ID code: '1SKN' 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' --------------------------------------------------------------------------------- 661 C1' A A 3 beta 657 662 660 682 C1' C A 4 beta 678 683 681 701 C1' A A 5 beta 697 702 700 722 C1' A A 6 beta 718 723 721 743 C1' T A 7 beta 739 744 742 763 C1' G A 8 beta 759 764 762 785 C1' T A 9 beta 781 786 784 805 C1' C A 10 beta 801 806 804 824 C1' A A 11 beta 820 825 823 845 C1' T A 12 beta 841 846 844 865 C1' C A 13 beta 861 866 864 884 C1' C A 14 beta 880 885 883 903 C1' C A 15 beta 899 904 902 960 C1' G B 3 beta 956 961 959 982 C1' G B 4 beta 978 983 981 1004 C1' G B 5 beta 1000 1005 1003 1026 C1' A B 6 beta 1022 1027 1025 1047 C1' T B 7 beta 1043 1048 1046 1067 C1' G B 8 beta 1063 1068 1066 1089 C1' A B 9 beta 1085 1090 1088 1110 C1' C B 10 beta 1106 1111 1109 1129 C1' A B 11 beta 1125 1130 1128 1150 C1' T B 12 beta 1146 1151 1149 1170 C1' T B 13 beta 1166 1171 1169 1190 C1' G B 14 beta 1186 1191 1189 1212 C1' T B 15 beta 1208 1213 1211 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 660 C2' A A 3 661 658 681 C2' C A 4 682 679 700 C2' A A 5 701 698 721 C2' A A 6 722 719 742 C2' T A 7 743 740 762 C2' G A 8 763 760 784 C2' T A 9 785 782 804 C2' C A 10 805 802 823 C2' A A 11 824 821 844 C2' T A 12 845 842 864 C2' C A 13 865 862 883 C2' C A 14 884 881 902 C2' C A 15 903 900 959 C2' G B 3 960 957 981 C2' G B 4 982 979 1003 C2' G B 5 1004 1001 1025 C2' A B 6 1026 1023 1046 C2' T B 7 1047 1044 1066 C2' G B 8 1067 1064 1088 C2' A B 9 1089 1086 1109 C2' C B 10 1110 1107 1128 C2' A B 11 1129 1126 1149 C2' T B 12 1150 1147 1169 C2' T B 13 1170 1167 1189 C2' G B 14 1190 1187 1211 C2' T B 15 1212 1209 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 658 C3' A A 3 OK 656 659 660 679 C3' C A 4 OK 677 680 681 698 C3' A A 5 OK 696 699 700 719 C3' A A 6 OK 717 720 721 740 C3' T A 7 OK 738 741 742 760 C3' G A 8 OK 758 761 762 782 C3' T A 9 OK 780 783 784 802 C3' C A 10 OK 800 803 804 821 C3' A A 11 OK 819 822 823 842 C3' T A 12 OK 840 843 844 862 C3' C A 13 OK 860 863 864 881 C3' C A 14 OK 879 882 883 900 C3' C A 15 OK 898 901 902 957 C3' G B 3 OK 955 958 959 979 C3' G B 4 OK 977 980 981 1001 C3' G B 5 OK 999 1002 1003 1023 C3' A B 6 OK 1021 1024 1025 1044 C3' T B 7 OK 1042 1045 1046 1064 C3' G B 8 OK 1062 1065 1066 1086 C3' A B 9 OK 1084 1087 1088 1107 C3' C B 10 OK 1105 1108 1109 1126 C3' A B 11 OK 1124 1127 1128 1147 C3' T B 12 OK 1145 1148 1149 1167 C3' T B 13 OK 1165 1168 1169 1187 C3' G B 14 OK 1185 1188 1189 1209 C3' T B 15 OK 1207 1210 1211 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 656 C4' A A 3 OK 658 655 657 677 C4' C A 4 OK 679 676 678 696 C4' A A 5 OK 698 695 697 717 C4' A A 6 OK 719 716 718 738 C4' T A 7 OK 740 737 739 758 C4' G A 8 OK 760 757 759 780 C4' T A 9 OK 782 779 781 800 C4' C A 10 OK 802 799 801 819 C4' A A 11 OK 821 818 820 840 C4' T A 12 OK 842 839 841 860 C4' C A 13 OK 862 859 861 879 C4' C A 14 OK 881 878 880 898 C4' C A 15 OK 900 897 899 955 C4' G B 3 OK 957 954 956 977 C4' G B 4 OK 979 976 978 999 C4' G B 5 OK 1001 998 1000 1021 C4' A B 6 OK 1023 1020 1022 1042 C4' T B 7 OK 1044 1041 1043 1062 C4' G B 8 OK 1064 1061 1063 1084 C4' A B 9 OK 1086 1083 1085 1105 C4' C B 10 OK 1107 1104 1106 1124 C4' A B 11 OK 1126 1123 1125 1145 C4' T B 12 OK 1147 1144 1146 1165 C4' T B 13 OK 1167 1164 1166 1185 C4' G B 14 OK 1187 1184 1186 1207 C4' T B 15 OK 1209 1206 1208 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 655 C5' A A 3 654 656 676 C5' C A 4 675 677 695 C5' A A 5 694 696 716 C5' A A 6 715 717 737 C5' T A 7 736 738 757 C5' G A 8 756 758 779 C5' T A 9 778 780 799 C5' C A 10 798 800 818 C5' A A 11 817 819 839 C5' T A 12 838 840 859 C5' C A 13 858 860 878 C5' C A 14 877 879 897 C5' C A 15 896 898 954 C5' G B 3 953 955 976 C5' G B 4 975 977 998 C5' G B 5 997 999 1020 C5' A B 6 1019 1021 1041 C5' T B 7 1040 1042 1061 C5' G B 8 1060 1062 1083 C5' A B 9 1082 1084 1104 C5' C B 10 1103 1105 1123 C5' A B 11 1122 1124 1144 C5' T B 12 1143 1145 1164 C5' T B 13 1163 1165 1184 C5' G B 14 1183 1185 1206 C5' T B 15 1205 1207 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 672 P C A 4 OK OK 659 673 674 675 691 P A A 5 OK OK 680 692 693 694 712 P A A 6 OK OK 699 713 714 715 733 P T A 7 OK OK 720 734 735 736 753 P G A 8 OK OK 741 754 755 756 775 P T A 9 OK OK 761 776 777 778 795 P C A 10 OK OK 783 796 797 798 814 P A A 11 OK OK 803 815 816 817 835 P T A 12 OK OK 822 836 837 838 855 P C A 13 OK OK 843 856 857 858 874 P C A 14 OK OK 863 875 876 877 893 P C A 15 OK OK 882 894 895 896 972 P G B 4 OK OK 958 973 974 975 994 P G B 5 OK OK 980 995 996 997 1016 P A B 6 OK OK 1002 1017 1018 1019 1037 P T B 7 OK OK 1024 1038 1039 1040 1057 P G B 8 OK OK 1045 1058 1059 1060 1079 P A B 9 OK OK 1065 1080 1081 1082 1100 P C B 10 OK OK 1087 1101 1102 1103 1119 P A B 11 OK OK 1108 1120 1121 1122 1140 P T B 12 OK OK 1127 1141 1142 1143 1160 P T B 13 OK OK 1148 1161 1162 1163 1180 P G B 14 OK OK 1168 1181 1182 1183 1202 P T B 15 OK OK 1188 1203 1204 1205 ---------------------------------------------------------------------------------