-kink 0.063 13 5 5 circular 0.104 80 1n3f pd0361 10 prot-nuc diff single-kink 0.154 11 4 6 circular 0.223 112 1ofx ahj040 10 nuc diff single-kink 0.144 25 4 6 circular 0.224 36 1pib ------ 10 nuc NMR single-kink 0.212 11 2 7 straight 0.229 circular 0.262 200 1ql5 ------ 10 nuc NMR single-kink 0.208 12 6 4 circular 0.228 96 1rn9 ------ 10 nuc NMR single-kink 0.362 17 4 6 circular 0.370 61 1zaa pdt006 10 prot-nuc diff single-kink 0.208 9 5 4 circular 0.211 121 straight 0.309 221d adj067 10 nuc diff single-kink 0.319 32 5 5 circular 0.322 27 222d ahj068 10 nuc diff single-kink 0.171 24 4 6 circular 0.274 38 226d ------ 10 nuc NMR single-kink 0.174 10 4 6 circular 0.190 124 straight 0.290 260d adj075 10 nuc diff single-kink 0.111 18 5 5 circular 0.179 48 320d adj081 10 nuc diff single-kink 0.391 31 5 5 circular 0.420 29 327d adjb88 10 nuc diff single-kink 0.221 20 5 5 circular 0.273 42 334d gdj054 10 nuc diff single-kink 0.309 19 7 3 circular 0.445 85 348d adj0102 10 nuc diff single-kink 0.398 26 5 5 circular 0.503 34 349d adj0103 10 nuc diff single-kink 0.397 24 5 5 circular 0.492 37 358d gdjb55 10 nuc diff single-kink 0.038 12 5 5 circular 0.044 79 365d gdj057 10 nuc diff single-kink 0.088 10 5 5 circular 0.113 109 383d adjb110 10 nuc diff single-kink 0.218 33 5 5 circular 0.270 25 384d adjb111 10 nuc diff single-kink 0.519 20 8 2 circular 0.564 74 straight 0.664 395d adj0112 10 nuc diff single-kink 0.051 19 5 5 circular 0.120 44 396d adj0113 10 nuc diff single-kink 0.279 28 5 5 circular 0.457 32 401d ad0001 10 nuc diff single-kink 0.356 26 5 5 circular 0.496 34 404d ah0001 10 nuc diff single-kink 0.232 21 5 5 circular 0.411 45 408d bdd003 10 nuc diff single-kink 0.188 7 5 5 circular 0.208 156 straight 0.261 411d ah0003 10 nuc diff single-kink 0.148 26 4 6 circular 0.256 35 412d ah0004 10 nuc diff single-kink 0.141 28 4 6 circular 0.246 32 414d ad0002 10 nuc diff single-kink 0.222 27 5 5 circular 0.323 34 440d ad0003 10 nuc diff single-kink 0.246 29 4 6 circular 0.374 32 474d gdjb58 10 nuc diff single-kink 0.029 4 4 6 circular 0.036 283 straight 0.054 1afz ------ 11 nuc NMR single-kink 0.116 5 5 6 circular 0.124 239 straight 0.143 1axv ------ 11 nuc NMR single-kink 0.467 19 6 5 circular 0.589 68 1djd ------ 11 nuc NMR single-kink 0.771 22 5 6 circular 0.844 62 1dsi ------ 11 nuc NMR single-kink 0.463 17 8 3 circular 0.530 89 1e3o pd0225 11 prot-nuc diff single-kink 0.563 24 7 4 circular 0.744 54 1eyu pd0147 11 prot-nuc diff single-kink 0.352 13 5 6 circular 0.414 96 1fj5 ------ 11 nuc NMR single-kink 0.387 30 6 5 circular 0.408 35 1gcc ------ 11 prot-nuc NMR single-kink 0.064 13 4 7 circular 0.140 96 1hwv ------ 11 nuc NMR single-kink 0.286 30 8 3 circular 0.464 60 1i7v ------ 11 nuc NMR single-kink 0.701 22 5 6 circular 0.874 60 1ijw pd0213 11 prot-nuc diff single-kink 0.208 13 4 7 circular 0.225 97 1l3u pd0302 11 prot-nuc diff single-kink 0.166 9 4 7 circular 0.179 138 straight 0.300 1lcc ------ 11 prot-nuc NMR single-kink 0.207 22 6 5 circular 0.216 47 1le9 pd0309 11 prot-nuc diff single-kink 0.171 10 5 6 circular 0.200 115 1msf ------ 11 prot-nuc NMR single-kink 0.323 12 