ID code: '3VAF' 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' --------------------------------------------------------------------------------- 2692 C1' DU P 2 beta 2688 2693 2691 2711 C1' DU P 3 beta 2707 2712 2710 2729 C1' BRU P 4 beta 2734 2720 2730 2749 C1' BRU P 5 beta 2754 2740 2750 2770 C1' DU P 6 beta 2766 2771 2769 2789 C1' DU P 7 beta 2785 2790 2788 2806 C1' DU E 2 beta 2802 2807 2805 2825 C1' DU E 3 beta 2821 2826 2824 2843 C1' BRU E 4 beta 2848 2834 2844 2863 C1' BRU E 5 beta 2868 2854 2864 2884 C1' DU E 6 beta 2880 2885 2883 2903 C1' DU E 7 beta 2899 2904 2902 2915 C1' DIO A 401 2918 2921 C1' DIO A 402 2924 2970 C1' DIO B 402 2973 2976 C1' DIO B 403 2979 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2691 C2' DU P 2 2692 2689 2710 C2' DU P 3 2711 2708 2730 C2' BRU P 4 2729 2731 2750 C2' BRU P 5 2749 2751 2769 C2' DU P 6 2770 2767 2788 C2' DU P 7 2789 2786 2805 C2' DU E 2 2806 2803 2824 C2' DU E 3 2825 2822 2844 C2' BRU E 4 2843 2845 2864 C2' BRU E 5 2863 2865 2883 C2' DU E 6 2884 2881 2902 C2' DU E 7 2903 2900 2916 C2' DIO A 401 2922 C2' DIO A 402 2971 C2' DIO B 402 2977 C2' DIO B 403 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2689 C3' DU P 2 OK 2687 2690 2691 2708 C3' DU P 3 OK 2706 2709 2710 2731 C3' BRU P 4 OK 2732 2733 2730 2751 C3' BRU P 5 OK 2752 2753 2750 2767 C3' DU P 6 OK 2765 2768 2769 2786 C3' DU P 7 OK 2784 2787 2788 2803 C3' DU E 2 OK 2801 2804 2805 2822 C3' DU E 3 OK 2820 2823 2824 2845 C3' BRU E 4 OK 2846 2847 2844 2865 C3' BRU E 5 OK 2866 2867 2864 2881 C3' DU E 6 OK 2879 2882 2883 2900 C3' DU E 7 OK 2898 2901 2902 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2687 C4' DU P 2 OK 2689 2686 2688 2706 C4' DU P 3 OK 2708 2705 2707 2732 C4' BRU P 4 OK 2731 2735 2734 2752 C4' BRU P 5 OK 2751 2755 2754 2765 C4' DU P 6 OK 2767 2764 2766 2784 C4' DU P 7 OK 2786 2783 2785 2801 C4' DU E 2 OK 2803 2800 2802 2820 C4' DU E 3 OK 2822 2819 2821 2846 C4' BRU E 4 OK 2845 2849 2848 2866 C4' BRU E 5 OK 2865 2869 2868 2879 C4' DU E 6 OK 2881 2878 2880 2898 C4' DU E 7 OK 2900 2897 2899 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2686 C5' DU P 2 2685 2687 2705 C5' DU P 3 2704 2706 2735 C5' BRU P 4 2736 2732 2755 C5' BRU P 5 2756 2752 2764 C5' DU P 6 2763 2765 2783 C5' DU P 7 2782 2784 2800 C5' DU E 2 2799 2801 2819 C5' DU E 3 2818 2820 2849 C5' BRU E 4 2850 2846 2869 C5' BRU E 5 2870 2866 2878 C5' DU E 6 2877 2879 2897 C5' DU E 7 2896 2898 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2701 P DU P 3 distorted distorted 2690 2702 2703 2704 2737 P BRU P 4 distorted distorted 2709 2738 2739 2736 2757 P BRU P 5 distorted distorted 2733 2758 2759 2756 2760 P DU P 6 distorted distorted 2753 2761 2762 2763 2779 P DU P 7 distorted distorted 2768 2780 2781 2782 2815 P DU E 3 distorted distorted 2804 2816 2817 2818 2851 P BRU E 4 distorted distorted 2823 2852 2853 2850 2871 P BRU E 5 distorted distorted 2847 2872 2873 2870 2874 P DU E 6 distorted distorted 2867 2875 2876 2877 2893 P DU E 7 distorted distorted 2882 2894 2895 2896 ---------------------------------------------------------------------------------