ID code: '4WAL' 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' --------------------------------------------------------------------------------- 1008 C1' U B 2 beta 1003 1009 1006 1028 C1' A B 3 beta 1023 1029 1026 1050 C1' C B 4 beta 1045 1051 1048 1070 C1' U B 5 beta 1065 1071 1068 1090 C1' A B 6 beta 1085 1091 1088 1112 C1' A B 7 beta 1107 1113 1110 1134 C1' C B 8 beta 1129 1135 1132 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1006 C2' U B 2 OK 1008 1004 1007 1026 C2' A B 3 OK 1028 1024 1027 1048 C2' C B 4 OK 1050 1046 1049 1068 C2' U B 5 OK 1070 1066 1069 1088 C2' A B 6 OK 1090 1086 1089 1110 C2' A B 7 OK 1112 1108 1111 1132 C2' C B 8 OK 1134 1130 1133 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1004 C3' U B 2 OK 1002 1005 1006 1024 C3' A B 3 OK 1022 1025 1026 1046 C3' C B 4 OK 1044 1047 1048 1066 C3' U B 5 OK 1064 1067 1068 1086 C3' A B 6 OK 1084 1087 1088 1108 C3' A B 7 OK 1106 1109 1110 1130 C3' C B 8 OK 1128 1131 1132 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1002 C4' U B 2 OK 1004 1001 1003 1022 C4' A B 3 OK 1024 1021 1023 1044 C4' C B 4 OK 1046 1043 1045 1064 C4' U B 5 OK 1066 1063 1065 1084 C4' A B 6 OK 1086 1083 1085 1106 C4' A B 7 OK 1108 1105 1107 1128 C4' C B 8 OK 1130 1127 1129 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1001 C5' U B 2 1000 1002 1021 C5' A B 3 1020 1022 1043 C5' C B 4 1042 1044 1063 C5' U B 5 1062 1064 1083 C5' A B 6 1082 1084 1105 C5' A B 7 1104 1106 1127 C5' C B 8 1126 1128 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 997 P U B 2 distorted distorted 996 998 999 1000 1017 P A B 3 distorted distorted 1005 1018 1019 1020 1039 P C B 4 distorted distorted 1025 1040 1041 1042 1059 P U B 5 distorted distorted 1047 1060 1061 1062 1079 P A B 6 distorted distorted 1067 1080 1081 1082 1101 P A B 7 distorted distorted 1087 1102 1103 1104 1123 P C B 8 distorted distorted 1109 1124 1125 1126 1143 P A B 9 distorted distorted 1131 1144 1145 1146 ---------------------------------------------------------------------------------