ID code: '1DRN' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 8 C1' DG A 1 beta 4 9 7 30 C1' DG A 2 beta 26 31 29 52 C1' DA A 3 beta 48 53 51 73 C1' DG A 4 beta 69 74 72 95 C1' DA A 5 beta 91 96 94 117 C1' U A 6 beta 112 118 115 137 C1' G A 7 beta 132 138 135 160 C1' A A 8 beta 155 161 158 182 C1' C A 9 beta 177 183 180 199 C1' DG B 10 beta 195 200 198 221 C1' DT B 11 beta 217 222 220 241 C1' DC B 12 beta 237 242 240 260 C1' DA B 13 beta 256 261 259 281 C1' DT B 14 beta 277 282 280 301 C1' DC B 15 beta 297 302 300 320 C1' DT B 16 beta 316 321 319 340 C1' DC B 17 beta 336 341 339 359 C1' DC B 18 beta 355 360 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG A 1 8 5 29 C2' DG A 2 30 27 51 C2' DA A 3 52 49 72 C2' DG A 4 73 70 94 C2' DA A 5 95 92 115 C2' U A 6 OK 117 113 116 135 C2' G A 7 OK 137 133 136 158 C2' A A 8 OK 160 156 159 180 C2' C A 9 OK 182 178 181 198 C2' DG B 10 199 196 220 C2' DT B 11 221 218 240 C2' DC B 12 241 238 259 C2' DA B 13 260 257 280 C2' DT B 14 281 278 300 C2' DC B 15 301 298 319 C2' DT B 16 320 317 339 C2' DC B 17 340 337 358 C2' DC B 18 359 356 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG A 1 OK 3 6 7 27 C3' DG A 2 OK 25 28 29 49 C3' DA A 3 OK 47 50 51 70 C3' DG A 4 OK 68 71 72 92 C3' DA A 5 OK 90 93 94 113 C3' U A 6 OK 111 114 115 133 C3' G A 7 OK 131 134 135 156 C3' A A 8 OK 154 157 158 178 C3' C A 9 OK 176 179 180 196 C3' DG B 10 OK 194 197 198 218 C3' DT B 11 OK 216 219 220 238 C3' DC B 12 OK 236 239 240 257 C3' DA B 13 OK 255 258 259 278 C3' DT B 14 OK 276 279 280 298 C3' DC B 15 OK 296 299 300 317 C3' DT B 16 OK 315 318 319 337 C3' DC B 17 OK 335 338 339 356 C3' DC B 18 OK 354 357 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG A 1 OK 5 2 4 25 C4' DG A 2 OK 27 24 26 47 C4' DA A 3 OK 49 46 48 68 C4' DG A 4 OK 70 67 69 90 C4' DA A 5 OK 92 89 91 111 C4' U A 6 OK 113 110 112 131 C4' G A 7 OK 133 130 132 154 C4' A A 8 OK 156 153 155 176 C4' C A 9 OK 178 175 177 194 C4' DG B 10 OK 196 193 195 216 C4' DT B 11 OK 218 215 217 236 C4' DC B 12 OK 238 235 237 255 C4' DA B 13 OK 257 254 256 276 C4' DT B 14 OK 278 275 277 296 C4' DC B 15 OK 298 295 297 315 C4' DT B 16 OK 317 314 316 335 C4' DC B 17 OK 337 334 336 354 C4' DC B 18 OK 356 353 355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG A 1 1 3 24 C5' DG A 2 23 25 46 C5' DA A 3 45 47 67 C5' DG A 4 66 68 89 C5' DA A 5 88 90 110 C5' U A 6 109 111 130 C5' G A 7 129 131 153 C5' A A 8 152 154 175 C5' C A 9 174 176 193 C5' DG B 10 192 194 215 C5' DT B 11 214 216 235 C5' DC B 12 234 236 254 C5' DA B 13 253 255 275 C5' DT B 14 274 276 295 C5' DC B 15 294 296 314 C5' DT B 16 313 315 334 C5' DC B 17 333 335 353 C5' DC B 18 352 354 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DG A 2 distorted distorted 6 21 22 23 42 P DA A 3 distorted distorted 28 43 44 45 63 P DG A 4 distorted distorted 50 64 65 66 85 P DA A 5 distorted distorted 71 86 87 88 106 P U A 6 distorted distorted 93 107 108 109 126 P G A 7 distorted distorted 114 127 128 129 149 P A A 8 distorted distorted 134 150 151 152 171 P C A 9 distorted distorted 157 172 173 174 211 P DT B 11 distorted distorted 197 212 213 214 231 P DC B 12 distorted distorted 219 232 233 234 250 P DA B 13 distorted distorted 239 251 252 253 271 P DT B 14 distorted distorted 258 272 273 274 291 P DC B 15 distorted distorted 279 292 293 294 310 P DT B 16 distorted distorted 299 311 312 313 330 P DC B 17 distorted distorted 318 331 332 333 349 P DC B 18 distorted distorted 338 350 351 352 ---------------------------------------------------------------------------------