ID code: '1A1G' 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' --------------------------------------------------------------------------------- 728 C1' G B 2 beta 724 729 727 750 C1' C B 3 beta 746 751 749 769 C1' G B 4 beta 765 770 768 791 C1' T B 5 beta 787 792 790 811 C1' G B 6 beta 807 812 810 833 C1' G B 7 beta 829 834 832 855 C1' G B 8 beta 851 856 854 877 C1' C B 9 beta 873 878 876 896 C1' G B 10 beta 892 897 895 918 C1' T B 11 beta 914 919 917 956 C1' A C 52 beta 952 957 955 977 C1' C C 53 beta 973 978 976 996 C1' G C 54 beta 992 997 995 1018 C1' C C 55 beta 1014 1019 1017 1037 C1' C C 56 beta 1033 1038 1036 1056 C1' C C 57 beta 1052 1057 1055 1075 C1' A C 58 beta 1071 1076 1074 1096 C1' C C 59 beta 1092 1097 1095 1115 C1' G C 60 beta 1111 1116 1114 1137 C1' C C 61 beta 1133 1138 1136 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 727 C2' G B 2 728 725 749 C2' C B 3 750 747 768 C2' G B 4 769 766 790 C2' T B 5 791 788 810 C2' G B 6 811 808 832 C2' G B 7 833 830 854 C2' G B 8 855 852 876 C2' C B 9 877 874 895 C2' G B 10 896 893 917 C2' T B 11 918 915 955 C2' A C 52 956 953 976 C2' C C 53 977 974 995 C2' G C 54 996 993 1017 C2' C C 55 1018 1015 1036 C2' C C 56 1037 1034 1055 C2' C C 57 1056 1053 1074 C2' A C 58 1075 1072 1095 C2' C C 59 1096 1093 1114 C2' G C 60 1115 1112 1136 C2' C C 61 1137 1134 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 725 C3' G B 2 OK 723 726 727 747 C3' C B 3 OK 745 748 749 766 C3' G B 4 OK 764 767 768 788 C3' T B 5 OK 786 789 790 808 C3' G B 6 OK 806 809 810 830 C3' G B 7 OK 828 831 832 852 C3' G B 8 OK 850 853 854 874 C3' C B 9 OK 872 875 876 893 C3' G B 10 OK 891 894 895 915 C3' T B 11 OK 913 916 917 953 C3' A C 52 OK 951 954 955 974 C3' C C 53 OK 972 975 976 993 C3' G C 54 OK 991 994 995 1015 C3' C C 55 OK 1013 1016 1017 1034 C3' C C 56 OK 1032 1035 1036 1053 C3' C C 57 OK 1051 1054 1055 1072 C3' A C 58 OK 1070 1073 1074 1093 C3' C C 59 OK 1091 1094 1095 1112 C3' G C 60 OK 1110 1113 1114 1134 C3' C C 61 OK 1132 1135 1136 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 723 C4' G B 2 OK 725 722 724 745 C4' C B 3 OK 747 744 746 764 C4' G B 4 OK 766 763 765 786 C4' T B 5 OK 788 785 787 806 C4' G B 6 OK 808 805 807 828 C4' G B 7 OK 830 827 829 850 C4' G B 8 OK 852 849 851 872 C4' C B 9 OK 874 871 873 891 C4' G B 10 OK 893 890 892 913 C4' T B 11 OK 915 912 914 951 C4' A C 52 OK 953 950 952 972 C4' C C 53 OK 974 971 973 991 C4' G C 54 OK 993 990 992 1013 C4' C C 55 OK 1015 1012 1014 1032 C4' C C 56 OK 1034 1031 1033 1051 C4' C C 57 OK 1053 1050 1052 1070 C4' A C 58 OK 1072 1069 1071 1091 C4' C C 59 OK 1093 1090 1092 1110 C4' G C 60 OK 1112 1109 1111 1132 C4' C C 61 OK 1134 1131 1133 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 722 C5' G B 2 721 723 744 C5' C B 3 743 745 763 C5' G B 4 762 764 785 C5' T B 5 784 786 805 C5' G B 6 804 806 827 C5' G B 7 826 828 849 C5' G B 8 848 850 871 C5' C B 9 870 872 890 C5' G B 10 889 891 912 C5' T B 11 911 913 950 C5' A C 52 949 951 971 C5' C C 53 970 972 990 C5' G C 54 989 991 1012 C5' C C 55 1011 1013 1031 C5' C C 56 1030 1032 1050 C5' C C 57 1049 1051 1069 C5' A C 58 1068 1070 1090 C5' C C 59 1089 1091 1109 C5' G C 60 1108 1110 1131 C5' C C 61 1130 1132 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 740 P C B 3 OK OK 726 741 742 743 759 P G B 4 OK OK 748 760 761 762 781 P T B 5 OK OK 767 782 783 784 801 P G B 6 distorted distorted 789 802 803 804 823 P G B 7 OK OK 809 824 825 826 845 P G B 8 OK OK 831 846 847 848 867 P C B 9 OK OK 853 868 869 870 886 P G B 10 OK OK 875 887 888 889 908 P T B 11 OK OK 894 909 910 911 967 P C C 53 OK OK 954 968 969 970 986 P G C 54 OK OK 975 987 988 989 1008 P C C 55 OK OK 994 1009 1010 1011 1027 P C C 56 OK OK 1016 1028 1029 1030 1046 P C C 57 OK OK 1035 1047 1048 1049 1065 P A C 58 OK OK 1054 1066 1067 1068 1086 P C C 59 OK OK 1073 1087 1088 1089 1105 P G C 60 OK OK 1094 1106 1107 1108 1127 P C C 61 OK OK 1113 1128 1129 1130 ---------------------------------------------------------------------------------