ID code: '5VZE' 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' --------------------------------------------------------------------------------- 2677 C1' DC T 1 beta 2673 2678 2676 2696 C1' DG T 2 beta 2692 2697 2695 2718 C1' DG T 3 beta 2714 2719 2717 2740 C1' DC T 4 beta 2736 2741 2739 2759 C1' DA T 5 beta 2755 2760 2758 2780 C1' DT T 6 beta 2776 2781 2779 2800 C1' DA T 7 beta 2796 2801 2799 2821 C1' DC T 8 beta 2817 2822 2820 2840 C1' DG T 9 beta 2836 2841 2839 2860 C1' DC P 1 beta 2856 2861 2859 2879 C1' DG P 2 beta 2875 2880 2878 2901 C1' DT P 3 beta 2897 2902 2900 2921 C1' DA P 4 beta 2917 2922 2920 2950 C1' DG D 1 beta 2946 2951 2949 2972 C1' DC D 2 beta 2968 2973 2971 3084 C1' UTP A 505 beta 3083 3089 3085 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2676 C2' DC T 1 2677 2674 2695 C2' DG T 2 2696 2693 2717 C2' DG T 3 2718 2715 2739 C2' DC T 4 2740 2737 2758 C2' DA T 5 2759 2756 2779 C2' DT T 6 2780 2777 2799 C2' DA T 7 2800 2797 2820 C2' DC T 8 2821 2818 2839 C2' DG T 9 2840 2837 2859 C2' DC P 1 2860 2857 2878 C2' DG P 2 2879 2876 2900 C2' DT P 3 2901 2898 2920 C2' DA P 4 2921 2918 2949 C2' DG D 1 2950 2947 2971 C2' DC D 2 2972 2969 3085 C2' UTP A 505 OK 3084 3087 3086 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2674 C3' DC T 1 OK 2672 2675 2676 2693 C3' DG T 2 OK 2691 2694 2695 2715 C3' DG T 3 OK 2713 2716 2717 2737 C3' DC T 4 OK 2735 2738 2739 2756 C3' DA T 5 OK 2754 2757 2758 2777 C3' DT T 6 OK 2775 2778 2779 2797 C3' DA T 7 OK 2795 2798 2799 2818 C3' DC T 8 OK 2816 2819 2820 2837 C3' DG T 9 OK 2835 2838 2839 2857 C3' DC P 1 OK 2855 2858 2859 2876 C3' DG P 2 OK 2874 2877 2878 2898 C3' DT P 3 OK 2896 2899 2900 2918 C3' DA P 4 OK 2916 2919 2920 2947 C3' DG D 1 OK 2945 2948 2949 2969 C3' DC D 2 OK 2967 2970 2971 3087 C3' UTP A 505 OK 3082 3088 3085 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2672 C4' DC T 1 OK 2674 2671 2673 2691 C4' DG T 2 OK 2693 2690 2692 2713 C4' DG T 3 OK 2715 2712 2714 2735 C4' DC T 4 OK 2737 2734 2736 2754 C4' DA T 5 OK 2756 2753 2755 2775 C4' DT T 6 OK 2777 2774 2776 2795 C4' DA T 7 OK 2797 2794 2796 2816 C4' DC T 8 OK 2818 2815 2817 2835 C4' DG T 9 OK 2837 2834 2836 2855 C4' DC P 1 OK 2857 2854 2856 2874 C4' DG P 2 OK 2876 2873 2875 2896 C4' DT P 3 OK 2898 2895 2897 2916 C4' DA P 4 OK 2918 2915 2917 2945 C4' DG D 1 OK 2947 2944 2946 2967 C4' DC D 2 OK 2969 2966 2968 3082 C4' UTP A 505 OK 3087 3081 3083 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2671 C5' DC T 1 2670 2672 2690 C5' DG T 2 2689 2691 2712 C5' DG T 3 2711 2713 2734 C5' DC T 4 2733 2735 2753 C5' DA T 5 2752 2754 2774 C5' DT T 6 2773 2775 2794 C5' DA T 7 2793 2795 2815 C5' DC T 8 2814 2816 2834 C5' DG T 9 2833 2835 2854 C5' DC P 1 2853 2855 2873 C5' DG P 2 2872 2874 2895 C5' DT P 3 2894 2896 2915 C5' DA P 4 2914 2916 2944 C5' DG D 1 2943 2945 2966 C5' DC D 2 2965 2967 3081 C5' UTP A 505 3072 3082 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2686 P DG T 2 distorted distorted 2675 2687 2688 2689 2708 P DG T 3 distorted distorted 2694 2709 2710 2711 2730 P DC T 4 distorted distorted 2716 2731 2732 2733 2749 P DA T 5 distorted distorted 2738 2750 2751 2752 2770 P DT T 6 distorted distorted 2757 2771 2772 2773 2790 P DA T 7 distorted distorted 2778 2791 2792 2793 2811 P DC T 8 distorted distorted 2798 2812 2813 2814 2830 P DG T 9 distorted distorted 2819 2831 2832 2833 2869 P DG P 2 distorted distorted 2858 2870 2871 2872 2891 P DT P 3 distorted distorted 2877 2892 2893 2894 2911 P DA P 4 distorted distorted 2899 2912 2913 2914 2932 P U P 5 2919 2940 P DG D 1 OK OK 2941 2942 2943 2962 P DC D 2 distorted distorted 2948 2963 2964 2965 2981 P DC D 3 2970 2982 P DC D 3 2970 3019 P DG D 4 3020 P DG D 4 ---------------------------------------------------------------------------------