ID code: '2XEA' 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' --------------------------------------------------------------------------------- 1225 C1' G R 4 beta 1220 1226 1223 1248 C1' A R 5 beta 1243 1249 1246 1270 C1' A R 6 beta 1265 1271 1268 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1223 C2' G R 4 OK 1225 1221 1224 1246 C2' A R 5 OK 1248 1244 1247 1268 C2' A R 6 OK 1270 1266 1269 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1221 C3' G R 4 OK 1219 1222 1223 1244 C3' A R 5 OK 1242 1245 1246 1266 C3' A R 6 OK 1264 1267 1268 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1219 C4' G R 4 OK 1221 1218 1220 1242 C4' A R 5 OK 1244 1241 1243 1264 C4' A R 6 OK 1266 1263 1265 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1218 C5' G R 4 1217 1219 1241 C5' A R 5 1240 1242 1263 C5' A R 6 1262 1264 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1214 P G R 4 OK OK 1215 1216 1217 1237 P A R 5 distorted distorted 1222 1238 1239 1240 1259 P A R 6 distorted distorted 1245 1260 1261 1262 ---------------------------------------------------------------------------------