ID code: '5VZ8' 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' --------------------------------------------------------------------------------- 2674 C1' DC T 1 beta 2670 2675 2673 2693 C1' DG T 2 beta 2689 2694 2692 2715 C1' DG T 3 beta 2711 2716 2714 2737 C1' DC T 4 beta 2733 2738 2736 2756 C1' DA T 5 beta 2752 2757 2755 2777 C1' DT T 6 beta 2773 2778 2776 2797 C1' DA T 7 beta 2793 2798 2796 2818 C1' DC T 8 beta 2814 2819 2817 2837 C1' DG T 9 beta 2833 2838 2836 2857 C1' DC P 1 beta 2853 2858 2856 2876 C1' DG P 2 beta 2872 2877 2875 2898 C1' DT P 3 beta 2894 2899 2897 2918 C1' DA P 4 beta 2914 2919 2917 2946 C1' DG D 1 beta 2942 2947 2945 2968 C1' DC D 2 beta 2964 2969 2967 3079 C1' UTP A 504 beta 3078 3084 3080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2673 C2' DC T 1 2674 2671 2692 C2' DG T 2 2693 2690 2714 C2' DG T 3 2715 2712 2736 C2' DC T 4 2737 2734 2755 C2' DA T 5 2756 2753 2776 C2' DT T 6 2777 2774 2796 C2' DA T 7 2797 2794 2817 C2' DC T 8 2818 2815 2836 C2' DG T 9 2837 2834 2856 C2' DC P 1 2857 2854 2875 C2' DG P 2 2876 2873 2897 C2' DT P 3 2898 2895 2917 C2' DA P 4 2918 2915 2945 C2' DG D 1 2946 2943 2967 C2' DC D 2 2968 2965 3080 C2' UTP A 504 OK 3079 3082 3081 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2671 C3' DC T 1 OK 2669 2672 2673 2690 C3' DG T 2 OK 2688 2691 2692 2712 C3' DG T 3 OK 2710 2713 2714 2734 C3' DC T 4 OK 2732 2735 2736 2753 C3' DA T 5 OK 2751 2754 2755 2774 C3' DT T 6 OK 2772 2775 2776 2794 C3' DA T 7 OK 2792 2795 2796 2815 C3' DC T 8 OK 2813 2816 2817 2834 C3' DG T 9 OK 2832 2835 2836 2854 C3' DC P 1 OK 2852 2855 2856 2873 C3' DG P 2 OK 2871 2874 2875 2895 C3' DT P 3 OK 2893 2896 2897 2915 C3' DA P 4 OK 2913 2916 2917 2943 C3' DG D 1 OK 2941 2944 2945 2965 C3' DC D 2 OK 2963 2966 2967 3082 C3' UTP A 504 OK 3077 3083 3080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2669 C4' DC T 1 OK 2671 2668 2670 2688 C4' DG T 2 OK 2690 2687 2689 2710 C4' DG T 3 OK 2712 2709 2711 2732 C4' DC T 4 OK 2734 2731 2733 2751 C4' DA T 5 OK 2753 2750 2752 2772 C4' DT T 6 OK 2774 2771 2773 2792 C4' DA T 7 OK 2794 2791 2793 2813 C4' DC T 8 OK 2815 2812 2814 2832 C4' DG T 9 OK 2834 2831 2833 2852 C4' DC P 1 OK 2854 2851 2853 2871 C4' DG P 2 OK 2873 2870 2872 2893 C4' DT P 3 OK 2895 2892 2894 2913 C4' DA P 4 OK 2915 2912 2914 2941 C4' DG D 1 OK 2943 2940 2942 2963 C4' DC D 2 OK 2965 2962 2964 3077 C4' UTP A 504 OK 3082 3076 3078 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2668 C5' DC T 1 2667 2669 2687 C5' DG T 2 2686 2688 2709 C5' DG T 3 2708 2710 2731 C5' DC T 4 2730 2732 2750 C5' DA T 5 2749 2751 2771 C5' DT T 6 2770 2772 2791 C5' DA T 7 2790 2792 2812 C5' DC T 8 2811 2813 2831 C5' DG T 9 2830 2832 2851 C5' DC P 1 2850 2852 2870 C5' DG P 2 2869 2871 2892 C5' DT P 3 2891 2893 2912 C5' DA P 4 2911 2913 2933 C5' U P 5 2932 2940 C5' DG D 1 2939 2941 2962 C5' DC D 2 2961 2963 3076 C5' UTP A 504 3067 3077 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2683 P DG T 2 distorted distorted 2672 2684 2685 2686 2705 P DG T 3 distorted distorted 2691 2706 2707 2708 2727 P DC T 4 distorted distorted 2713 2728 2729 2730 2746 P DA T 5 distorted distorted 2735 2747 2748 2749 2767 P DT T 6 distorted distorted 2754 2768 2769 2770 2787 P DA T 7 distorted distorted 2775 2788 2789 2790 2808 P DC T 8 distorted distorted 2795 2809 2810 2811 2827 P DG T 9 distorted distorted 2816 2828 2829 2830 2866 P DG P 2 distorted distorted 2855 2867 2868 2869 2888 P DT P 3 distorted distorted 2874 2889 2890 2891 2908 P DA P 4 distorted distorted 2896 2909 2910 2911 2929 P U P 5 distorted distorted 2916 2930 2931 2932 2936 P DG D 1 OK OK 2937 2938 2939 2958 P DC D 2 distorted distorted 2944 2959 2960 2961 2977 P DC D 3 2966 2978 P DC D 3 2966 3015 P DG D 4 3016 P DG D 4 ---------------------------------------------------------------------------------