ID code: '7ICT' 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' --------------------------------------------------------------------------------- 2635 C1' C T 2 beta 2631 2636 2634 2654 C1' A T 3 beta 2650 2655 2653 2675 C1' T T 4 beta 2671 2676 2674 2695 C1' C T 5 beta 2691 2696 2694 2714 C1' T T 6 beta 2710 2715 2713 2734 C1' G T 7 beta 2730 2735 2733 2762 C1' C P 1 beta 2758 2763 2761 2781 C1' A P 2 beta 2777 2782 2780 2802 C1' G P 3 beta 2798 2803 2801 2824 C1' A P 4 beta 2820 2825 2823 2845 C1' T P 5 beta 2841 2846 2844 2865 C1' G P 6 beta 2861 2866 2864 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2634 C2' C T 2 2635 2632 2653 C2' A T 3 2654 2651 2674 C2' T T 4 2675 2672 2694 C2' C T 5 2695 2692 2713 C2' T T 6 2714 2711 2733 C2' G T 7 2734 2731 2761 C2' C P 1 2762 2759 2780 C2' A P 2 2781 2778 2801 C2' G P 3 2802 2799 2823 C2' A P 4 2824 2821 2844 C2' T P 5 2845 2842 2864 C2' G P 6 2865 2862 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2632 C3' C T 2 OK 2630 2633 2634 2651 C3' A T 3 OK 2649 2652 2653 2672 C3' T T 4 OK 2670 2673 2674 2692 C3' C T 5 OK 2690 2693 2694 2711 C3' T T 6 OK 2709 2712 2713 2731 C3' G T 7 OK 2729 2732 2733 2759 C3' C P 1 OK 2757 2760 2761 2778 C3' A P 2 OK 2776 2779 2780 2799 C3' G P 3 OK 2797 2800 2801 2821 C3' A P 4 OK 2819 2822 2823 2842 C3' T P 5 OK 2840 2843 2844 2862 C3' G P 6 OK 2860 2863 2864 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2630 C4' C T 2 OK 2632 2629 2631 2649 C4' A T 3 OK 2651 2648 2650 2670 C4' T T 4 OK 2672 2669 2671 2690 C4' C T 5 OK 2692 2689 2691 2709 C4' T T 6 OK 2711 2708 2710 2729 C4' G T 7 OK 2731 2728 2730 2757 C4' C P 1 OK 2759 2756 2758 2776 C4' A P 2 OK 2778 2775 2777 2797 C4' G P 3 OK 2799 2796 2798 2819 C4' A P 4 OK 2821 2818 2820 2840 C4' T P 5 OK 2842 2839 2841 2860 C4' G P 6 OK 2862 2859 2861 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2629 C5' C T 2 2628 2630 2648 C5' A T 3 2647 2649 2669 C5' T T 4 2668 2670 2689 C5' C T 5 2688 2690 2708 C5' T T 6 2707 2709 2728 C5' G T 7 2727 2729 2756 C5' C P 1 2755 2757 2775 C5' A P 2 2774 2776 2796 C5' G P 3 2795 2797 2818 C5' A P 4 2817 2819 2839 C5' T P 5 2838 2840 2859 C5' G P 6 2858 2860 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2644 P A T 3 OK OK 2633 2645 2646 2647 2665 P T T 4 OK OK 2652 2666 2667 2668 2685 P C T 5 OK OK 2673 2686 2687 2688 2704 P T T 6 OK OK 2693 2705 2706 2707 2724 P G T 7 OK OK 2712 2725 2726 2727 2771 P A P 2 OK OK 2760 2772 2773 2774 2792 P G P 3 OK OK 2779 2793 2794 2795 2814 P A P 4 OK OK 2800 2815 2816 2817 2835 P T P 5 distorted distorted 2822 2836 2837 2838 2855 P G P 6 distorted distorted 2843 2856 2857 2858 ---------------------------------------------------------------------------------