ID code: '2BOP' 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' --------------------------------------------------------------------------------- 828 C1' C B 2 beta 824 829 827 847 C1' G B 3 beta 843 848 846 869 C1' A B 4 beta 865 870 868 890 C1' C B 5 beta 886 891 889 909 C1' C B 6 beta 905 910 908 928 C1' G B 7 beta 924 929 927 950 C1' A B 8 beta 946 951 949 971 C1' C B 9 beta 967 972 970 990 C1' G B 10 beta 986 991 989 1012 C1' T B 11 beta 1008 1013 1011 1032 C1' C B 12 beta 1028 1033 1031 1051 C1' G B 13 beta 1047 1052 1050 1073 C1' G B 14 beta 1069 1074 1072 1095 C1' T B 15 beta 1091 1096 1094 1115 C1' C B 16 beta 1111 1116 1114 1134 C1' G B 17 beta 1130 1135 1133 828 C1' C B 2 beta 824 829 827 847 C1' G B 3 beta 843 848 846 869 C1' A B 4 beta 865 870 868 890 C1' C B 5 beta 886 891 889 909 C1' C B 6 beta 905 910 908 928 C1' G B 7 beta 924 929 927 950 C1' A B 8 beta 946 951 949 971 C1' C B 9 beta 967 972 970 990 C1' G B 10 beta 986 991 989 1012 C1' T B 11 beta 1008 1013 1011 1032 C1' C B 12 beta 1028 1033 1031 1051 C1' G B 13 beta 1047 1052 1050 1073 C1' G B 14 beta 1069 1074 1072 1095 C1' T B 15 beta 1091 1096 1094 1115 C1' C B 16 beta 1111 1116 1114 1134 C1' G B 17 beta 1130 1135 1133 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 827 C2' C B 2 828 825 846 C2' G B 3 847 844 868 C2' A B 4 869 866 889 C2' C B 5 890 887 908 C2' C B 6 909 906 927 C2' G B 7 928 925 949 C2' A B 8 950 947 970 C2' C B 9 971 968 989 C2' G B 10 990 987 1011 C2' T B 11 1012 1009 1031 C2' C B 12 1032 1029 1050 C2' G B 13 1051 1048 1072 C2' G B 14 1073 1070 1094 C2' T B 15 1095 1092 1114 C2' C B 16 1115 1112 1133 C2' G B 17 1134 1131 827 C2' C B 2 828 825 846 C2' G B 3 847 844 868 C2' A B 4 869 866 889 C2' C B 5 890 887 908 C2' C B 6 909 906 927 C2' G B 7 928 925 949 C2' A B 8 950 947 970 C2' C B 9 971 968 989 C2' G B 10 990 987 1011 C2' T B 11 1012 1009 1031 C2' C B 12 1032 1029 1050 C2' G B 13 1051 1048 1072 C2' G B 14 1073 1070 1094 C2' T B 15 1095 1092 1114 C2' C B 16 1115 1112 1133 C2' G B 17 1134 1131 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 825 C3' C B 2 OK 823 826 827 844 C3' G B 3 OK 842 845 846 866 C3' A B 4 OK 864 867 868 887 C3' C B 5 OK 885 888 889 906 C3' C B 6 OK 904 907 908 925 C3' G B 7 OK 923 926 927 947 C3' A B 8 OK 945 948 949 968 C3' C B 9 OK 966 969 970 987 C3' G B 10 OK 985 988 989 1009 C3' T B 11 OK 1007 1010 1011 1029 C3' C B 12 OK 1027 1030 1031 1048 C3' G B 13 OK 1046 1049 1050 1070 C3' G B 14 OK 1068 1071 1072 1092 C3' T B 15 OK 1090 1093 1094 1112 C3' C B 16 OK 1110 1113 1114 1131 C3' G B 17 OK 1129 1132 1133 825 C3' C B 2 OK 823 826 827 844 C3' G B 3 OK 842 845 846 866 C3' A B 4 OK 864 867 868 887 C3' C B 5 OK 885 888 889 906 C3' C B 6 OK 904 907 908 925 C3' G B 7 OK 923 926 927 947 C3' A B 8 OK 945 948 949 968 C3' C B 9 OK 966 969 970 987 C3' G B 10 OK 985 988 989 1009 C3' T B 11 OK 1007 1010 1011 1029 C3' C B 12 OK 1027 1030 1031 1048 C3' G B 13 OK 1046 1049 1050 1070 C3' G B 14 OK 1068 1071 1072 1092 C3' T B 15 OK 1090 1093 1094 1112 C3' C B 16 OK 1110 1113 1114 1131 C3' G B 17 OK 1129 1132 1133 