ID code: '1FNX' 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' --------------------------------------------------------------------------------- 2727 C1' U R 0 alpha beta 2722 2742 2728 2725 2758 C1' A R 1 alpha beta 2753 2775 2759 2756 2791 C1' U R 2 alpha beta 2786 2806 2792 2789 2821 C1' U R 3 alpha beta 2816 2836 2822 2819 2851 C1' U R 4 alpha beta 2846 2866 2852 2849 2881 C1' A R 5 alpha beta 2876 2898 2882 2879 2914 C1' U R 6 alpha beta 2909 2929 2915 2912 2944 C1' U R 7 alpha beta 2939 2959 2945 2942 2974 C1' U R 8 alpha beta 2969 2989 2975 2972 3004 C1' U R 9 alpha beta 2999 3020 3005 3002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2725 C2' U R 0 OK OK 2727 2723 2740 2726 2756 C2' A R 1 OK OK 2758 2754 2773 2757 2789 C2' U R 2 OK OK 2791 2787 2804 2790 2819 C2' U R 3 OK OK 2821 2817 2834 2820 2849 C2' U R 4 OK OK 2851 2847 2864 2850 2879 C2' A R 5 OK OK 2881 2877 2896 2880 2912 C2' U R 6 OK OK 2914 2910 2927 2913 2942 C2' U R 7 OK OK 2944 2940 2957 2943 2972 C2' U R 8 OK OK 2974 2970 2987 2973 3002 C2' U R 9 OK OK 3004 3000 3018 3003 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2723 C3' U R 0 OK OK 2721 2739 2724 2725 2754 C3' A R 1 OK OK 2752 2772 2755 2756 2787 C3' U R 2 OK OK 2785 2803 2788 2789 2817 C3' U R 3 OK OK 2815 2833 2818 2819 2847 C3' U R 4 OK OK 2845 2863 2848 2849 2877 C3' A R 5 OK OK 2875 2895 2878 2879 2910 C3' U R 6 OK OK 2908 2926 2911 2912 2940 C3' U R 7 OK OK 2938 2956 2941 2942 2970 C3' U R 8 OK OK 2968 2986 2971 2972 3000 C3' U R 9 OK OK 2998 3016 3001 3002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2721 C4' U R 0 OK OK 2723 2738 2720 2722 2752 C4' A R 1 OK OK 2754 2771 2751 2753 2785 C4' U R 2 OK OK 2787 2802 2784 2786 2815 C4' U R 3 OK OK 2817 2832 2814 2816 2845 C4' U R 4 OK OK 2847 2862 2844 2846 2875 C4' A R 5 OK OK 2877 2894 2874 2876 2908 C4' U R 6 OK OK 2910 2925 2907 2909 2938 C4' U R 7 OK OK 2940 2955 2937 2939 2968 C4' U R 8 OK OK 2970 2985 2967 2969 2998 C4' U R 9 OK OK 3000 3015 2997 2999 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2720 C5' U R 0 OK OK 2719 2736 2737 2721 2751 C5' A R 1 OK OK 2750 2769 2770 2752 2784 C5' U R 2 OK OK 2783 2800 2801 2785 2814 C5' U R 3 OK OK 2813 2830 2831 2815 2844 C5' U R 4 OK OK 2843 2860 2861 2845 2874 C5' A R 5 OK OK 2873 2892 2893 2875 2907 C5' U R 6 OK OK 2906 2923 2924 2908 2937 C5' U R 7 OK OK 2936 2953 2954 2938 2967 C5' U R 8 OK OK 2966 2983 2984 2968 2997 C5' U R 9 OK OK 2996 3013 3014 2998 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2716 P U R 0 OK OK 2717 2718 2719 2747 P A R 1 distorted distorted 2724 2748 2749 2750 2780 P U R 2 distorted distorted 2755 2781 2782 2783 2810 P U R 3 distorted distorted 2788 2811 2812 2813 2840 P U R 4 distorted distorted 2818 2841 2842 2843 2870 P A R 5 distorted distorted 2848 2871 2872 2873 2903 P U R 6 distorted distorted 2878 2904 2905 2906 2933 P U R 7 distorted distorted 2911 2934 2935 2936 2963 P U R 8 distorted distorted 2941 2964 2965 2966 2993 P U R 9 distorted distorted 2971 2994 2995 2996 ---------------------------------------------------------------------------------