ID code: '9ICK' 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' --------------------------------------------------------------------------------- 2634 C1' C T 2 beta 2630 2635 2633 2653 C1' A T 3 beta 2649 2654 2652 2674 C1' T T 4 beta 2670 2675 2673 2694 C1' C T 5 beta 2690 2695 2693 2713 C1' T T 6 beta 2709 2714 2712 2733 C1' G T 7 beta 2729 2734 2732 2761 C1' C P 1 beta 2757 2762 2760 2780 C1' A P 2 beta 2776 2781 2779 2801 C1' G P 3 beta 2797 2802 2800 2823 C1' A P 4 beta 2819 2824 2822 2844 C1' T P 5 beta 2840 2845 2843 2864 C1' G P 6 beta 2860 2865 2863 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2633 C2' C T 2 2634 2631 2652 C2' A T 3 2653 2650 2673 C2' T T 4 2674 2671 2693 C2' C T 5 2694 2691 2712 C2' T T 6 2713 2710 2732 C2' G T 7 2733 2730 2760 C2' C P 1 2761 2758 2779 C2' A P 2 2780 2777 2800 C2' G P 3 2801 2798 2822 C2' A P 4 2823 2820 2843 C2' T P 5 2844 2841 2863 C2' G P 6 2864 2861 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2631 C3' C T 2 OK 2629 2632 2633 2650 C3' A T 3 OK 2648 2651 2652 2671 C3' T T 4 OK 2669 2672 2673 2691 C3' C T 5 OK 2689 2692 2693 2710 C3' T T 6 OK 2708 2711 2712 2730 C3' G T 7 OK 2728 2731 2732 2758 C3' C P 1 OK 2756 2759 2760 2777 C3' A P 2 OK 2775 2778 2779 2798 C3' G P 3 OK 2796 2799 2800 2820 C3' A P 4 OK 2818 2821 2822 2841 C3' T P 5 OK 2839 2842 2843 2861 C3' G P 6 OK 2859 2862 2863 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2629 C4' C T 2 OK 2631 2628 2630 2648 C4' A T 3 OK 2650 2647 2649 2669 C4' T T 4 OK 2671 2668 2670 2689 C4' C T 5 OK 2691 2688 2690 2708 C4' T T 6 OK 2710 2707 2709 2728 C4' G T 7 OK 2730 2727 2729 2756 C4' C P 1 OK 2758 2755 2757 2775 C4' A P 2 OK 2777 2774 2776 2796 C4' G P 3 OK 2798 2795 2797 2818 C4' A P 4 OK 2820 2817 2819 2839 C4' T P 5 OK 2841 2838 2840 2859 C4' G P 6 OK 2861 2858 2860 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2628 C5' C T 2 2627 2629 2647 C5' A T 3 2646 2648 2668 C5' T T 4 2667 2669 2688 C5' C T 5 2687 2689 2707 C5' T T 6 2706 2708 2727 C5' G T 7 2726 2728 2755 C5' C P 1 2754 2756 2774 C5' A P 2 2773 2775 2795 C5' G P 3 2794 2796 2817 C5' A P 4 2816 2818 2838 C5' T P 5 2837 2839 2858 C5' G P 6 2857 2859 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2643 P A T 3 OK OK 2632 2644 2645 2646 2664 P T T 4 OK OK 2651 2665 2666 2667 2684 P C T 5 OK OK 2672 2685 2686 2687 2703 P T T 6 OK OK 2692 2704 2705 2706 2723 P G T 7 OK OK 2711 2724 2725 2726 2770 P A P 2 OK OK 2759 2771 2772 2773 2791 P G P 3 OK OK 2778 2792 2793 2794 2813 P A P 4 OK OK 2799 2814 2815 2816 2834 P T P 5 distorted distorted 2821 2835 2836 2837 2854 P G P 6 distorted distorted 2842 2855 2856 2857 ---------------------------------------------------------------------------------