ID code: '1A1F' 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' --------------------------------------------------------------------------------- 731 C1' G B 2 beta 727 732 730 753 C1' C B 3 beta 749 754 752 772 C1' G B 4 beta 768 773 771 794 C1' T B 5 beta 790 795 793 814 C1' G B 6 beta 810 815 813 836 C1' G B 7 beta 832 837 835 858 C1' G B 8 beta 854 859 857 880 C1' A B 9 beta 876 881 879 901 C1' C B 10 beta 897 902 900 920 C1' C B 11 beta 916 921 919 957 C1' G C 52 beta 953 958 956 979 C1' G C 53 beta 975 980 978 1001 C1' T C 54 beta 997 1002 1000 1021 C1' C C 55 beta 1017 1022 1020 1040 C1' C C 56 beta 1036 1041 1039 1059 C1' C C 57 beta 1055 1060 1058 1078 C1' A C 58 beta 1074 1079 1077 1099 C1' C C 59 beta 1095 1100 1098 1118 C1' G C 60 beta 1114 1119 1117 1140 C1' C C 61 beta 1136 1141 1139 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 730 C2' G B 2 731 728 752 C2' C B 3 753 750 771 C2' G B 4 772 769 793 C2' T B 5 794 791 813 C2' G B 6 814 811 835 C2' G B 7 836 833 857 C2' G B 8 858 855 879 C2' A B 9 880 877 900 C2' C B 10 901 898 919 C2' C B 11 920 917 956 C2' G C 52 957 954 978 C2' G C 53 979 976 1000 C2' T C 54 1001 998 1020 C2' C C 55 1021 1018 1039 C2' C C 56 1040 1037 1058 C2' C C 57 1059 1056 1077 C2' A C 58 1078 1075 1098 C2' C C 59 1099 1096 1117 C2' G C 60 1118 1115 1139 C2' C C 61 1140 1137 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 728 C3' G B 2 OK 726 729 730 750 C3' C B 3 OK 748 751 752 769 C3' G B 4 OK 767 770 771 791 C3' T B 5 OK 789 792 793 811 C3' G B 6 OK 809 812 813 833 C3' G B 7 OK 831 834 835 855 C3' G B 8 OK 853 856 857 877 C3' A B 9 OK 875 878 879 898 C3' C B 10 OK 896 899 900 917 C3' C B 11 OK 915 918 919 954 C3' G C 52 OK 952 955 956 976 C3' G C 53 OK 974 977 978 998 C3' T C 54 OK 996 999 1000 1018 C3' C C 55 OK 1016 1019 1020 1037 C3' C C 56 OK 1035 1038 1039 1056 C3' C C 57 OK 1054 1057 1058 1075 C3' A C 58 OK 1073 1076 1077 1096 C3' C C 59 OK 1094 1097 1098 1115 C3' G C 60 OK 1113 1116 1117 1137 C3' C C 61 OK 1135 1138 1139 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 726 C4' G B 2 OK 728 725 727 748 C4' C B 3 OK 750 747 749 767 C4' G B 4 OK 769 766 768 789 C4' T B 5 OK 791 788 790 809 C4' G B 6 OK 811 808 810 831 C4' G B 7 OK 833 830 832 853 C4' G B 8 OK 855 852 854 875 C4' A B 9 OK 877 874 876 896 C4' C B 10 OK 898 895 897 915 C4' C B 11 OK 917 914 916 952 C4' G C 52 OK 954 951 953 974 C4' G C 53 OK 976 973 975 996 C4' T C 54 OK 998 995 997 1016 C4' C C 55 OK 1018 1015 1017 1035 C4' C C 56 OK 1037 1034 1036 1054 C4' C C 57 OK 1056 1053 1055 1073 C4' A C 58 OK 1075 1072 1074 1094 C4' C C 59 OK 1096 1093 1095 1113 C4' G C 60 OK 1115 1112 1114 1135 C4' C C 61 OK 1137 1134 1136 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 725 C5' G B 2 724 726 747 C5' C B 3 746 748 766 C5' G B 4 765 767 788 C5' T B 5 787 789 808 C5' G B 6 807 809 830 C5' G B 7 829 831 852 C5' G B 8 851 853 874 C5' A B 9 873 875 895 C5' C B 10 894 896 914 C5' C B 11 913 915 951 C5' G C 52 950 952 973 C5' G C 53 972 974 995 C5' T C 54 994 996 1015 C5' C C 55 1014 1016 1034 C5' C C 56 1033 1035 1053 C5' C C 57 1052 1054 1072 C5' A C 58 1071 1073 1093 C5' C C 59 1092 1094 1112 C5' G C 60 1111 1113 1134 C5' C C 61 1133 1135 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 743 P C B 3 OK OK 729 744 745 746 762 P G B 4 OK OK 751 763 764 765 784 P T B 5 OK OK 770 785 786 787 804 P G B 6 distorted distorted 792 805 806 807 826 P G B 7 OK OK 812 827 828 829 848 P G B 8 OK OK 834 849 850 851 870 P A B 9 OK OK 856 871 872 873 891 P C B 10 OK OK 878 892 893 894 910 P C B 11 OK OK 899 911 912 913 969 P G C 53 OK OK 955 970 971 972 991 P T C 54 OK OK 977 992 993 994 1011 P C C 55 OK OK 999 1012 1013 1014 1030 P C C 56 OK OK 1019 1031 1032 1033 1049 P C C 57 OK OK 1038 1050 1051 1052 1068 P A C 58 OK OK 1057 1069 1070 1071 1089 P C C 59 OK OK 1076 1090 1091 1092 1108 P G C 60 OK OK 1097 1109 1110 1111 1130 P C C 61 OK OK 1116 1131 1132 1133 ---------------------------------------------------------------------------------