ID code: '1WZH' 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' --------------------------------------------------------------------------------- 651 C1' T D 501 beta 647 652 650 671 C1' T D 502 beta 667 672 670 691 C1' T D 503 beta 687 692 690 711 C1' T D 504 beta 707 712 710 731 C1' C D 505 beta 727 732 730 750 C1' G D 506 beta 746 751 749 772 C1' C D 507 beta 768 773 771 791 C1' G D 508 beta 787 792 790 813 C1' C D 509 beta 809 814 812 832 C1' G D 510 beta 828 833 831 854 C1' G D 511 beta 850 855 853 876 C1' T D 512 beta 872 877 875 896 C1' T D 513 beta 892 897 895 916 C1' T D 514 beta 912 917 915 936 C1' T D 515 beta 932 937 935 957 C1' A E 601 beta 953 958 956 978 C1' A E 602 beta 974 979 977 999 C1' A E 603 beta 995 1000 998 1020 C1' A E 604 beta 1016 1021 1019 1041 C1' C E 605 beta 1037 1042 1040 1060 C1' C E 606 beta 1056 1061 1059 1079 C1' G E 607 beta 1075 1080 1078 1101 C1' C E 608 beta 1097 1102 1100 1120 C1' G E 609 beta 1116 1121 1119 1142 C1' C E 610 beta 1138 1143 1141 1161 C1' G E 611 beta 1157 1162 1160 1183 C1' A E 612 beta 1179 1184 1182 1204 C1' A E 613 beta 1200 1205 1203 1225 C1' A E 614 beta 1221 1226 1224 1246 C1' A E 615 beta 1242 1247 1245 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 650 C2' T D 501 651 648 670 C2' T D 502 671 668 690 C2' T D 503 691 688 710 C2' T D 504 711 708 730 C2' C D 505 731 728 749 C2' G D 506 750 747 771 C2' C D 507 772 769 790 C2' G D 508 791 788 812 C2' C D 509 813 810 831 C2' G D 510 832 829 853 C2' G D 511 854 851 875 C2' T D 512 876 873 895 C2' T D 513 896 893 915 C2' T D 514 916 913 935 C2' T D 515 936 933 956 C2' A E 601 957 954 977 C2' A E 602 978 975 998 C2' A E 603 999 996 1019 C2' A E 604 1020 1017 1040 C2' C E 605 1041 1038 1059 C2' C E 606 1060 1057 1078 C2' G E 607 1079 1076 1100 C2' C E 608 1101 1098 1119 C2' G E 609 1120 1117 1141 C2' C E 610 1142 1139 1160 C2' G E 611 1161 1158 1182 C2' A E 612 1183 1180 1203 C2' A E 613 1204 1201 1224 C2' A E 614 1225 1222 1245 C2' A E 615 1246 1243 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 648 C3' T D 501 OK 646 649 650 668 C3' T D 502 OK 666 669 670 688 C3' T D 503 OK 686 689 690 708 C3' T D 504 OK 706 709 710 728 C3' C D 505 OK 726 729 730 747 C3' G D 506 OK 745 748 749 769 C3' C D 507 OK 767 770 771 788 C3' G D 508 OK 786 789 790 810 C3' C D 509 OK 808 811 812 829 C3' G D 510 OK 827 830 831 851 C3' G D 511 OK 849 852 853 873 C3' T D 512 OK 871 874 875 893 C3' T D 513 OK 891 894 895 913 C3' T D 514 OK 911 914 915 933 C3' T D 515 OK 931 934 935 954 C3' A E 601 OK 952 955 956 975 C3' A E 602 OK 973 976 977 996 C3' A E 603 OK 994 997 998 1017 C3' A E 604 OK 1015 1018 1019 1038 C3' C E 605 OK 1036 1039 1040 1057 C3' C E 606 OK 1055 1058 1059 1076 C3' G E 607 OK 1074 1077 1078 1098 C3' C E 608 OK 1096 1099 1100 1117 C3' G E 609 OK 1115 1118 1119 1139 C3' C E 610 OK 1137 1140 1141 1158 C3' G E 611 OK 1156 1159 1160 1180 C3' A E 612 OK 1178 1181 1182 1201 C3' A E 613 OK 1199 1202 1203 1222 C3' A E 614 OK 1220 1223 1224 1243 C3' A E 615 OK 1241 1244 1245 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 646 C4' T D 501 OK 648 645 647 666 C4' T D 502 OK 668 665 667 686 C4' T D 503 OK 688 685 687 706 C4' T D 504 OK 708 705 707 726 C4' C D 505 OK 728 725 727 745 C4' G D 506 OK 747 744 746 