ID code: '1WWE' 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' --------------------------------------------------------------------------------- 901 C1' U B 517 alpha beta 896 916 902 899 931 C1' U B 518 alpha beta 926 946 932 929 961 C1' U B 519 alpha beta 956 976 962 959 991 C1' U B 520 alpha beta 986 1006 992 989 1021 C1' G B 521 alpha beta 1016 1039 1022 1019 1055 C1' C B 522 alpha beta 1050 1070 1056 1053 1086 C1' U B 523 alpha beta 1081 1101 1087 1084 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 899 C2' U B 517 OK OK 901 897 914 900 929 C2' U B 518 OK OK 931 927 944 930 959 C2' U B 519 OK OK 961 957 974 960 989 C2' U B 520 OK OK 991 987 1004 990 1019 C2' G B 521 OK OK 1021 1017 1037 1020 1053 C2' C B 522 OK OK 1055 1051 1068 1054 1084 C2' U B 523 OK OK 1086 1082 1099 1085 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 897 C3' U B 517 OK OK 895 913 898 899 927 C3' U B 518 OK OK 925 943 928 929 957 C3' U B 519 OK OK 955 973 958 959 987 C3' U B 520 OK OK 985 1003 988 989 1017 C3' G B 521 OK OK 1015 1036 1018 1019 1051 C3' C B 522 OK OK 1049 1067 1052 1053 1082 C3' U B 523 OK OK 1080 1098 1083 1084 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 895 C4' U B 517 OK OK 897 912 894 896 925 C4' U B 518 OK OK 927 942 924 926 955 C4' U B 519 OK OK 957 972 954 956 985 C4' U B 520 OK OK 987 1002 984 986 1015 C4' G B 521 OK OK 1017 1035 1014 1016 1049 C4' C B 522 OK OK 1051 1066 1048 1050 1080 C4' U B 523 OK OK 1082 1097 1079 1081 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 894 C5' U B 517 OK OK 893 910 911 895 924 C5' U B 518 OK OK 923 940 941 925 954 C5' U B 519 OK OK 953 970 971 955 984 C5' U B 520 OK OK 983 1000 1001 985 1014 C5' G B 521 OK OK 1013 1033 1034 1015 1048 C5' C B 522 OK OK 1047 1064 1065 1049 1079 C5' U B 523 OK OK 1078 1095 1096 1080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 890 P U B 517 distorted distorted 891 892 893 920 P U B 518 distorted distorted 898 921 922 923 950 P U B 519 distorted distorted 928 951 952 953 980 P U B 520 distorted distorted 958 981 982 983 1010 P G B 521 distorted distorted 988 1011 1012 1013 1044 P C B 522 distorted distorted 1018 1045 1046 1047 1075 P U B 523 distorted distorted 1052 1076 1077 1078 ---------------------------------------------------------------------------------