ID code: '3O7V' 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' --------------------------------------------------------------------------------- 884 C1' G A 1 beta 879 885 882 907 C1' C A 2 beta 902 908 905 927 C1' G A 3 beta 922 928 925 950 C1' A A 4 beta 945 951 948 972 C1' A A 5 beta 967 973 970 994 C1' U A 6 beta 989 995 992 1014 C1' A A 7 beta 1009 1015 1012 1036 C1' U A 8 beta 1031 1037 1034 1056 C1' U A 9 beta 1051 1057 1054 1076 C1' C A 10 beta 1071 1077 1074 1096 C1' G A 11 beta 1091 1097 1094 1119 C1' C A 12 beta 1114 1120 1117 1139 C1' U A 13 beta 1134 1140 1137 1156 C1' OMU A 14 beta 1163 1148 1157 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 882 C2' G A 1 OK 884 880 883 905 C2' C A 2 OK 907 903 906 925 C2' G A 3 OK 927 923 926 948 C2' A A 4 OK 950 946 949 970 C2' A A 5 OK 972 968 971 992 C2' U A 6 OK 994 990 993 1012 C2' A A 7 OK 1014 1010 1013 1034 C2' U A 8 OK 1036 1032 1035 1054 C2' U A 9 OK 1056 1052 1055 1074 C2' C A 10 OK 1076 1072 1075 1094 C2' G A 11 OK 1096 1092 1095 1117 C2' C A 12 OK 1119 1115 1118 1137 C2' U A 13 OK 1139 1135 1138 1157 C2' OMU A 14 OK 1156 1160 1158 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 880 C3' G A 1 OK 878 881 882 903 C3' C A 2 OK 901 904 905 923 C3' G A 3 OK 921 924 925 946 C3' A A 4 OK 944 947 948 968 C3' A A 5 OK 966 969 970 990 C3' U A 6 OK 988 991 992 1010 C3' A A 7 OK 1008 1011 1012 1032 C3' U A 8 OK 1030 1033 1034 1052 C3' U A 9 OK 1050 1053 1054 1072 C3' C A 10 OK 1070 1073 1074 1092 C3' G A 11 OK 1090 1093 1094 1115 C3' C A 12 OK 1113 1116 1117 1135 C3' U A 13 OK 1133 1136 1137 1160 C3' OMU A 14 OK 1161 1162 1157 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 878 C4' G A 1 OK 880 877 879 901 C4' C A 2 OK 903 900 902 921 C4' G A 3 OK 923 920 922 944 C4' A A 4 OK 946 943 945 966 C4' A A 5 OK 968 965 967 988 C4' U A 6 OK 990 987 989 1008 C4' A A 7 OK 1010 1007 1009 1030 C4' U A 8 OK 1032 1029 1031 1050 C4' U A 9 OK 1052 1049 1051 1070 C4' C A 10 OK 1072 1069 1071 1090 C4' G A 11 OK 1092 1089 1091 1113 C4' C A 12 OK 1115 1112 1114 1133 C4' U A 13 OK 1135 1132 1134 1161 C4' OMU A 14 OK 1160 1164 1163 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 877 C5' G A 1 876 878 900 C5' C A 2 899 901 920 C5' G A 3 919 921 943 C5' A A 4 942 944 965 C5' A A 5 964 966 987 C5' U A 6 986 988 1007 C5' A A 7 1006 1008 1029 C5' U A 8 1028 1030 1049 C5' U A 9 1048 1050 1069 C5' C A 10 1068 1070 1089 C5' G A 11 1088 1090 1112 C5' C A 12 1111 1113 1132 C5' U A 13 1131 1133 1164 C5' OMU A 14 1165 1161 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 896 P C A 2 distorted distorted 881 897 898 899 916 P G A 3 distorted distorted 904 917 918 919 939 P A A 4 distorted distorted 924 940 941 942 961 P A A 5 distorted distorted 947 962 963 964 983 P U A 6 distorted distorted 969 984 985 986 1003 P A A 7 distorted distorted 991 1004 1005 1006 1025 P U A 8 distorted distorted 1011 1026 1027 1028 1045 P U A 9 distorted distorted 1033 1046 1047 1048 1065 P C A 10 distorted distorted 1053 1066 1067 1068 1085 P G A 11 distorted distorted 1073 1086 1087 1088 1108 P C A 12 distorted distorted 1093 1109 1110 1111 1128 P U A 13 distorted distorted 1116 1129 1130 1131 1166 P OMU A 14 distorted distorted 1136 1167 1168 1165 ---------------------------------------------------------------------------------