ID code: '2L41' 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' --------------------------------------------------------------------------------- 1260 C1' U B 78 alpha beta 1255 1275 1261 1258 1290 C1' C B 79 alpha beta 1285 1305 1291 1288 1321 C1' U B 80 alpha beta 1316 1336 1322 1319 1351 C1' U B 81 alpha beta 1346 1366 1352 1349 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1258 C2' U B 78 OK OK 1260 1256 1273 1259 1288 C2' C B 79 OK OK 1290 1286 1303 1289 1319 C2' U B 80 OK OK 1321 1317 1334 1320 1349 C2' U B 81 OK OK 1351 1347 1364 1350 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1256 C3' U B 78 OK OK 1254 1272 1257 1258 1286 C3' C B 79 OK OK 1284 1302 1287 1288 1317 C3' U B 80 OK OK 1315 1333 1318 1319 1347 C3' U B 81 OK OK 1345 1363 1348 1349 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1254 C4' U B 78 OK OK 1256 1271 1253 1255 1284 C4' C B 79 OK OK 1286 1301 1283 1285 1315 C4' U B 80 OK OK 1317 1332 1314 1316 1345 C4' U B 81 OK OK 1347 1362 1344 1346 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1253 C5' U B 78 OK OK 1252 1269 1270 1254 1283 C5' C B 79 OK OK 1282 1299 1300 1284 1314 C5' U B 80 OK OK 1313 1330 1331 1315 1344 C5' U B 81 OK OK 1343 1360 1361 1345 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1249 P U B 78 distorted distorted 1250 1251 1252 1279 P C B 79 distorted distorted 1257 1280 1281 1282 1310 P U B 80 distorted distorted 1287 1311 1312 1313 1340 P U B 81 distorted distorted 1318 1341 1342 1343 ---------------------------------------------------------------------------------