767 C4' C D 507 OK 769 766 768 786 C4' G D 508 OK 788 785 787 808 C4' C D 509 OK 810 807 809 827 C4' G D 510 OK 829 826 828 849 C4' G D 511 OK 851 848 850 871 C4' T D 512 OK 873 870 872 891 C4' T D 513 OK 893 890 892 911 C4' T D 514 OK 913 910 912 931 C4' T D 515 OK 933 930 932 952 C4' A E 601 OK 954 951 953 973 C4' A E 602 OK 975 972 974 994 C4' A E 603 OK 996 993 995 1015 C4' A E 604 OK 1017 1014 1016 1036 C4' C E 605 OK 1038 1035 1037 1055 C4' C E 606 OK 1057 1054 1056 1074 C4' G E 607 OK 1076 1073 1075 1096 C4' C E 608 OK 1098 1095 1097 1115 C4' G E 609 OK 1117 1114 1116 1137 C4' C E 610 OK 1139 1136 1138 1156 C4' G E 611 OK 1158 1155 1157 1178 C4' A E 612 OK 1180 1177 1179 1199 C4' A E 613 OK 1201 1198 1200 1220 C4' A E 614 OK 1222 1219 1221 1241 C4' A E 615 OK 1243 1240 1242 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 645 C5' T D 501 644 646 665 C5' T D 502 664 666 685 C5' T D 503 684 686 705 C5' T D 504 704 706 725 C5' C D 505 724 726 744 C5' G D 506 743 745 766 C5' C D 507 765 767 785 C5' G D 508 784 786 807 C5' C D 509 806 808 826 C5' G D 510 825 827 848 C5' G D 511 847 849 870 C5' T D 512 869 871 890 C5' T D 513 889 891 910 C5' T D 514 909 911 930 C5' T D 515 929 931 951 C5' A E 601 950 952 972 C5' A E 602 971 973 993 C5' A E 603 992 994 1014 C5' A E 604 1013 1015 1035 C5' C E 605 1034 1036 1054 C5' C E 606 1053 1055 1073 C5' G E 607 1072 1074 1095 C5' C E 608 1094 1096 1114 C5' G E 609 1113 1115 1136 C5' C E 610 1135 1137 1155 C5' G E 611 1154 1156 1177 C5' A E 612 1176 1178 1198 C5' A E 613 1197 1199 1219 C5' A E 614 1218 1220 1240 C5' A E 615 1239 1241 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 641 P T D 501 distorted distorted 642 643 644 661 P T D 502 distorted distorted 649 662 663 664 681 P T D 503 distorted distorted 669 682 683 684 701 P T D 504 distorted distorted 689 702 703 704 721 P C D 505 distorted distorted 709 722 723 724 740 P G D 506 distorted distorted 729 741 742 743 762 P C D 507 distorted distorted 748 763 764 765 781 P G D 508 distorted distorted 770 782 783 784 803 P C D 509 distorted distorted 789 804 805 806 822 P G D 510 distorted distorted 811 823 824 825 844 P G D 511 distorted distorted 830 845 846 847 866 P T D 512 distorted distorted 852 867 868 869 886 P T D 513 distorted distorted 874 887 888 889 906 P T D 514 distorted distorted 894 907 908 909 926 P T D 515 distorted distorted 914 927 928 929 947 P A E 601 OK OK 948 949 950 968 P A E 602 distorted distorted 955 969 970 971 989 P A E 603 distorted distorted 976 990 991 992 1010 P A E 604 distorted distorted 997 1011 1012 1013 1031 P C E 605 distorted distorted 1018 1032 1033 1034 1050 P C E 606 distorted distorted 1039 1051 1052 1053 1069 P G E 607 distorted distorted 1058 1070 1071 1072 1091 P C E 608 distorted distorted 1077 1092 1093 1094 1110 P G E 609 distorted distorted 1099 1111 1112 1113 1132 P C E 610 distorted distorted 1118 1133 1134 1135 1151 P G E 611 distorted distorted 1140 1152 1153 1154 1173 P A E 612 distorted distorted 1159 1174 1175 1176 1194 P A E 613 distorted distorted 1181 1195 1196 1197 1215 P A E 614 distorted distorted 1202 1216 1217 1218 1236 P A E 615 distorted distorted 1223 1237 1238 1239 ---------------------------------------------------------------------------------