ID code: '3O6E' 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' --------------------------------------------------------------------------------- 865 C1' G A 1 beta 860 866 863 888 C1' C A 2 beta 883 889 886 908 C1' G A 3 beta 903 909 906 931 C1' A A 4 beta 926 932 929 953 C1' A A 5 beta 948 954 951 975 C1' U A 6 beta 970 976 973 995 C1' A A 7 beta 990 996 993 1017 C1' U A 8 beta 1012 1018 1015 1037 C1' U A 9 beta 1032 1038 1035 1057 C1' C A 10 beta 1052 1058 1055 1077 C1' G A 11 beta 1072 1078 1075 1100 C1' C A 12 beta 1095 1101 1098 1120 C1' U A 13 beta 1115 1121 1118 1137 C1' OMU A 14 beta 1144 1129 1138 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 863 C2' G A 1 OK 865 861 864 886 C2' C A 2 OK 888 884 887 906 C2' G A 3 OK 908 904 907 929 C2' A A 4 OK 931 927 930 951 C2' A A 5 OK 953 949 952 973 C2' U A 6 OK 975 971 974 993 C2' A A 7 OK 995 991 994 1015 C2' U A 8 OK 1017 1013 1016 1035 C2' U A 9 OK 1037 1033 1036 1055 C2' C A 10 OK 1057 1053 1056 1075 C2' G A 11 OK 1077 1073 1076 1098 C2' C A 12 OK 1100 1096 1099 1118 C2' U A 13 OK 1120 1116 1119 1138 C2' OMU A 14 OK 1137 1141 1139 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 861 C3' G A 1 OK 859 862 863 884 C3' C A 2 OK 882 885 886 904 C3' G A 3 OK 902 905 906 927 C3' A A 4 OK 925 928 929 949 C3' A A 5 OK 947 950 951 971 C3' U A 6 OK 969 972 973 991 C3' A A 7 OK 989 992 993 1013 C3' U A 8 OK 1011 1014 1015 1033 C3' U A 9 OK 1031 1034 1035 1053 C3' C A 10 OK 1051 1054 1055 1073 C3' G A 11 OK 1071 1074 1075 1096 C3' C A 12 OK 1094 1097 1098 1116 C3' U A 13 OK 1114 1117 1118 1141 C3' OMU A 14 OK 1142 1143 1138 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 859 C4' G A 1 OK 861 858 860 882 C4' C A 2 OK 884 881 883 902 C4' G A 3 OK 904 901 903 925 C4' A A 4 OK 927 924 926 947 C4' A A 5 OK 949 946 948 969 C4' U A 6 OK 971 968 970 989 C4' A A 7 OK 991 988 990 1011 C4' U A 8 OK 1013 1010 1012 1031 C4' U A 9 OK 1033 1030 1032 1051 C4' C A 10 OK 1053 1050 1052 1071 C4' G A 11 OK 1073 1070 1072 1094 C4' C A 12 OK 1096 1093 1095 1114 C4' U A 13 OK 1116 1113 1115 1142 C4' OMU A 14 OK 1141 1145 1144 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 858 C5' G A 1 857 859 881 C5' C A 2 880 882 901 C5' G A 3 900 902 924 C5' A A 4 923 925 946 C5' A A 5 945 947 968 C5' U A 6 967 969 988 C5' A A 7 987 989 1010 C5' U A 8 1009 1011 1030 C5' U A 9 1029 1031 1050 C5' C A 10 1049 1051 1070 C5' G A 11 1069 1071 1093 C5' C A 12 1092 1094 1113 C5' U A 13 1112 1114 1145 C5' OMU A 14 1146 1142 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 877 P C A 2 distorted distorted 862 878 879 880 897 P G A 3 distorted distorted 885 898 899 900 920 P A A 4 distorted distorted 905 921 922 923 942 P A A 5 distorted distorted 928 943 944 945 964 P U A 6 distorted distorted 950 965 966 967 984 P A A 7 distorted distorted 972 985 986 987 1006 P U A 8 distorted distorted 992 1007 1008 1009 1026 P U A 9 distorted distorted 1014 1027 1028 1029 1046 P C A 10 distorted distorted 1034 1047 1048 1049 1066 P G A 11 distorted distorted 1054 1067 1068 1069 1089 P C A 12 distorted distorted 1074 1090 1091 1092 1109 P U A 13 distorted distorted 1097 1110 1111 1112 1147 P OMU A 14 distorted distorted 1117 1148 1149 1146 ---------------------------------------------------------------------------------