ID code: '3VYX' 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' --------------------------------------------------------------------------------- 779 C1' G B 1 beta 774 780 777 802 C1' C B 2 beta 797 803 800 822 C1' G B 3 beta 817 823 820 845 C1' C B 4 beta 840 846 843 865 C1' G B 5 beta 860 866 863 888 C1' C B 6 beta 883 889 886 908 C1' G B 7 beta 903 909 906 931 C1' C B 8 beta 926 932 929 951 C1' G B 9 beta 946 952 949 974 C1' C B 10 beta 969 975 972 996 C1' G C 1 beta 991 997 994 1019 C1' C C 2 beta 1014 1020 1017 1039 C1' G C 3 beta 1034 1040 1037 1062 C1' C C 4 beta 1057 1063 1060 1082 C1' G C 5 beta 1077 1083 1080 1105 C1' C C 6 beta 1100 1106 1103 1125 C1' G C 7 beta 1120 1126 1123 1148 C1' C C 8 beta 1143 1149 1146 1168 C1' G C 9 beta 1163 1169 1166 1191 C1' C C 10 beta 1186 1192 1189 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 777 C2' G B 1 OK 779 775 778 800 C2' C B 2 OK 802 798 801 820 C2' G B 3 OK 822 818 821 843 C2' C B 4 OK 845 841 844 863 C2' G B 5 OK 865 861 864 886 C2' C B 6 OK 888 884 887 906 C2' G B 7 OK 908 904 907 929 C2' C B 8 OK 931 927 930 949 C2' G B 9 OK 951 947 950 972 C2' C B 10 OK 974 970 973 994 C2' G C 1 OK 996 992 995 1017 C2' C C 2 OK 1019 1015 1018 1037 C2' G C 3 OK 1039 1035 1038 1060 C2' C C 4 OK 1062 1058 1061 1080 C2' G C 5 OK 1082 1078 1081 1103 C2' C C 6 OK 1105 1101 1104 1123 C2' G C 7 OK 1125 1121 1124 1146 C2' C C 8 OK 1148 1144 1147 1166 C2' G C 9 OK 1168 1164 1167 1189 C2' C C 10 OK 1191 1187 1190 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 775 C3' G B 1 OK 773 776 777 798 C3' C B 2 OK 796 799 800 818 C3' G B 3 OK 816 819 820 841 C3' C B 4 OK 839 842 843 861 C3' G B 5 OK 859 862 863 884 C3' C B 6 OK 882 885 886 904 C3' G B 7 OK 902 905 906 927 C3' C B 8 OK 925 928 929 947 C3' G B 9 OK 945 948 949 970 C3' C B 10 OK 968 971 972 992 C3' G C 1 OK 990 993 994 1015 C3' C C 2 OK 1013 1016 1017 1035 C3' G C 3 OK 1033 1036 1037 1058 C3' C C 4 OK 1056 1059 1060 1078 C3' G C 5 OK 1076 1079 1080 1101 C3' C C 6 OK 1099 1102 1103 1121 C3' G C 7 OK 1119 1122 1123 1144 C3' C C 8 OK 1142 1145 1146 1164 C3' G C 9 OK 1162 1165 1166 1187 C3' C C 10 OK 1185 1188 1189 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 773 C4' G B 1 OK 775 772 774 796 C4' C B 2 OK 798 795 797 816 C4' G B 3 OK 818 815 817 839 C4' C B 4 OK 841 838 840 859 C4' G B 5 OK 861 858 860 882 C4' C B 6 OK 884 881 883 902 C4' G B 7 OK 904 901 903 925 C4' C B 8 OK 927 924 926 945 C4' G B 9 OK 947 944 946 968 C4' C B 10 OK 970 967 969 990 C4' G C 1 OK 992 989 991 1013 C4' C C 2 OK 1015 1012 1014 1033 C4' G C 3 OK 1035 1032 1034 1056 C4' C C 4 OK 1058 1055 1057 1076 C4' G C 5 OK 1078 1075 1077 1099 C4' C C 6 OK 1101 1098 1100 1119 C4' G C 7 OK 1121 1118 1120 1142 C4' C C 8 OK 1144 1141 1143 1162 C4' G C 9 OK 1164 1161 1163 1185 C4' C C 10 OK 1187 1184 1186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 772 C5' G B 1 771 773 795 C5' C B 2 794 796 815 C5' G B 3 814 816 838 C5' C B 4 837 839 858 C5' G B 5 857 859 881 C5' C B 6 880 882 901 C5' G B 7 900 902 924 C5' C B 8 923 925 944 C5' G B 9 943 945 967 C5' C B 10 966 968 989 C5' G C 1 988 990 1012 C5' C C 2 1011 1013 1032 C5' G C 3 1031 1033 1055 C5' C C 4 1054 1056 1075 C5' G C 5 1074 1076 1098 C5' C C 6 1097 1099 1118 C5' G C 7 1117 1119 1141 C5' C C 8 1140 1142 1161 C5' G C 9 1160 1162 1184 C5' C C 10 1183 1185 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 768 P G B 1 distorted distorted 769 770 771 791 P C B 2 distorted distorted 776 792 793 794 811 P G B 3 distorted distorted 799 812 813 814 834 P C B 4 distorted distorted 819 835 836 837 854 P G B 5 distorted distorted 842 855 856 857 877 P C B 6 distorted distorted 862 878 879 880 897 P G B 7 distorted distorted 885 898 899 900 920 P C B 8 distorted distorted 905 921 922 923 940 P G B 9 distorted distorted 928 941 942 943 963 P C B 10 distorted distorted 948 964 965 966 985 P G C 1 distorted distorted 986 987 988 1008 P C C 2 distorted distorted 993 1009 1010 1011 1028 P G C 3 distorted distorted 1016 1029 1030 1031 1051 P C C 4 distorted distorted 1036 1052 1053 1054 1071 P G C 5 distorted distorted 1059 1072 1073 1074 1094 P C C 6 distorted distorted 1079 1095 1096 1097 1114 P G C 7 distorted distorted 1102 1115 1116 1117 1137 P C C 8 distorted distorted 1122 1138 1139 1140 1157 P G C 9 distorted distorted 1145 1158 1159 1160 1180 P C C 10 distorted distorted 1165 1181 1182 1183 ---------------------------------------------------------------------------------