ID code: '3PF5' 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' --------------------------------------------------------------------------------- 1069 C1' U R 1 beta 1064 1070 1067 1091 C1' U R 2 beta 1084 1092 1089 1117 C1' U R 3 beta 1112 1118 1115 1137 C1' U R 4 beta 1132 1138 1135 1157 C1' U R 5 beta 1152 1158 1155 1175 C1' U S 1 beta 1170 1176 1173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1067 C2' U R 1 OK 1069 1065 1068 1089 C2' U R 2 1091 1090 1115 C2' U R 3 OK 1117 1113 1116 1135 C2' U R 4 OK 1137 1133 1136 1155 C2' U R 5 OK 1157 1153 1156 1173 C2' U S 1 OK 1175 1171 1174 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1065 C3' U R 1 OK 1063 1066 1067 1113 C3' U R 3 1114 1115 1133 C3' U R 4 OK 1131 1134 1135 1153 C3' U R 5 OK 1151 1154 1155 1171 C3' U S 1 OK 1169 1172 1173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1063 C4' U R 1 OK 1065 1062 1064 1083 C4' U R 2 1082 1084 1131 C4' U R 4 OK 1133 1130 1132 1151 C4' U R 5 OK 1153 1150 1152 1169 C4' U S 1 OK 1171 1168 1170 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1062 C5' U R 1 1061 1063 1082 C5' U R 2 1081 1083 1130 C5' U R 4 1129 1131 1150 C5' U R 5 1149 1151 1168 C5' U S 1 1167 1169 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1058 P U R 1 OK OK 1059 1060 1061 1078 P U R 2 distorted distorted 1066 1079 1080 1081 1100 P U R 3 1101 P U R 3 1126 P U R 4 distorted distorted 1114 1127 1128 1129 1146 P U R 5 distorted distorted 1134 1147 1148 1149 ---------------------------------------------------------------------------------