ID code: '4XUS' 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' --------------------------------------------------------------------------------- 2504 C1' DG D 1 beta 2500 2505 2503 2526 C1' DC D 2 beta 2522 2527 2525 2545 C1' DC D 3 beta 2541 2546 2544 2564 C1' DG D 4 beta 2560 2565 2563 2584 C1' DC P 1 beta 2580 2585 2583 2603 C1' DA P 2 beta 2599 2604 2602 2624 C1' DG P 3 beta 2620 2625 2623 2646 C1' DT P 4 beta 2642 2647 2645 2666 C1' DA P 5 beta 2662 2667 2665 2685 C1' DC T 1 beta 2681 2686 2684 2704 C1' DG T 2 beta 2700 2705 2703 2726 C1' DG T 3 beta 2722 2727 2725 2748 C1' DC T 4 beta 2744 2749 2747 2767 C1' DA T 5 beta 2763 2768 2766 2788 C1' DG T 6 beta 2784 2789 2787 2810 C1' DT T 7 beta 2806 2811 2809 2830 C1' DA T 8 beta 2826 2831 2829 2851 C1' DC T 9 beta 2847 2852 2850 2870 C1' DT T 10 beta 2866 2871 2869 2890 C1' DG T 11 beta 2886 2891 2889 2922 C1' TTP A 601 beta 2918 2923 2921 2942 C1' DOC P 101 beta 2946 2934 2943 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2503 C2' DG D 1 2504 2501 2525 C2' DC D 2 2526 2523 2544 C2' DC D 3 2545 2542 2563 C2' DG D 4 2564 2561 2583 C2' DC P 1 2584 2581 2602 C2' DA P 2 2603 2600 2623 C2' DG P 3 2624 2621 2645 C2' DT P 4 2646 2643 2665 C2' DA P 5 2666 2663 2684 C2' DC T 1 2685 2682 2703 C2' DG T 2 2704 2701 2725 C2' DG T 3 2726 2723 2747 C2' DC T 4 2748 2745 2766 C2' DA T 5 2767 2764 2787 C2' DG T 6 2788 2785 2809 C2' DT T 7 2810 2807 2829 C2' DA T 8 2830 2827 2850 C2' DC T 9 2851 2848 2869 C2' DT T 10 2870 2867 2889 C2' DG T 11 2890 2887 2921 C2' TTP A 601 2922 2919 2943 C2' DOC P 101 2942 2944 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2501 C3' DG D 1 OK 2499 2502 2503 2523 C3' DC D 2 OK 2521 2524 2525 2542 C3' DC D 3 OK 2540 2543 2544 2561 C3' DG D 4 OK 2559 2562 2563 2581 C3' DC P 1 OK 2579 2582 2583 2600 C3' DA P 2 OK 2598 2601 2602 2621 C3' DG P 3 OK 2619 2622 2623 2643 C3' DT P 4 OK 2641 2644 2645 2663 C3' DA P 5 OK 2661 2664 2665 2682 C3' DC T 1 OK 2680 2683 2684 2701 C3' DG T 2 OK 2699 2702 2703 2723 C3' DG T 3 OK 2721 2724 2725 2745 C3' DC T 4 OK 2743 2746 2747 2764 C3' DA T 5 OK 2762 2765 2766 2785 C3' DG T 6 OK 2783 2786 2787 2807 C3' DT T 7 OK 2805 2808 2809 2827 C3' DA T 8 OK 2825 2828 2829 2848 C3' DC T 9 OK 2846 2849 2850 2867 C3' DT T 10 OK 2865 2868 2869 2887 C3' DG T 11 OK 2885 2888 2889 2919 C3' TTP A 601 OK 2917 2920 2921 2944 C3' DOC P 101 2945 2943 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2499 C4' DG D 1 OK 2501 2498 2500 2521 C4' DC D 2 OK 2523 2520 2522 2540 C4' DC D 3 OK 2542 2539 2541 2559 C4' DG D 4 OK 2561 2558 2560 2579 C4' DC P 1 OK 2581 2578 2580 2598 C4' DA P 2 OK 2600 2597 2599 2619 C4' DG P 3 OK 2621 2618 2620 2641 C4' DT P 4 OK 2643 2640 2642 2661 C4' DA P 5 OK 2663 2660 2662 2680 C4' DC T 1 OK 2682 2679 2681 2699 C4' DG T 2 OK 2701 2698 2700 2721 C4' DG T 3 OK 2723 2720 2722 2743 C4' DC T 4 OK 2745 2742 2744 2762 C4' DA T 5 OK 2764 2761 2763 2783 C4' DG T 6 OK 2785 2782 2784 2805 C4' DT T 7 OK 2807 2804 2806 2825 C4' DA T 8 OK 2827 2824 2826 2846 C4' DC T 9 OK 2848 2845 2847 2865 C4' DT T 10 OK 2867 2864 2866 2885 C4' DG T 11 OK 2887 2884 2886 2917 C4' TTP A 601 OK 2919 2916 2918 2945 C4' DOC P 101 OK 2944 2947 2946 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2498 C5' DG D 1 2497 2499 2520 C5' DC D 2 2519 2521 2539 C5' DC D 3 2538 2540 2558 C5' DG D 4 2557 2559 2578 C5' DC P 1 2577 2579 2597 C5' DA P 2 2596 2598 2618 C5' DG P 3 2617 2619 2640 C5' DT P 4 2639 2641 2660 C5' DA P 5 2659 2661 2679 C5' DC T 1 2678 2680 2698 C5' DG T 2 2697 2699 2720 C5' DG T 3 2719 2721 2742 C5' DC T 4 2741 2743 2761 C5' DA T 5 2760 2762 2782 C5' DG T 6 2781 2783 2804 C5' DT T 7 2803 2805 2824 C5' DA T 8 2823 2825 2845 C5' DC T 9 2844 2846 2864 C5' DT T 10 2863 2865 2884 C5' DG T 11 2883 2885 2916 C5' TTP A 601 2915 2917 2947 C5' DOC P 101 2948 2945 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2494 P DG D 1 distorted distorted 2495 2496 2497 2516 P DC D 2 distorted distorted 2502 2517 2518 2519 2535 P DC D 3 distorted distorted 2524 2536 2537 2538 2554 P DG D 4 distorted distorted 2543 2555 2556 2557 2593 P DA P 2 distorted distorted 2582 2594 2595 2596 2614 P DG P 3 distorted distorted 2601 2615 2616 2617 2636 P DT P 4 distorted distorted 2622 2637 2638 2639 2656 P DA P 5 distorted distorted 2644 2657 2658 2659 2694 P DG T 2 distorted distorted 2683 2695 2696 2697 2716 P DG T 3 distorted distorted 2702 2717 2718 2719 2738 P DC T 4 distorted distorted 2724 2739 2740 2741 2757 P DA T 5 distorted distorted 2746 2758 2759 2760 2778 P DG T 6 distorted distorted 2765 2779 2780 2781 2800 P DT T 7 distorted distorted 2786 2801 2802 2803 2820 P DA T 8 distorted distorted 2808 2821 2822 2823 2841 P DC T 9 distorted distorted 2828 2842 2843 2844 2860 P DT T 10 distorted distorted 2849 2861 2862 2863 2880 P DG T 11 distorted distorted 2868 2881 2882 2883 2949 P DOC P 101 OK OK 2664 2950 2951 2948 ---------------------------------------------------------------------------------