ID code: '1DHH' 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 53 C1' A A 3 beta 48 54 51 75 C1' G A 4 beta 70 76 73 98 C1' A A 5 beta 93 99 96 120 C1' U A 6 beta 115 121 118 139 C1' DG A 7 beta 135 140 138 161 C1' DA A 8 beta 157 162 160 182 C1' DC A 9 beta 178 183 181 199 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' A A 3 OK 53 49 52 73 C2' G A 4 OK 75 71 74 96 C2' A A 5 OK 98 94 97 118 C2' U A 6 OK 120 116 119 138 C2' DG A 7 139 136 160 C2' DA A 8 161 158 181 C2' DC A 9 182 179 198 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' A A 3 OK 47 50 51 71 C3' G A 4 OK 69 72 73 94 C3' A A 5 OK 92 95 96 116 C3' U A 6 OK 114 117 118 136 C3' DG A 7 OK 134 137 138 158 C3' DA A 8 OK 156 159 160 179 C3' DC A 9 OK 177 180 181 196 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' A A 3 OK 49 46 48 69 C4' G A 4 OK 71 68 70 92 C4' A A 5 OK 94 91 93 114 C4' U A 6 OK 116 113 115 134 C4' DG A 7 OK 136 133 135 156 C4' DA A 8 OK 158 155 157 177 C4' DC A 9 OK 179 176 178 194 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' A A 3 45 47 68 C5' G A 4 67 69 91 C5' A A 5 90 92 113 C5' U A 6 112 114 133 C5' DG A 7 132 134 155 C5' DA A 8 154 156 176 C5' DC A 9 175 177 193 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 A A 3 distorted distorted 28 43 44 45 64 P G A 4 distorted distorted 50 65 66 67 87 P A A 5 distorted distorted 72 88 89 90 109 P U A 6 distorted distorted 95 110 111 112 129 P DG A 7 distorted distorted 117 130 131 132 151 P DA A 8 distorted distorted 137 152 153 154 172 P DC A 9 distorted distorted 159 173 174 175 211 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 ---------------------------------------------------------------------------------