ID code: '3J06' 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' --------------------------------------------------------------------------------- 1232 C1' A R 4 beta 1227 1233 1230 1254 C1' U R 5 beta 1249 1255 1252 1274 C1' G R 6 beta 1269 1275 1272 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1230 C2' A R 4 OK 1232 1228 1231 1252 C2' U R 5 OK 1254 1250 1253 1272 C2' G R 6 OK 1274 1270 1273 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1228 C3' A R 4 OK 1226 1229 1230 1250 C3' U R 5 OK 1248 1251 1252 1270 C3' G R 6 OK 1268 1271 1272 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1226 C4' A R 4 OK 1228 1225 1227 1248 C4' U R 5 OK 1250 1247 1249 1268 C4' G R 6 OK 1270 1267 1269 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1225 C5' A R 4 1224 1226 1247 C5' U R 5 1246 1248 1267 C5' G R 6 1266 1268 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1221 P A R 4 OK OK 1222 1223 1224 1243 P U R 5 distorted distorted 1229 1244 1245 1246 1263 P G R 6 distorted distorted 1251 1264 1265 1266 ---------------------------------------------------------------------------------