ID code: '2DRP' 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' --------------------------------------------------------------------------------- 555 C1' T B 2 beta 551 556 554 575 C1' A B 3 beta 571 576 574 596 C1' A B 4 beta 592 597 595 617 C1' T B 5 beta 613 618 616 637 C1' A B 6 beta 633 638 636 658 C1' A B 7 beta 654 659 657 679 C1' G B 8 beta 675 680 678 701 C1' G B 9 beta 697 702 700 723 C1' A B 10 beta 719 724 722 744 C1' T B 11 beta 740 745 743 764 C1' A B 12 beta 760 765 763 785 C1' A B 13 beta 781 786 784 806 C1' C B 14 beta 802 807 805 825 C1' G B 15 beta 821 826 824 847 C1' T B 16 beta 843 848 846 867 C1' C B 17 beta 863 868 866 886 C1' C B 18 beta 882 887 885 905 C1' G B 19 beta 901 906 904 945 C1' C C 22 beta 941 946 944 964 C1' G C 23 beta 960 965 963 986 C1' G C 24 beta 982 987 985 1008 C1' A C 25 beta 1004 1009 1007 1029 C1' C C 26 beta 1025 1030 1028 1048 C1' G C 27 beta 1044 1049 1047 1070 C1' T C 28 beta 1066 1071 1069 1090 C1' T C 29 beta 1086 1091 1089 1110 C1' A C 30 beta 1106 1111 1109 1131 C1' T C 31 beta 1127 1132 1130 1151 C1' C C 32 beta 1147 1152 1150 1170 C1' C C 33 beta 1166 1171 1169 1189 C1' T C 34 beta 1185 1190 1188 1209 C1' T C 35 beta 1205 1210 1208 1229 C1' A C 36 beta 1225 1230 1228 1250 C1' T C 37 beta 1246 1251 1249 1270 C1' T C 38 beta 1266 1271 1269 1290 C1' A C 39 beta 1286 1291 1289 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 554 C2' T B 2 555 552 574 C2' A B 3 575 572 595 C2' A B 4 596 593 616 C2' T B 5 617 614 636 C2' A B 6 637 634 657 C2' A B 7 658 655 678 C2' G B 8 679 676 700 C2' G B 9 701 698 722 C2' A B 10 723 720 743 C2' T B 11 744 741 763 C2' A B 12 764 761 784 C2' A B 13 785 782 805 C2' C B 14 806 803 824 C2' G B 15 825 822 846 C2' T B 16 847 844 866 C2' C B 17 867 864 885 C2' C B 18 886 883 904 C2' G B 19 905 902 944 C2' C C 22 945 942 963 C2' G C 23 964 961 985 C2' G C 24 986 983 1007 C2' A C 25 1008 1005 1028 C2' C C 26 1029 1026 1047 C2' G C 27 1048 1045 1069 C2' T C 28 1070 1067 1089 C2' T C 29 1090 1087 1109 C2' A C 30 1110 1107 1130 C2' T C 31 1131 1128 1150 C2' C C 32 1151 1148 1169 C2' C C 33 1170 1167 1188 C2' T C 34 1189 1186 1208 C2' T C 35 1209 1206 1228 C2' A C 36 1229 1226 1249 C2' T C 37 1250 1247 1269 C2' T C 38 1270 1267 1289 C2' A C 39 1290 1287 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 552 C3' T B 2 OK 550 553 554 572 C3' A B 3 OK 570 573 574 593 C3' A B 4 OK 591 594 595 614 C3' T B 5 OK 612 615 616 634 C3' A B 6 OK 632 635 636 655 C3' A B 7 OK 653 656 657 676 C3' G B 8 OK 674 677 678 698 C3' G B 9 OK 696 699 700 720 C3' A B 10 OK 718 721 722 741 C3' T B 11 OK 739 742 743 761 C3' A B 12 OK 759 762 763 782 C3' A B 13 OK 780 783 784 803 C3' C B 14 OK 801 804 805 822 C3' G B 15 OK 820 823 824 844 C3' T B 16 OK 842 845 846 864 C3' C B 17 OK 862 865 866 883 C3' C B 18 OK 881 884 885 902 C3' G B 19 OK 900 903 904 942 C3' C C 22 OK 940 943 944 961 C3' G C 23 OK 959 962 963 983 C3' G C 24 OK 981 984 985 1005 C3' A C 25 OK 1003 1006 1007 1026 C3' C C 26 OK 1024 1027 1028 1045 C3' G C 27 OK 1043 1046 1047 1067 C3' T C 28 OK 1065 1068 1069 1087 C3' T C 29 OK 1085 1088 1089 1107 C3' A C 30 OK 1105 1108 1109 1128 C3' T C 31 OK 1126 1129 1130 1148 C3' C C 32 OK 1146 1149 1150 1167 C3' C C 33 OK 1165 1168 1169 1186 C3' T C 34 OK 1184 1187 1188 1206 C3' T C 35 OK 1204 1207 1208 1226 C3' A C 36 OK 1224 1227 1228 1247 C3' T C 37 OK 1245 1248 1249 1267 C3' T C 38 OK 1265 1268 1269 1287 C3' A C 39 OK 1285 1288 1289 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 550 C4' T B 2 OK 552 549 551 570 C4' A B 3 OK 572 569 571 591 C4' A B 4 OK 593 590 592 612 C4' T B 5 OK 614 611 613 632 C4' A B 6 OK 634 631 633 653 C4' A B 7 OK 655 652 654 674 C4' G B 8 OK 676 673 