ID code: '4I2A' 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' --------------------------------------------------------------------------------- 2907 C1' DA C 1 beta 2903 2908 2906 2928 C1' DA C 2 beta 2924 2929 2927 2948 C1' BRU C 3 beta 2953 2939 2949 2969 C1' DA C 4 beta 2965 2970 2968 2990 C1' DA C 5 beta 2986 2991 2989 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2906 C2' DA C 1 2907 2904 2927 C2' DA C 2 2928 2925 2949 C2' BRU C 3 2948 2950 2968 C2' DA C 4 2969 2966 2989 C2' DA C 5 2990 2987 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2904 C3' DA C 1 OK 2902 2905 2906 2925 C3' DA C 2 OK 2923 2926 2927 2950 C3' BRU C 3 OK 2951 2952 2949 2966 C3' DA C 4 OK 2964 2967 2968 2987 C3' DA C 5 OK 2985 2988 2989 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2902 C4' DA C 1 OK 2904 2901 2903 2923 C4' DA C 2 OK 2925 2922 2924 2951 C4' BRU C 3 OK 2950 2954 2953 2964 C4' DA C 4 OK 2966 2963 2965 2985 C4' DA C 5 OK 2987 2984 2986 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2901 C5' DA C 1 2900 2902 2922 C5' DA C 2 2921 2923 2954 C5' BRU C 3 2955 2951 2963 C5' DA C 4 2962 2964 2984 C5' DA C 5 2983 2985 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2918 P DA C 2 distorted distorted 2905 2919 2920 2921 2956 P BRU C 3 distorted distorted 2926 2957 2958 2955 2959 P DA C 4 distorted distorted 2952 2960 2961 2962 2980 P DA C 5 distorted distorted 2967 2981 2982 2983 ---------------------------------------------------------------------------------