ID code: '4UDV' 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' --------------------------------------------------------------------------------- 1219 C1' G R 4 beta 1214 1220 1217 1242 C1' A R 5 beta 1237 1243 1240 1264 C1' A R 6 beta 1259 1265 1262 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1217 C2' G R 4 OK 1219 1215 1218 1240 C2' A R 5 OK 1242 1238 1241 1262 C2' A R 6 OK 1264 1260 1263 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1215 C3' G R 4 OK 1213 1216 1217 1238 C3' A R 5 OK 1236 1239 1240 1260 C3' A R 6 OK 1258 1261 1262 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1213 C4' G R 4 OK 1215 1212 1214 1236 C4' A R 5 OK 1238 1235 1237 1258 C4' A R 6 OK 1260 1257 1259 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1212 C5' G R 4 1211 1213 1235 C5' A R 5 1234 1236 1257 C5' A R 6 1256 1258 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1208 P G R 4 distorted distorted 1209 1210 1211 1231 P A R 5 distorted distorted 1216 1232 1233 1234 1253 P A R 6 distorted distorted 1239 1254 1255 1256 ---------------------------------------------------------------------------------