ID code: '4I27' 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' --------------------------------------------------------------------------------- 2878 C1' DA C 1 beta 2874 2879 2877 2899 C1' DA C 2 beta 2895 2900 2898 2920 C1' DA C 3 beta 2916 2921 2919 2941 C1' DA C 4 beta 2937 2942 2940 2962 C1' DA C 5 beta 2958 2963 2961 2990 C1' 2DT C 6 beta 2989 2977 2986 3001 C1' D3T A 602 beta 3000 3002 3011 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2877 C2' DA C 1 2878 2875 2898 C2' DA C 2 2899 2896 2919 C2' DA C 3 2920 2917 2940 C2' DA C 4 2941 2938 2961 C2' DA C 5 2962 2959 2986 C2' 2DT C 6 2990 2991 3011 C2' D3T A 602 3001 3012 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2875 C3' DA C 1 OK 2873 2876 2877 2896 C3' DA C 2 OK 2894 2897 2898 2917 C3' DA C 3 OK 2915 2918 2919 2938 C3' DA C 4 OK 2936 2939 2940 2959 C3' DA C 5 OK 2957 2960 2961 2991 C3' 2DT C 6 2988 2986 3012 C3' D3T A 602 2999 3011 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2873 C4' DA C 1 OK 2875 2872 2874 2894 C4' DA C 2 OK 2896 2893 2895 2915 C4' DA C 3 OK 2917 2914 2916 2936 C4' DA C 4 OK 2938 2935 2937 2957 C4' DA C 5 OK 2959 2956 2958 2988 C4' 2DT C 6 OK 2991 2987 2989 2999 C4' D3T A 602 OK 3012 2998 3000 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2872 C5' DA C 1 2871 2873 2893 C5' DA C 2 2892 2894 2914 C5' DA C 3 2913 2915 2935 C5' DA C 4 2934 2936 2956 C5' DA C 5 2955 2957 2987 C5' 2DT C 6 2976 2988 2998 C5' D3T A 602 2997 2999 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2889 P DA C 2 distorted distorted 2876 2890 2891 2892 2910 P DA C 3 distorted distorted 2897 2911 2912 2913 2931 P DA C 4 distorted distorted 2918 2932 2933 2934 2952 P DA C 5 distorted distorted 2939 2953 2954 2955 2973 P 2DT C 6 distorted distorted 2960 2974 2975 2976 ---------------------------------------------------------------------------------