ID code: '1A1H' 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' --------------------------------------------------------------------------------- 747 C1' G B 2 beta 743 748 746 769 C1' C B 3 beta 765 770 768 788 C1' G B 4 beta 784 789 787 810 C1' T B 5 beta 806 811 809 830 C1' G B 6 beta 826 831 829 852 C1' G B 7 beta 848 853 851 874 C1' G B 8 beta 870 875 873 896 C1' C B 9 beta 892 897 895 915 C1' A B 10 beta 911 916 914 936 C1' C B 11 beta 932 937 935 973 C1' G C 52 beta 969 974 972 995 C1' T C 53 beta 991 996 994 1015 C1' G C 54 beta 1011 1016 1014 1037 C1' C C 55 beta 1033 1038 1036 1056 C1' C C 56 beta 1052 1057 1055 1075 C1' C C 57 beta 1071 1076 1074 1094 C1' A C 58 beta 1090 1095 1093 1115 C1' C C 59 beta 1111 1116 1114 1134 C1' G C 60 beta 1130 1135 1133 1156 C1' C C 61 beta 1152 1157 1155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 746 C2' G B 2 747 744 768 C2' C B 3 769 766 787 C2' G B 4 788 785 809 C2' T B 5 810 807 829 C2' G B 6 830 827 851 C2' G B 7 852 849 873 C2' G B 8 874 871 895 C2' C B 9 896 893 914 C2' A B 10 915 912 935 C2' C B 11 936 933 972 C2' G C 52 973 970 994 C2' T C 53 995 992 1014 C2' G C 54 1015 1012 1036 C2' C C 55 1037 1034 1055 C2' C C 56 1056 1053 1074 C2' C C 57 1075 1072 1093 C2' A C 58 1094 1091 1114 C2' C C 59 1115 1112 1133 C2' G C 60 1134 1131 1155 C2' C C 61 1156 1153 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 744 C3' G B 2 OK 742 745 746 766 C3' C B 3 OK 764 767 768 785 C3' G B 4 OK 783 786 787 807 C3' T B 5 OK 805 808 809 827 C3' G B 6 OK 825 828 829 849 C3' G B 7 OK 847 850 851 871 C3' G B 8 OK 869 872 873 893 C3' C B 9 OK 891 894 895 912 C3' A B 10 OK 910 913 914 933 C3' C B 11 OK 931 934 935 970 C3' G C 52 OK 968 971 972 992 C3' T C 53 OK 990 993 994 1012 C3' G C 54 OK 1010 1013 1014 1034 C3' C C 55 OK 1032 1035 1036 1053 C3' C C 56 OK 1051 1054 1055 1072 C3' C C 57 OK 1070 1073 1074 1091 C3' A C 58 OK 1089 1092 1093 1112 C3' C C 59 OK 1110 1113 1114 1131 C3' G C 60 OK 1129 1132 1133 1153 C3' C C 61 OK 1151 1154 1155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 742 C4' G B 2 OK 744 741 743 764 C4' C B 3 OK 766 763 765 783 C4' G B 4 OK 785 782 784 805 C4' T B 5 OK 807 804 806 825 C4' G B 6 OK 827 824 826 847 C4' G B 7 OK 849 846 848 869 C4' G B 8 OK 871 868 870 891 C4' C B 9 OK 893 890 892 910 C4' A B 10 OK 912 909 911 931 C4' C B 11 OK 933 930 932 968 C4' G C 52 OK 970 967 969 990 C4' T C 53 OK 992 989 991 1010 C4' G C 54 OK 1012 1009 1011 1032 C4' C C 55 OK 1034 1031 1033 1051 C4' C C 56 OK 1053 1050 1052 1070 C4' C C 57 OK 1072 1069 1071 1089 C4' A C 58 OK 1091 1088 1090 1110 C4' C C 59 OK 1112 1109 1111 1129 C4' G C 60 OK 1131 1128 1130 1151 C4' C C 61 OK 1153 1150 1152 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 741 C5' G B 2 740 742 763 C5' C B 3 762 764 782 C5' G B 4 781 783 804 C5' T B 5 803 805 824 C5' G B 6 823 825 846 C5' G B 7 845 847 868 C5' G B 8 867 869 890 C5' C B 9 889 891 909 C5' A B 10 908 910 930 C5' C B 11 929 931 967 C5' G C 52 966 968 989 C5' T C 53 988 990 1009 C5' G C 54 1008 1010 1031 C5' C C 55 1030 1032 1050 C5' C C 56 1049 1051 1069 C5' C C 57 1068 1070 1088 C5' A C 58 1087 1089 1109 C5' C C 59 1108 1110 1128 C5' G C 60 1127 1129 1150 C5' C C 61 1149 1151 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 759 P C B 3 OK OK 745 760 761 762 778 P G B 4 OK OK 767 779 780 781 800 P T B 5 OK OK 786 801 802 803 820 P G B 6 distorted distorted 808 821 822 823 842 P G B 7 OK OK 828 843 844 845 864 P G B 8 OK OK 850 865 866 867 886 P C B 9 OK OK 872 887 888 889 905 P A B 10 OK OK 894 906 907 908 926 P C B 11 OK OK 913 927 928 929 985 P T C 53 OK OK 971 986 987 988 1005 P G C 54 OK OK 993 1006 1007 1008 1027 P C C 55 OK OK 1013 1028 1029 1030 1046 P C C 56 OK OK 1035 1047 1048 1049 1065 P C C 57 OK OK 1054 1066 1067 1068 1084 P A C 58 OK OK 1073 1085 1086 1087 1105 P C C 59 OK OK 1092 1106 1107 1108 1124 P G C 60 OK OK 1113 1125 1126 1127 1146 P C C 61 OK OK 1132 1147 1148 1149 ---------------------------------------------------------------------------------