ID code: '3PF4' 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' --------------------------------------------------------------------------------- 1140 C1' U R 3 beta 1135 1141 1138 1160 C1' U R 4 beta 1155 1161 1158 1180 C1' U R 5 beta 1175 1181 1178 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1138 C2' U R 3 OK 1140 1136 1139 1158 C2' U R 4 OK 1160 1156 1159 1178 C2' U R 5 OK 1180 1176 1179 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1136 C3' U R 3 OK 1134 1137 1138 1156 C3' U R 4 OK 1154 1157 1158 1176 C3' U R 5 OK 1174 1177 1178 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1134 C4' U R 3 1136 1135 1154 C4' U R 4 OK 1156 1153 1155 1174 C4' U R 5 OK 1176 1173 1175 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1153 C5' U R 4 1152 1154 1173 C5' U R 5 1172 1174 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1087 P C R 2 1124 P U R 3 1125 P U R 3 1149 P U R 4 distorted distorted 1137 1150 1151 1152 1169 P U R 5 distorted distorted 1157 1170 1171 1172 ---------------------------------------------------------------------------------