7 4 circular 0.448 121 1mxj ------ 11 nuc NMR single-kink 0.063 11 4 7 circular 0.106 111 1njw pd0372 11 prot-nuc diff single-kink 0.101 9 5 6 circular 0.117 131 straight 0.276 1njx pd0373 11 prot-nuc diff single-kink 0.205 14 5 6 circular 0.281 83 1nk0 pd0376 11 prot-nuc diff single-kink 0.059 7 5 6 circular 0.069 175 straight 0.157 1o3q pd0398 11 prot-nuc diff single-kink 0.663 27 6 5 circular 0.713 43 1o3r pd0399 11 prot-nuc diff single-kink 0.347 33 6 5 circular 0.391 34 1onm ------ 11 nuc NMR single-kink 0.050 11 4 7 circular 0.096 111 1pqq ------ 11 nuc NMR single-kink 0.700 24 5 6 circular 0.730 45 1qby ------ 11 nuc NMR single-kink 0.215 14 8 3 circular 0.393 174 1skp ------ 11 nuc NMR single-kink 0.144 15 6 5 circular 0.199 64 1t7p pde0135 11 prot-nuc diff single-kink 0.248 9 4 7 circular 0.268 142 straight 0.358 1vkx pdr033 11 prot-nuc diff single-kink 0.113 9 7 4 circular 0.175 172 straight 0.253 1yui ------ 11 prot-nuc NMR single-kink 0.118 15 5 6 circular 0.138 84 1yuj ------ 11 prot-nuc NMR single-kink 0.097 13 6 5 circular 0.127 97 4bdp pde0133 11 prot-nuc diff single-kink 0.131 14 5 6 circular 0.204 80 101d gdlb31 12 nuc diff single-kink 0.061 7 7 5 circular 0.071 178 straight 0.224 102d gdl032 12 nuc diff single-kink 0.053 8 4 8 circular 0.073 175 straight 0.234 127d gdl022 12 nuc diff single-kink 0.099 10 5 7 circular 0.124 132 128d gdlb19 12 nuc diff single-kink 0.097 9 5 7 circular 0.167 168 129d gdl021 12 nuc diff single-kink 0.097 9 5 7 circular 0.104 151 130d gdlb20 12 nuc diff single-kink 0.149 10 5 6 circular 0.210 124 166d gdl027 12 nuc diff single-kink 0.060 9 4 8 circular 0.095 162 194d bdl059 12 nuc diff single-kink 0.104 14 4 8 circular 0.195 115 1a66 ------ 12 prot-nuc NMR single-kink 0.118 11 3 9 circular 0.169 181 straight 0.300 1aio ddlb73 12 nuc diff single-kink 0.221 30 6 6 circular 0.383 35 1bbx ------ 12 prot-nuc NMR single-kink 0.692 12 6 6 circular 0.702 115 1bna bdl001 12 nuc diff single-kink 0.070 11 5 7 circular 0.076 118 1bw7 ------ 12 nuc NMR single-kink 0.214 8 4 8 circular 0.257 207 straight 0.271 1coc ------ 12 nuc NMR single-kink 0.262 24 5 7 circular 0.271 58 1d30 gdl008 12 nuc diff single-kink 0.056 9 4 8 circular 0.104 189 straight 0.240 1d45 gdl012 12 nuc diff single-kink 0.069 12 4 8 circular 0.097 124 1d46 gdl013 12 nuc diff single-kink 0.071 10 2 10 straight 0.115 circular 0.119 462 1d85 gdlb17 12 nuc diff single-kink 0.126 10 6 6 circular 0.158 128 1d99 bdl011 12 nuc diff single-kink 0.088 14 5 7 circular 0.102 91 1dn9 bdl007 12 nuc diff single-kink 0.085 6 3 9 straight 0.101 circular 0.107 511 1dnh gdl002 12 nuc diff single-kink 0.108 10 5 7 circular 0.132 130 1dxn ------ 12 nuc NMR single-kink 0.608 20 3 9 circular 0.729 106 1eel dd0025 12 nuc diff single-kink 0.107 8 3 8 circular 0.142 226 straight 0.213 1flo pd0178 12 prot-nuc diff single-kink 0.129 21 5 7 circular 0.281 62 1fmq dd0034 12 nuc diff single-kink 0.090 11 4 8 circular 0.147 149 1fms dd0035 12 nuc diff single-kink 0.075 11 4 8 circular 0.105 131 1hq7 bd0047 12 nuc diff single-kink 0.094 5 5 7 circular 0.104 253 straight 0.152 1i3t bd0048 12 nuc diff