675 696 C4' G B 9 OK 698 695 697 718 C4' A B 10 OK 720 717 719 739 C4' T B 11 OK 741 738 740 759 C4' A B 12 OK 761 758 760 780 C4' A B 13 OK 782 779 781 801 C4' C B 14 OK 803 800 802 820 C4' G B 15 OK 822 819 821 842 C4' T B 16 OK 844 841 843 862 C4' C B 17 OK 864 861 863 881 C4' C B 18 OK 883 880 882 900 C4' G B 19 OK 902 899 901 940 C4' C C 22 OK 942 939 941 959 C4' G C 23 OK 961 958 960 981 C4' G C 24 OK 983 980 982 1003 C4' A C 25 OK 1005 1002 1004 1024 C4' C C 26 OK 1026 1023 1025 1043 C4' G C 27 OK 1045 1042 1044 1065 C4' T C 28 OK 1067 1064 1066 1085 C4' T C 29 OK 1087 1084 1086 1105 C4' A C 30 OK 1107 1104 1106 1126 C4' T C 31 OK 1128 1125 1127 1146 C4' C C 32 OK 1148 1145 1147 1165 C4' C C 33 OK 1167 1164 1166 1184 C4' T C 34 OK 1186 1183 1185 1204 C4' T C 35 OK 1206 1203 1205 1224 C4' A C 36 OK 1226 1223 1225 1245 C4' T C 37 OK 1247 1244 1246 1265 C4' T C 38 OK 1267 1264 1266 1285 C4' A C 39 OK 1287 1284 1286 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 549 C5' T B 2 548 550 569 C5' A B 3 568 570 590 C5' A B 4 589 591 611 C5' T B 5 610 612 631 C5' A B 6 630 632 652 C5' A B 7 651 653 673 C5' G B 8 672 674 695 C5' G B 9 694 696 717 C5' A B 10 716 718 738 C5' T B 11 737 739 758 C5' A B 12 757 759 779 C5' A B 13 778 780 800 C5' C B 14 799 801 819 C5' G B 15 818 820 841 C5' T B 16 840 842 861 C5' C B 17 860 862 880 C5' C B 18 879 881 899 C5' G B 19 898 900 939 C5' C C 22 938 940 958 C5' G C 23 957 959 980 C5' G C 24 979 981 1002 C5' A C 25 1001 1003 1023 C5' C C 26 1022 1024 1042 C5' G C 27 1041 1043 1064 C5' T C 28 1063 1065 1084 C5' T C 29 1083 1085 1104 C5' A C 30 1103 1105 1125 C5' T C 31 1124 1126 1145 C5' C C 32 1144 1146 1164 C5' C C 33 1163 1165 1183 C5' T C 34 1182 1184 1203 C5' T C 35 1202 1204 1223 C5' A C 36 1222 1224 1244 C5' T C 37 1243 1245 1264 C5' T C 38 1263 1265 1284 C5' A C 39 1283 1285 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 565 P A B 3 distorted distorted 553 566 567 568 586 P A B 4 distorted distorted 573 587 588 589 607 P T B 5 distorted distorted 594 608 609 610 627 P A B 6 distorted distorted 615 628 629 630 648 P A B 7 distorted distorted 635 649 650 651 669 P G B 8 distorted distorted 656 670 671 672 691 P G B 9 distorted distorted 677 692 693 694 713 P A B 10 distorted distorted 699 714 715 716 734 P T B 11 distorted distorted 721 735 736 737 754 P A B 12 distorted distorted 742 755 756 757 775 P A B 13 distorted distorted 762 776 777 778 796 P C B 14 distorted distorted 783 797 798 799 815 P G B 15 distorted distorted 804 816 817 818 837 P T B 16 distorted distorted 823 838 839 840 857 P C B 17 distorted distorted 845 858 859 860 876 P C B 18 distorted distorted 865 877 878 879 895 P G B 19 distorted distorted 884 896 897 898 954 P G C 23 distorted distorted 943 955 956 957 976 P G C 24 distorted distorted 962 977 978 979 998 P A C 25 distorted distorted 984 999 1000 1001 1019 P C C 26 distorted distorted 1006 1020 1021 1022 1038 P G C 27 distorted distorted 1027 1039 1040 1041 1060 P T C 28 distorted distorted 1046 1061 1062 1063 1080 P T C 29 distorted distorted 1068 1081 1082 1083 1100 P A C 30 distorted distorted 1088 1101 1102 1103 1121 P T C 31 distorted distorted 1108 1122 1123 1124 1141 P C C 32 distorted distorted 1129 1142 1143 1144 1160 P C C 33 distorted distorted 1149 1161 1162 1163 1179 P T C 34 distorted distorted 1168 1180 1181 1182 1199 P T C 35 distorted distorted 1187 1200 1201 1202 1219 P A C 36 distorted distorted 1207 1220 1221 1222 1240 P T C 37 distorted distorted 1227 1241 1242 1243 1260 P T C 38 distorted distorted 1248 1261 1262 1263 1280 P A C 39 distorted distorted 1268 1281 1282 1283 ---------------------------------------------------------------------------------