ID code: '1O9M' 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' --------------------------------------------------------------------------------- 12 C1' C A1409 beta 7 13 10 32 C1' A A1410 beta 27 33 30 54 C1' C A1411 beta 49 55 52 74 C1' C A1412 beta 69 75 72 94 C1' G A1488 beta 89 95 92 117 C1' G A1489 beta 112 118 115 140 C1' U A1490 beta 135 141 138 160 C1' G A1491 beta 155 161 158 184 C1' C B1409 beta 179 185 182 204 C1' A B1410 beta 199 205 202 226 C1' C B1411 beta 221 227 224 246 C1' C B1412 beta 241 247 244 266 C1' G B1488 beta 261 267 264 289 C1' G B1489 beta 284 290 287 312 C1' U B1490 beta 307 313 310 332 C1' G B1491 beta 327 333 330 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C A1409 OK 12 8 11 30 C2' A A1410 OK 32 28 31 52 C2' C A1411 OK 54 50 53 72 C2' C A1412 OK 74 70 73 92 C2' G A1488 OK 94 90 93 115 C2' G A1489 OK 117 113 116 138 C2' U A1490 OK 140 136 139 158 C2' G A1491 OK 160 156 159 182 C2' C B1409 OK 184 180 183 202 C2' A B1410 OK 204 200 203 224 C2' C B1411 OK 226 222 225 244 C2' C B1412 OK 246 242 245 264 C2' G B1488 OK 266 262 265 287 C2' G B1489 OK 289 285 288 310 C2' U B1490 OK 312 308 311 330 C2' G B1491 OK 332 328 331 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A1409 OK 6 9 10 28 C3' A A1410 OK 26 29 30 50 C3' C A1411 OK 48 51 52 70 C3' C A1412 OK 68 71 72 90 C3' G A1488 OK 88 91 92 113 C3' G A1489 OK 111 114 115 136 C3' U A1490 OK 134 137 138 156 C3' G A1491 OK 154 157 158 180 C3' C B1409 OK 178 181 182 200 C3' A B1410 OK 198 201 202 222 C3' C B1411 OK 220 223 224 242 C3' C B1412 OK 240 243 244 262 C3' G B1488 OK 260 263 264 285 C3' G B1489 OK 283 286 287 308 C3' U B1490 OK 306 309 310 328 C3' G B1491 OK 326 329 330 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A1409 OK 8 5 7 26 C4' A A1410 OK 28 25 27 48 C4' C A1411 OK 50 47 49 68 C4' C A1412 OK 70 67 69 88 C4' G A1488 OK 90 87 89 111 C4' G A1489 OK 113 110 112 134 C4' U A1490 OK 136 133 135 154 C4' G A1491 OK 156 153 155 178 C4' C B1409 OK 180 177 179 198 C4' A B1410 OK 200 197 199 220 C4' C B1411 OK 222 219 221 240 C4' C B1412 OK 242 239 241 260 C4' G B1488 OK 262 259 261 283 C4' G B1489 OK 285 282 284 306 C4' U B1490 OK 308 305 307 326 C4' G B1491 OK 328 325 327 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A1409 4 6 25 C5' A A1410 24 26 47 C5' C A1411 46 48 67 C5' C A1412 66 68 87 C5' G A1488 86 88 110 C5' G A1489 109 111 133 C5' U A1490 132 134 153 C5' G A1491 152 154 177 C5' C B1409 176 178 197 C5' A B1410 196 198 219 C5' C B1411 218 220 239 C5' C B1412 238 240 259 C5' G B1488 258 260 282 C5' G B1489 281 283 305 C5' U B1490 304 306 325 C5' G B1491 324 326 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A1409 distorted distorted 2 3 4 21 P A A1410 distorted distorted 9 22 23 24 43 P C A1411 distorted distorted 29 44 45 46 63 P C A1412 distorted distorted 51 64 65 66 83 P G A1488 distorted distorted 71 84 85 86 106 P G A1489 distorted distorted 91 107 108 109 129 P U A1490 distorted distorted 114 130 131 132 149 P G A1491 distorted distorted 137 150 151 152 173 P C B1409 distorted distorted 174 175 176 193 P A B1410 distorted distorted 181 194 195 196 215 P C B1411 distorted distorted 201 216 217 218 235 P C B1412 distorted distorted 223 236 237 238 255 P G B1488 distorted distorted 243 256 257 258 278 P G B1489 distorted distorted 263 279 280 281 301 P U B1490 distorted distorted 286 302 303 304 321 P G B1491 distorted distorted 309 322 323 324 ---------------------------------------------------------------------------------