ID code: '5VZH' 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' --------------------------------------------------------------------------------- 2645 C1' DC T 1 beta 2641 2646 2644 2664 C1' DG T 2 beta 2660 2665 2663 2686 C1' DG T 3 beta 2682 2687 2685 2708 C1' DC T 4 beta 2704 2709 2707 2727 C1' DA T 5 beta 2723 2728 2726 2748 C1' DT T 6 beta 2744 2749 2747 2768 C1' DA T 7 beta 2764 2769 2767 2789 C1' DC T 8 beta 2785 2790 2788 2808 C1' DG T 9 beta 2804 2809 2807 2828 C1' DC P 1 beta 2824 2829 2827 2847 C1' DG P 2 beta 2843 2848 2846 2869 C1' DT P 3 beta 2865 2870 2868 2889 C1' DA P 4 beta 2885 2890 2888 2918 C1' DG D 1 beta 2914 2919 2917 2940 C1' DC D 2 beta 2936 2941 2939 3053 C1' UTP A 506 beta 3052 3058 3054 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2644 C2' DC T 1 2645 2642 2663 C2' DG T 2 2664 2661 2685 C2' DG T 3 2686 2683 2707 C2' DC T 4 2708 2705 2726 C2' DA T 5 2727 2724 2747 C2' DT T 6 2748 2745 2767 C2' DA T 7 2768 2765 2788 C2' DC T 8 2789 2786 2807 C2' DG T 9 2808 2805 2827 C2' DC P 1 2828 2825 2846 C2' DG P 2 2847 2844 2868 C2' DT P 3 2869 2866 2888 C2' DA P 4 2889 2886 2917 C2' DG D 1 2918 2915 2939 C2' DC D 2 2940 2937 3054 C2' UTP A 506 OK 3053 3056 3055 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2642 C3' DC T 1 OK 2640 2643 2644 2661 C3' DG T 2 OK 2659 2662 2663 2683 C3' DG T 3 OK 2681 2684 2685 2705 C3' DC T 4 OK 2703 2706 2707 2724 C3' DA T 5 OK 2722 2725 2726 2745 C3' DT T 6 OK 2743 2746 2747 2765 C3' DA T 7 OK 2763 2766 2767 2786 C3' DC T 8 OK 2784 2787 2788 2805 C3' DG T 9 OK 2803 2806 2807 2825 C3' DC P 1 OK 2823 2826 2827 2844 C3' DG P 2 OK 2842 2845 2846 2866 C3' DT P 3 OK 2864 2867 2868 2886 C3' DA P 4 OK 2884 2887 2888 2915 C3' DG D 1 OK 2913 2916 2917 2937 C3' DC D 2 OK 2935 2938 2939 3056 C3' UTP A 506 OK 3051 3057 3054 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2640 C4' DC T 1 OK 2642 2639 2641 2659 C4' DG T 2 OK 2661 2658 2660 2681 C4' DG T 3 OK 2683 2680 2682 2703 C4' DC T 4 OK 2705 2702 2704 2722 C4' DA T 5 OK 2724 2721 2723 2743 C4' DT T 6 OK 2745 2742 2744 2763 C4' DA T 7 OK 2765 2762 2764 2784 C4' DC T 8 OK 2786 2783 2785 2803 C4' DG T 9 OK 2805 2802 2804 2823 C4' DC P 1 OK 2825 2822 2824 2842 C4' DG P 2 OK 2844 2841 2843 2864 C4' DT P 3 OK 2866 2863 2865 2884 C4' DA P 4 OK 2886 2883 2885 2905 C4' U P 5 2904 2913 C4' DG D 1 OK 2915 2912 2914 2935 C4' DC D 2 OK 2937 2934 2936 3051 C4' UTP A 506 OK 3056 3050 3052 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2639 C5' DC T 1 2638 2640 2658 C5' DG T 2 2657 2659 2680 C5' DG T 3 2679 2681 2702 C5' DC T 4 2701 2703 2721 C5' DA T 5 2720 2722 2742 C5' DT T 6 2741 2743 2762 C5' DA T 7 2761 2763 2783 C5' DC T 8 2782 2784 2802 C5' DG T 9 2801 2803 2822 C5' DC P 1 2821 2823 2841 C5' DG P 2 2840 2842 2863 C5' DT P 3 2862 2864 2883 C5' DA P 4 2882 2884 2904 C5' U P 5 2903 2905 2912 C5' DG D 1 2911 2913 2934 C5' DC D 2 2933 2935 3050 C5' UTP A 506 3041 3051 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2654 P DG T 2 distorted distorted 2643 2655 2656 2657 2676 P DG T 3 distorted distorted 2662 2677 2678 2679 2698 P DC T 4 distorted distorted 2684 2699 2700 2701 2717 P DA T 5 distorted distorted 2706 2718 2719 2720 2738 P DT T 6 distorted distorted 2725 2739 2740 2741 2758 P DA T 7 distorted distorted 2746 2759 2760 2761 2779 P DC T 8 distorted distorted 2766 2780 2781 2782 2798 P DG T 9 distorted distorted 2787 2799 2800 2801 2837 P DG P 2 distorted distorted 2826 2838 2839 2840 2859 P DT P 3 distorted distorted 2845 2860 2861 2862 2879 P DA P 4 distorted distorted 2867 2880 2881 2882 2900 P U P 5 distorted distorted 2887 2901 2902 2903 2908 P DG D 1 OK OK 2909 2910 2911 2930 P DC D 2 distorted distorted 2916 2931 2932 2933 2949 P DC D 3 2938 2950 P DC D 3 2938 2987 P DG D 4 2988 P DG D 4 ---------------------------------------------------------------------------------