ID code: '3HWT' 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' --------------------------------------------------------------------------------- 2419 C1' DC T 1 beta 2415 2420 2418 2438 C1' DG T 2 beta 2434 2439 2437 2460 C1' DG T 3 beta 2456 2461 2459 2482 C1' DC T 4 beta 2478 2483 2481 2501 C1' DA T 5 beta 2497 2502 2500 2522 C1' DA T 6 beta 2518 2523 2521 2543 C1' DA T 7 beta 2539 2544 2542 2564 C1' DT T 8 beta 2560 2565 2563 2584 C1' DA T 9 beta 2580 2585 2583 2605 C1' DC T 10 beta 2601 2606 2604 2624 C1' DT T 11 beta 2620 2625 2623 2644 C1' DG T 12 beta 2640 2645 2643 2664 C1' DC P 1 beta 2660 2665 2663 2683 C1' DA P 2 beta 2679 2684 2682 2704 C1' DG P 3 beta 2700 2705 2703 2726 C1' DT P 4 beta 2722 2727 2725 2746 C1' DA P 5 beta 2742 2747 2745 2774 C1' 2DT P 6 beta 2773 2761 2770 2788 C1' DG D 1 beta 2784 2789 2787 2810 C1' DC D 2 beta 2806 2811 2809 2829 C1' DC D 3 beta 2825 2830 2828 2848 C1' DG D 4 beta 2844 2849 2847 2868 C1' D3T A 576 beta 2867 2869 2878 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2418 C2' DC T 1 2419 2416 2437 C2' DG T 2 2438 2435 2459 C2' DG T 3 2460 2457 2481 C2' DC T 4 2482 2479 2500 C2' DA T 5 2501 2498 2521 C2' DA T 6 2522 2519 2542 C2' DA T 7 2543 2540 2563 C2' DT T 8 2564 2561 2583 C2' DA T 9 2584 2581 2604 C2' DC T 10 2605 2602 2623 C2' DT T 11 2624 2621 2643 C2' DG T 12 2644 2641 2663 C2' DC P 1 2664 2661 2682 C2' DA P 2 2683 2680 2703 C2' DG P 3 2704 2701 2725 C2' DT P 4 2726 2723 2745 C2' DA P 5 2746 2743 2770 C2' 2DT P 6 2774 2775 2787 C2' DG D 1 2788 2785 2809 C2' DC D 2 2810 2807 2828 C2' DC D 3 2829 2826 2847 C2' DG D 4 2848 2845 2878 C2' D3T A 576 2868 2879 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2416 C3' DC T 1 OK 2414 2417 2418 2435 C3' DG T 2 OK 2433 2436 2437 2457 C3' DG T 3 OK 2455 2458 2459 2479 C3' DC T 4 OK 2477 2480 2481 2498 C3' DA T 5 OK 2496 2499 2500 2519 C3' DA T 6 OK 2517 2520 2521 2540 C3' DA T 7 OK 2538 2541 2542 2561 C3' DT T 8 OK 2559 2562 2563 2581 C3' DA T 9 OK 2579 2582 2583 2602 C3' DC T 10 OK 2600 2603 2604 2621 C3' DT T 11 OK 2619 2622 2623 2641 C3' DG T 12 OK 2639 2642 2643 2661 C3' DC P 1 OK 2659 2662 2663 2680 C3' DA P 2 OK 2678 2681 2682 2701 C3' DG P 3 OK 2699 2702 2703 2723 C3' DT P 4 OK 2721 2724 2725 2743 C3' DA P 5 OK 2741 2744 2745 2775 C3' 2DT P 6 2772 2770 2785 C3' DG D 1 OK 2783 2786 2787 2807 C3' DC D 2 OK 2805 2808 2809 2826 C3' DC D 3 OK 2824 2827 2828 2845 C3' DG D 4 OK 2843 2846 2847 2879 C3' D3T A 576 2866 2878 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2414 C4' DC T 1 OK 2416 2413 2415 2433 C4' DG T 2 OK 2435 