ID code: '3AEV' 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' --------------------------------------------------------------------------------- 2819 C1' G C 1 beta 2814 2820 2817 2842 C1' G C 2 beta 2837 2843 2840 2865 C1' A C 3 beta 2860 2866 2863 2887 C1' U C 4 beta 2882 2888 2885 2907 C1' C C 5 beta 2902 2908 2905 2927 C1' A C 6 beta 2922 2928 2925 2949 C1' C C 7 beta 2944 2950 2947 2969 C1' C C 8 beta 2964 2970 2967 2989 C1' U C 9 beta 2984 2990 2987 3009 C1' C C 10 beta 3004 3010 3007 3029 C1' C C 11 beta 3024 3030 3027 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2817 C2' G C 1 OK 2819 2815 2818 2840 C2' G C 2 OK 2842 2838 2841 2863 C2' A C 3 OK 2865 2861 2864 2885 C2' U C 4 OK 2887 2883 2886 2905 C2' C C 5 OK 2907 2903 2906 2925 C2' A C 6 OK 2927 2923 2926 2947 C2' C C 7 OK 2949 2945 2948 2967 C2' C C 8 OK 2969 2965 2968 2987 C2' U C 9 OK 2989 2985 2988 3007 C2' C C 10 OK 3009 3005 3008 3027 C2' C C 11 OK 3029 3025 3028 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2815 C3' G C 1 OK 2813 2816 2817 2838 C3' G C 2 OK 2836 2839 2840 2861 C3' A C 3 OK 2859 2862 2863 2883 C3' U C 4 OK 2881 2884 2885 2903 C3' C C 5 OK 2901 2904 2905 2923 C3' A C 6 OK 2921 2924 2925 2945 C3' C C 7 OK 2943 2946 2947 2965 C3' C C 8 OK 2963 2966 2967 2985 C3' U C 9 OK 2983 2986 2987 3005 C3' C C 10 OK 3003 3006 3007 3025 C3' C C 11 OK 3023 3026 3027 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2813 C4' G C 1 OK 2815 2812 2814 2836 C4' G C 2 OK 2838 2835 2837 2859 C4' A C 3 OK 2861 2858 2860 2881 C4' U C 4 OK 2883 2880 2882 2901 C4' C C 5 OK 2903 2900 2902 2921 C4' A C 6 OK 2923 2920 2922 2943 C4' C C 7 OK 2945 2942 2944 2963 C4' C C 8 OK 2965 2962 2964 2983 C4' U C 9 OK 2985 2982 2984 3003 C4' C C 10 OK 3005 3002 3004 3023 C4' C C 11 OK 3025 3022 3024 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2812 C5' G C 1 2811 2813 2835 C5' G C 2 2834 2836 2858 C5' A C 3 2857 2859 2880 C5' U C 4 2879 2881 2900 C5' C C 5 2899 2901 2920 C5' A C 6 2919 2921 2942 C5' C C 7 2941 2943 2962 C5' C C 8 2961 2963 2982 C5' U C 9 2981 2983 3002 C5' C C 10 3001 3003 3022 C5' C C 11 3021 3023 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2831 P G C 2 distorted distorted 2816 2832 2833 2834 2854 P A C 3 distorted distorted 2839 2855 2856 2857 2876 P U C 4 distorted distorted 2862 2877 2878 2879 2896 P C C 5 distorted distorted 2884 2897 2898 2899 2916 P A C 6 distorted distorted 2904 2917 2918 2919 2938 P C C 7 distorted distorted 2924 2939 2940 2941 2958 P C C 8 distorted distorted 2946 2959 2960 2961 2978 P U C 9 distorted distorted 2966 2979 2980 2981 2998 P C C 10 distorted distorted 2986 2999 3000 3001 3018 P C C 11 distorted distorted 3006 3019 3020 3021 ---------------------------------------------------------------------------------