single-kink 0.080 11 5 7 circular 0.107 122 1i47 bd0049 12 nuc diff single-kink 0.080 10 4 8 circular 0.109 141 1jxl pd0252 12 prot-nuc diff single-kink 0.123 10 5 7 circular 0.133 122 1l5u pd0304 12 prot-nuc diff single-kink 0.127 10 5 6 circular 0.158 116 1llm pd0312 12 prot-nuc diff single-kink 0.138 14 6 6 circular 0.143 86 1lu5 dd0050 12 nuc diff single-kink 0.175 27 6 6 circular 0.184 39 1m6x pd0336 12 prot-nuc diff single-kink 0.153 19 5 7 circular 0.272 66 1ndn bdl032 12 nuc diff single-kink 0.212 9 4 8 circular 0.278 216 straight 0.321 1nk9 pd0382 12 prot-nuc diff single-kink 0.306 30 6 6 circular 0.330 39 1p4e pd0425 12 prot-nuc diff single-kink 0.159 20 5 7 circular 0.342 66 1pgc ------ 12 nuc NMR single-kink 0.338 22 8 4 circular 0.519 66 1qms ------ 12 nuc NMR single-kink 0.018 7 7 5 circular 0.026 181 straight 0.132 1qss pd0066 12 prot-nuc diff single-kink 0.287 17 5 7 circular 0.458 77 1qsx ------ 12 nuc NMR single-kink 0.065 12 7 5 circular 0.127 109 1qv8 dd0060 12 nuc diff single-kink 0.067 8 5 7 circular 0.071 162 straight 0.257 1qxb ------ 12 nuc NMR single-kink 0.173 13 6 6 circular 0.188 87 1sdr arl062 12 nuc diff single-kink 0.102 16 6 6 circular 0.144 64 1ttd ------ 12 nuc NMR single-kink 0.190 23 6 6 circular 0.292 56 218d bdlb58 12 nuc diff single-kink 0.145 21 5 7 circular 0.187 61 227d gdl036 12 nuc diff single-kink 0.035 10 4 8 circular 0.079 163 268d gdlb42 12 nuc diff single-kink 0.067 9 5 7 circular 0.079 141 289d gdl045 12 nuc diff single-kink 0.079 11 4 8 circular 0.112 130 2bna bdl002 12 nuc diff single-kink 0.067 11 4 8 circular 0.094 139 2dbe gdl009 12 nuc diff single-kink 0.061 9 4 8 circular 0.095 187 straight 0.230 2ezf ------ 12 prot-nuc NMR single-kink 0.072 6 8 4 circular 0.074 276 straight 0.179 2ezg ------ 12 prot-nuc NMR single-kink 0.069 11 3 9 circular 0.176 238 311d gdl052 12 nuc diff single-kink 0.052 10 4 8 circular 0.102 156 360d gdl056 12 nuc diff single-kink 0.088 12 4 8 circular 0.125 123 388d bdlb84 12 nuc diff single-kink 0.076 11 4 8 circular 0.130 140 389d bdlb85 12 nuc diff single-kink 0.080 12 4 8 circular 0.085 117 3hts pd0073 12 prot-nuc diff single-kink 0.080 9 6 6 circular 0.117 138 3pvi pd0006 12 prot-nuc diff single-kink 0.870 12 7 5 circular 0.976 127 442d dd0003 12 nuc diff single-kink 0.331 20 8 4 circular 0.406 80 443d dd0004 12 nuc diff single-kink 0.267 20 8 4 circular 0.355 79 444d dd0005 12 nuc diff single-kink 0.044 8 4 8 circular 0.058 184 straight 0.209 468d ar0016 12 nuc diff single-kink 0.047 5 8 4 circular 0.055 251 straight 0.060 469d ar0015 12 nuc diff single-kink 0.043 6 8 4 circular 0.055 177 straight 0.079 470d ar0017 12 nuc diff single-kink 0.097 6 5 6 circular 0.106 166 straight 0.128 471d ar0018 12 nuc diff single-kink 0.121 8 7 5 circular 0.152 146 straight 0.183 4dnb bdlb13 12 nuc diff single-kink 0.078 14 5 7 circular 0.103 91 6bna gdlb05 12 nuc diff single-kink 0.063 10 6 6 circular 0.064 127 9bna bdl020 12 nuc diff single-kink 0.066 12 5 7 circular 0.068 109 -------------------------------------------------------------------------- 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)