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 823 C4' C B 2 OK 825 822 824 842 C4' G B 3 OK 844 841 843 864 C4' A B 4 OK 866 863 865 885 C4' C B 5 OK 887 884 886 904 C4' C B 6 OK 906 903 905 923 C4' G B 7 OK 925 922 924 945 C4' A B 8 OK 947 944 946 966 C4' C B 9 OK 968 965 967 985 C4' G B 10 OK 987 984 986 1007 C4' T B 11 OK 1009 1006 1008 1027 C4' C B 12 OK 1029 1026 1028 1046 C4' G B 13 OK 1048 1045 1047 1068 C4' G B 14 OK 1070 1067 1069 1090 C4' T B 15 OK 1092 1089 1091 1110 C4' C B 16 OK 1112 1109 1111 1129 C4' G B 17 OK 1131 1128 1130 823 C4' C B 2 OK 825 822 824 842 C4' G B 3 OK 844 841 843 864 C4' A B 4 OK 866 863 865 885 C4' C B 5 OK 887 884 886 904 C4' C B 6 OK 906 903 905 923 C4' G B 7 OK 925 922 924 945 C4' A B 8 OK 947 944 946 966 C4' C B 9 OK 968 965 967 985 C4' G B 10 OK 987 984 986 1007 C4' T B 11 OK 1009 1006 1008 1027 C4' C B 12 OK 1029 1026 1028 1046 C4' G B 13 OK 1048 1045 1047 1068 C4' G B 14 OK 1070 1067 1069 1090 C4' T B 15 OK 1092 1089 1091 1110 C4' C B 16 OK 1112 1109 1111 1129 C4' G B 17 OK 1131 1128 1130 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 822 C5' C B 2 821 823 841 C5' G B 3 840 842 863 C5' A B 4 862 864 884 C5' C B 5 883 885 903 C5' C B 6 902 904 922 C5' G B 7 921 923 944 C5' A B 8 943 945 965 C5' C B 9 964 966 984 C5' G B 10 983 985 1006 C5' T B 11 1005 1007 1026 C5' C B 12 1025 1027 1045 C5' G B 13 1044 1046 1067 C5' G B 14 1066 1068 1089 C5' T B 15 1088 1090 1109 C5' C B 16 1108 1110 1128 C5' G B 17 1127 1129 822 C5' C B 2 821 823 841 C5' G B 3 840 842 863 C5' A B 4 862 864 884 C5' C B 5 883 885 903 C5' C B 6 902 904 922 C5' G B 7 921 923 944 C5' A B 8 943 945 965 C5' C B 9 964 966 984 C5' G B 10 983 985 1006 C5' T B 11 1005 1007 1026 C5' C B 12 1025 1027 1045 C5' G B 13 1044 1046 1067 C5' G B 14 1066 1068 1089 C5' T B 15 1088 1090 1109 C5' C B 16 1108 1110 1128 C5' G B 17 1127 1129 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 837 P G B 3 OK OK 826 838 839 840 859 P A B 4 OK OK 845 860 861 862 880 P C B 5 OK OK 867 881 882 883 899 P C B 6 OK OK 888 900 901 902 918 P G B 7 OK OK 907 919 920 921 940 P A B 8 OK OK 926 941 942 943 961 P C B 9 distorted distorted 948 962 963 964 980 P G B 10 OK OK 969 981 982 983 1002 P T B 11 OK OK 988 1003 1004 1005 1022 P C B 12 OK OK 1010 1023 1024 1025 1041 P G B 13 OK OK 1030 1042 1043 1044 1063 P G B 14 OK OK 1049 1064 1065 1066 1085 P T B 15 OK OK 1071 1086 1087 1088 1105 P C B 16 OK OK 1093 1106 1107 1108 1124 P G B 17 OK OK 1113 1125 1126 1127 837 P G B 3 OK OK 826 838 839 840 859 P A B 4 OK OK 845 860 861 862 880 P C B 5 OK OK 867 881 882 883 899 P C B 6 OK OK 888 900 901 902 918 P G B 7 OK OK 907 919 920 921 940 P A B 8 OK OK 926 941 942 943 961 P C B 9 distorted distorted 948 962 963 964 980 P G B 10 OK OK 969 981 982 983 1002 P T B 11 OK OK 988 1003 1004 1005 1022 P C B 12 OK OK 1010 1023 1024 1025 1041 P G B 13 OK OK 1030 1042 1043 1044 1063 P G B 14 OK OK 1049 1064 1065 1066 1085 P T B 15 OK OK 1071 1086 1087 1088 1105 P C B 16 OK OK 1093 1106 1107 1108 1124 P G B 17 OK OK 1113 1125 1126 1127 ---------------------------------------------------------------------------------