ID code: '1WWD' 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' A B 493 alpha beta 896 918 902 899 934 C1' A B 494 alpha beta 929 951 935 932 967 C1' C B 495 alpha beta 962 982 968 965 998 C1' A B 496 alpha beta 993 1015 999 996 1031 C1' G B 497 alpha beta 1026 1049 1032 1029 1065 C1' U B 498 alpha beta 1060 1080 1066 1063 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 899 C2' A B 493 OK OK 901 897 916 900 932 C2' A B 494 OK OK 934 930 949 933 965 C2' C B 495 OK OK 967 963 980 966 996 C2' A B 496 OK OK 998 994 1013 997 1029 C2' G B 497 OK OK 1031 1027 1047 1030 1063 C2' U B 498 OK OK 1065 1061 1078 1064 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 897 C3' A B 493 OK OK 895 915 898 899 930 C3' A B 494 OK OK 928 948 931 932 963 C3' C B 495 OK OK 961 979 964 965 994 C3' A B 496 OK OK 992 1012 995 996 1027 C3' G B 497 OK OK 1025 1046 1028 1029 1061 C3' U B 498 OK OK 1059 1077 1062 1063 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 895 C4' A B 493 OK OK 897 914 894 896 928 C4' A B 494 OK OK 930 947 927 929 961 C4' C B 495 OK OK 963 978 960 962 992 C4' A B 496 OK OK 994 1011 991 993 1025 C4' G B 497 OK OK 1027 1045 1024 1026 1059 C4' U B 498 OK OK 1061 1076 1058 1060 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 894 C5' A B 493 OK OK 893 912 913 895 927 C5' A B 494 OK OK 926 945 946 928 960 C5' C B 495 OK OK 959 976 977 961 991 C5' A B 496 OK OK 990 1009 1010 992 1024 C5' G B 497 OK OK 1023 1043 1044 1025 1058 C5' U B 498 OK OK 1057 1074 1075 1059 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 890 P A B 493 distorted distorted 891 892 893 923 P A B 494 distorted distorted 898 924 925 926 956 P C B 495 distorted distorted 931 957 958 959 987 P A B 496 distorted distorted 964 988 989 990 1020 P G B 497 distorted distorted 995 1021 1022 1023 1054 P U B 498 distorted distorted 1028 1055 1056 1057 ---------------------------------------------------------------------------------