ID code: '3VAI' 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' --------------------------------------------------------------------------------- 2706 C1' DU P 3 beta 2702 2707 2705 2725 C1' DU P 4 beta 2721 2726 2724 2743 C1' BRU P 5 beta 2748 2734 2744 2764 C1' DU P 6 beta 2760 2765 2763 2783 C1' DC P 7 beta 2779 2784 2782 2800 C1' DU E 3 beta 2796 2801 2799 2819 C1' DU E 4 beta 2815 2820 2818 2837 C1' BRU E 5 beta 2842 2828 2838 2858 C1' DU E 6 beta 2854 2859 2857 2877 C1' DC E 7 beta 2873 2878 2876 2889 C1' DIO A 401 2892 2895 C1' DIO A 402 2898 2921 C1' DIO B 401 2924 2927 C1' DIO B 402 2930 2933 C1' DIO B 403 2936 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2705 C2' DU P 3 2706 2703 2724 C2' DU P 4 2725 2722 2744 C2' BRU P 5 2743 2745 2763 C2' DU P 6 2764 2761 2782 C2' DC P 7 2783 2780 2799 C2' DU E 3 2800 2797 2818 C2' DU E 4 2819 2816 2838 C2' BRU E 5 2837 2839 2857 C2' DU E 6 2858 2855 2876 C2' DC E 7 2877 2874 2890 C2' DIO A 401 2896 C2' DIO A 402 2922 C2' DIO B 401 2928 C2' DIO B 402 2934 C2' DIO B 403 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2703 C3' DU P 3 OK 2701 2704 2705 2722 C3' DU P 4 OK 2720 2723 2724 2745 C3' BRU P 5 OK 2746 2747 2744 2761 C3' DU P 6 OK 2759 2762 2763 2780 C3' DC P 7 OK 2778 2781 2782 2797 C3' DU E 3 OK 2795 2798 2799 2816 C3' DU E 4 OK 2814 2817 2818 2839 C3' BRU E 5 OK 2840 2841 2838 2855 C3' DU E 6 OK 2853 2856 2857 2874 C3' DC E 7 OK 2872 2875 2876 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2701 C4' DU P 3 OK 2703 2700 2702 2720 C4' DU P 4 OK 2722 2719 2721 2746 C4' BRU P 5 OK 2745 2749 2748 2759 C4' DU P 6 OK 2761 2758 2760 2778 C4' DC P 7 OK 2780 2777 2779 2795 C4' DU E 3 OK 2797 2794 2796 2814 C4' DU E 4 OK 2816 2813 2815 2840 C4' BRU E 5 OK 2839 2843 2842 2853 C4' DU E 6 OK 2855 2852 2854 2872 C4' DC E 7 OK 2874 2871 2873 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2700 C5' DU P 3 2699 2701 2719 C5' DU P 4 2718 2720 2749 C5' BRU P 5 2750 2746 2758 C5' DU P 6 2757 2759 2777 C5' DC P 7 2776 2778 2794 C5' DU E 3 2793 2795 2813 C5' DU E 4 2812 2814 2843 C5' BRU E 5 2844 2840 2852 C5' DU E 6 2851 2853 2871 C5' DC E 7 2870 2872 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2715 P DU P 4 distorted distorted 2704 2716 2717 2718 2751 P BRU P 5 distorted distorted 2723 2752 2753 2750 2754 P DU P 6 distorted distorted 2747 2755 2756 2757 2773 P DC P 7 distorted distorted 2762 2774 2775 2776 2809 P DU E 4 distorted distorted 2798 2810 2811 2812 2845 P BRU E 5 distorted distorted 2817 2846 2847 2844 2848 P DU E 6 distorted distorted 2841 2849 2850 2851 2867 P DC E 7 distorted distorted 2856 2868 2869 2870 ---------------------------------------------------------------------------------