ID code: '7ICJ' 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 2756 C1' C P 1 beta 2752 2757 2755 2775 C1' A P 2 beta 2771 2776 2774 2796 C1' G P 3 beta 2792 2797 2795 2818 C1' A P 4 beta 2814 2819 2817 2839 C1' T P 5 beta 2835 2840 2838 2859 C1' G P 6 beta 2855 2860 2858 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 2755 C2' C P 1 2756 2753 2774 C2' A P 2 2775 2772 2795 C2' G P 3 2796 2793 2817 C2' A P 4 2818 2815 2838 C2' T P 5 2839 2836 2858 C2' G P 6 2859 2856 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 2753 C3' C P 1 OK 2751 2754 2755 2772 C3' A P 2 OK 2770 2773 2774 2793 C3' G P 3 OK 2791 2794 2795 2815 C3' A P 4 OK 2813 2816 2817 2836 C3' T P 5 OK 2834 2837 2838 2856 C3' G P 6 OK 2854 2857 2858 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 2751 C4' C P 1 OK 2753 2750 2752 2770 C4' A P 2 OK 2772 2769 2771 2791 C4' G P 3 OK 2793 2790 2792 2813 C4' A P 4 OK 2815 2812 2814 2834 C4' T P 5 OK 2836 2833 2835 2854 C4' G P 6 OK 2856 2853 2855 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 2750 C5' C P 1 2749 2751 2769 C5' A P 2 2768 2770 2790 C5' G P 3 2789 2791 2812 C5' A P 4 2811 2813 2833 C5' T P 5 2832 2834 2853 C5' G P 6 2852 2854 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 2765 P A P 2 OK OK 2754 2766 2767 2768 2786 P G P 3 OK OK 2773 2787 2788 2789 2808 P A P 4 OK OK 2794 2809 2810 2811 2829 P T P 5 distorted distorted 2816 2830 2831 2832 2849 P G P 6 distorted distorted 2837 2850 2851 2852 ---------------------------------------------------------------------------------