ID code: '1A1J' 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' --------------------------------------------------------------------------------- 745 C1' G B 2 beta 741 746 744 767 C1' C B 3 beta 763 768 766 786 C1' G B 4 beta 782 787 785 808 C1' T B 5 beta 804 809 807 828 C1' G B 6 beta 824 829 827 850 C1' G B 7 beta 846 851 849 872 C1' G B 8 beta 868 873 871 894 C1' C B 9 beta 890 895 893 913 C1' G B 10 beta 909 914 912 935 C1' T B 11 beta 931 936 934 972 C1' A C 52 beta 968 973 971 993 C1' C C 53 beta 989 994 992 1012 C1' G C 54 beta 1008 1013 1011 1034 C1' C C 55 beta 1030 1035 1033 1053 C1' C C 56 beta 1049 1054 1052 1072 C1' C C 57 beta 1068 1073 1071 1091 C1' A C 58 beta 1087 1092 1090 1112 C1' C C 59 beta 1108 1113 1111 1131 C1' G C 60 beta 1127 1132 1130 1153 C1' C C 61 beta 1149 1154 1152 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 744 C2' G B 2 745 742 766 C2' C B 3 767 764 785 C2' G B 4 786 783 807 C2' T B 5 808 805 827 C2' G B 6 828 825 849 C2' G B 7 850 847 871 C2' G B 8 872 869 893 C2' C B 9 894 891 912 C2' G B 10 913 910 934 C2' T B 11 935 932 971 C2' A C 52 972 969 992 C2' C C 53 993 990 1011 C2' G C 54 1012 1009 1033 C2' C C 55 1034 1031 1052 C2' C C 56 1053 1050 1071 C2' C C 57 1072 1069 1090 C2' A C 58 1091 1088 1111 C2' C C 59 1112 1109 1130 C2' G C 60 1131 1128 1152 C2' C C 61 1153 1150 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 742 C3' G B 2 OK 740 743 744 764 C3' C B 3 OK 762 765 766 783 C3' G B 4 OK 781 784 785 805 C3' T B 5 OK 803 806 807 825 C3' G B 6 OK 823 826 827 847 C3' G B 7 OK 845 848 849 869 C3' G B 8 OK 867 870 871 891 C3' C B 9 OK 889 892 893 910 C3' G B 10 OK 908 911 912 932 C3' T B 11 OK 930 933 934 969 C3' A C 52 OK 967 970 971 990 C3' C C 53 OK 988 991 992 1009 C3' G C 54 OK 1007 1010 1011 1031 C3' C C 55 OK 1029 1032 1033 1050 C3' C C 56 OK 1048 1051 1052 1069 C3' C C 57 OK 1067 1070 1071 1088 C3' A C 58 OK 1086 1089 1090 1109 C3' C C 59 OK 1107 1110 1111 1128 C3' G C 60 OK 1126 1129 1130 1150 C3' C C 61 OK 1148 1151 1152 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 740 C4' G B 2 OK 742 739 741 762 C4' C B 3 OK 764 761 763 781 C4' G B 4 OK 783 780 782 803 C4' T B 5 OK 805 802 804 823 C4' G B 6 OK 825 822 824 845 C4' G B 7 OK 847 844 846 867 C4' G B 8 OK 869 866 868 889 C4' C B 9 OK 891 888 890 908 C4' G B 10 OK 910 907 909 930 C4' T B 11 OK 932 929 931 967 C4' A C 52 OK 969 966 968 988 C4' C C 53 OK 990 987 989 1007 C4' G C 54 OK 1009 1006 1008 1029 C4' C C 55 OK 1031 1028 1030 1048 C4' C C 56 OK 1050 1047 1049 1067 C4' C C 57 OK 1069 1066 1068 1086 C4' A C 58 OK 1088 1085 1087 1107 C4' C C 59 OK 1109 1106 1108 1126 C4' G C 60 OK 1128 1125 1127 1148 C4' C C 61 OK 1150 1147 1149 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 739 C5' G B 2 738 740 761 C5' C B 3 760 762 780 C5' G B 4 779 781 802 C5' T B 5 801 803 822 C5' G B 6 821 823 844 C5' G B 7 843 845 866 C5' G B 8 865 867 888 C5' C B 9 887 889 907 C5' G B 10 906 908 929 C5' T B 11 928 930 966 C5' A C 52 965 967 987 C5' C C 53 986 988 1006 C5' G C 54 1005 1007 1028 C5' C C 55 1027 1029 1047 C5' C C 56 1046 1048 1066 C5' C C 57 1065 1067 1085 C5' A C 58 1084 1086 1106 C5' C C 59 1105 1107 1125 C5' G C 60 1124 1126 1147 C5' C C 61 1146 1148 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 757 P C B 3 OK OK 743 758 759 760 776 P G B 4 OK OK 765 777 778 779 798 P T B 5 OK OK 784 799 800 801 818 P G B 6 distorted distorted 806 819 820 821 840 P G B 7 OK OK 826 841 842 843 862 P G B 8 OK OK 848 863 864 865 884 P C B 9 OK OK 870 885 886 887 903 P G B 10 OK OK 892 904 905 906 925 P T B 11 OK OK 911 926 927 928 983 P C C 53 OK OK 970 984 985 986 1002 P G C 54 OK OK 991 1003 1004 1005 1024 P C C 55 OK OK 1010 1025 1026 1027 1043 P C C 56 OK OK 1032 1044 1045 1046 1062 P C C 57 OK OK 1051 1063 1064 1065 1081 P A C 58 OK OK 1070 1082 1083 1084 1102 P C C 59 OK OK 1089 1103 1104 1105 1121 P G C 60 OK OK 1110 1122 1123 1124 1143 P C C 61 OK OK 1129 1144 1145 1146 ---------------------------------------------------------------------------------