2432 2434 2455 C4' DG T 3 OK 2457 2454 2456 2477 C4' DC T 4 OK 2479 2476 2478 2496 C4' DA T 5 OK 2498 2495 2497 2517 C4' DA T 6 OK 2519 2516 2518 2538 C4' DA T 7 OK 2540 2537 2539 2559 C4' DT T 8 OK 2561 2558 2560 2579 C4' DA T 9 OK 2581 2578 2580 2600 C4' DC T 10 OK 2602 2599 2601 2619 C4' DT T 11 OK 2621 2618 2620 2639 C4' DG T 12 OK 2641 2638 2640 2659 C4' DC P 1 OK 2661 2658 2660 2678 C4' DA P 2 OK 2680 2677 2679 2699 C4' DG P 3 OK 2701 2698 2700 2721 C4' DT P 4 OK 2723 2720 2722 2741 C4' DA P 5 OK 2743 2740 2742 2772 C4' 2DT P 6 OK 2775 2771 2773 2783 C4' DG D 1 OK 2785 2782 2784 2805 C4' DC D 2 OK 2807 2804 2806 2824 C4' DC D 3 OK 2826 2823 2825 2843 C4' DG D 4 OK 2845 2842 2844 2866 C4' D3T A 576 OK 2879 2865 2867 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2413 C5' DC T 1 2412 2414 2432 C5' DG T 2 2431 2433 2454 C5' DG T 3 2453 2455 2476 C5' DC T 4 2475 2477 2495 C5' DA T 5 2494 2496 2516 C5' DA T 6 2515 2517 2537 C5' DA T 7 2536 2538 2558 C5' DT T 8 2557 2559 2578 C5' DA T 9 2577 2579 2599 C5' DC T 10 2598 2600 2618 C5' DT T 11 2617 2619 2638 C5' DG T 12 2637 2639 2658 C5' DC P 1 2657 2659 2677 C5' DA P 2 2676 2678 2698 C5' DG P 3 2697 2699 2720 C5' DT P 4 2719 2721 2740 C5' DA P 5 2739 2741 2771 C5' 2DT P 6 2760 2772 2782 C5' DG D 1 2781 2783 2804 C5' DC D 2 2803 2805 2823 C5' DC D 3 2822 2824 2842 C5' DG D 4 2841 2843 2865 C5' D3T A 576 2864 2866 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2428 P DG T 2 distorted distorted 2417 2429 2430 2431 2450 P DG T 3 distorted distorted 2436 2451 2452 2453 2472 P DC T 4 distorted distorted 2458 2473 2474 2475 2491 P DA T 5 distorted distorted 2480 2492 2493 2494 2512 P DA T 6 distorted distorted 2499 2513 2514 2515 2533 P DA T 7 distorted distorted 2520 2534 2535 2536 2554 P DT T 8 distorted distorted 2541 2555 2556 2557 2574 P DA T 9 distorted distorted 2562 2575 2576 2577 2595 P DC T 10 distorted distorted 2582 2596 2597 2598 2614 P DT T 11 distorted distorted 2603 2615 2616 2617 2634 P DG T 12 distorted distorted 2622 2635 2636 2637 2673 P DA P 2 distorted distorted 2662 2674 2675 2676 2694 P DG P 3 distorted distorted 2681 2695 2696 2697 2716 P DT P 4 distorted distorted 2702 2717 2718 2719 2736 P DA P 5 distorted distorted 2724 2737 2738 2739 2757 P 2DT P 6 distorted distorted 2744 2758 2759 2760 2778 P DG D 1 OK OK 2779 2780 2781 2800 P DC D 2 distorted distorted 2786 2801 2802 2803 2819 P DC D 3 distorted distorted 2808 2820 2821 2822 2838 P DG D 4 distorted distorted 2827 2839 2840 2841 ---------------------------------------------------------------------------------