ID code: '5IIJ' 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' --------------------------------------------------------------------------------- 2401 C1' DG D 1 beta 2397 2402 2400 2423 C1' DC D 2 beta 2419 2424 2422 2442 C1' DC D 3 beta 2438 2443 2441 2461 C1' DG D 4 beta 2457 2462 2460 2481 C1' DC P 1 beta 2477 2482 2480 2500 C1' DA P 2 beta 2496 2501 2499 2521 C1' DG P 3 beta 2517 2522 2520 2543 C1' DT P 4 beta 2539 2544 2542 2563 C1' DA P 5 beta 2559 2564 2562 2582 C1' DOC P 6 beta 2586 2574 2583 2600 C1' DC T 1 beta 2596 2601 2599 2619 C1' DG T 2 beta 2615 2620 2618 2641 C1' DG T 3 beta 2637 2642 2640 2663 C1' DC T 4 beta 2659 2664 2662 2682 C1' 8OG T 5 beta 2678 2683 2681 2705 C1' DG T 6 beta 2701 2706 2704 2727 C1' DT T 7 beta 2723 2728 2726 2747 C1' DA T 8 beta 2743 2748 2746 2768 C1' DC T 9 beta 2764 2769 2767 2787 C1' DT T 10 beta 2783 2788 2786 2807 C1' DG T 11 beta 2803 2808 2806 2828 C1' DCT A 601 beta 2832 2820 2829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2400 C2' DG D 1 2401 2398 2422 C2' DC D 2 2423 2420 2441 C2' DC D 3 2442 2439 2460 C2' DG D 4 2461 2458 2480 C2' DC P 1 2481 2478 2499 C2' DA P 2 2500 2497 2520 C2' DG P 3 2521 2518 2542 C2' DT P 4 2543 2540 2562 C2' DA P 5 2563 2560 2583 C2' DOC P 6 2582 2584 2599 C2' DC T 1 2600 2597 2618 C2' DG T 2 2619 2616 2640 C2' DG T 3 2641 2638 2662 C2' DC T 4 2663 2660 2681 C2' 8OG T 5 2682 2679 2704 C2' DG T 6 2705 2702 2726 C2' DT T 7 2727 2724 2746 C2' DA T 8 2747 2744 2767 C2' DC T 9 2768 2765 2786 C2' DT T 10 2787 2784 2806 C2' DG T 11 2807 2804 2829 C2' DCT A 601 2828 2830 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2398 C3' DG D 1 OK 2396 2399 2400 2420 C3' DC D 2 OK 2418 2421 2422 2439 C3' DC D 3 OK 2437 2440 2441 2458 C3' DG D 4 OK 2456 2459 2460 2478 C3' DC P 1 OK 2476 2479 2480 2497 C3' DA P 2 OK 2495 2498 2499 2518 C3' DG P 3 OK 2516 2519 2520 2540 C3' DT P 4 OK 2538 2541 2542 2560 C3' DA P 5 OK 2558 2561 2562 2584 C3' DOC P 6 2585 2583 2597 C3' DC T 1 OK 2595 2598 2599 2616 C3' DG T 2 OK 2614 2617 2618 2638 C3' DG T 3 OK 2636 2639 2640 2660 C3' DC T 4 OK 2658 2661 2662 2679 C3' 8OG T 5 OK 2677 2680 2681 2702 C3' DG T 6 OK 2700 2703 2704 2724 C3' DT T 7 OK 2722 2725 2726 2744 C3' DA T 8 OK 2742 2745 2746 2765 C3' DC T 9 OK 2763 2766 2767 2784 C3' DT T 10 OK 2782 2785 2786 2804 C3' DG T 11 OK 2802 2805 2806 2830 C3' DCT A 601 2831 2829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2396 C4' DG D 1 OK 2398 2395 2397 2418 C4' DC D 2 OK 2420 2417 2419 2437 C4' DC D 3 OK 2439 2436 2438 2456 C4' DG D 4 OK 2458 2455 2457 2476 C4' DC P 1 OK 2478 2475 2477 2495 C4' DA P 2 OK 2497 2494 2496 2516 C4' DG P 3 OK 2518 2515 2517 2538 C4' DT P 4 OK 2540 2537 2539 2558 C4' DA P 5 OK 2560 2557 2559 2585 C4' DOC P 6 OK 2584 2587 2586 2595 C4' DC T 1 OK 2597 2594 2596 2614 C4' DG T 2 OK 2616 2613 2615 2636 C4' DG T 3 OK 2638 2635 2637 2658 C4' DC T 4 OK 2660 2657 2659 2677 C4' 8OG T 5 OK 2679 2676 2678 2700 C4' DG T 6 OK 2702 2699 2701 2722 C4' DT T 7 OK 2724 2721 2723 2742 C4' DA T 8 OK 2744 2741 2743 2763 C4' DC T 9 OK 2765 2762 2764 2782 C4' DT T 10 OK 2784 2781 2783 2802 C4' DG T 11 OK 2804 2801 2803 2831 C4' DCT A 601 OK 2830 2833 2832 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2395 C5' DG D 1 2394 2396 2417 C5' DC D 2 2416 2418 2436 C5' DC D 3 2435 2437 2455 C5' DG D 4 2454 2456 2475 C5' DC P 1 2474 2476 2494 C5' DA P 2 2493 2495 2515 C5' DG P 3 2514 2516 2537 C5' DT P 4 2536 2538 2557 C5' DA P 5 2556 2558 2587 C5' DOC P 6 2588 2585 2594 C5' DC T 1 2593 2595 2613 C5' DG T 2 2612 2614 2635 C5' DG T 3 2634 2636 2657 C5' DC T 4 2656 2658 2676 C5' 8OG T 5 2675 2677 2699 C5' DG T 6 2698 2700 2721 C5' DT T 7 2720 2722 2741 C5' DA T 8 2740 2742 2762 C5' DC T 9 2761 2763 2781 C5' DT T 10 2780 2782 2801 C5' DG T 11 2800 2802 2833 C5' DCT A 601 2834 2831 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2391 P DG D 1 OK OK 2392 2393 2394 2413 P DC D 2 distorted distorted 2399 2414 2415 2416 2432 P DC D 3 distorted distorted 2421 2433 2434 2435 2451 P DG D 4 distorted distorted 2440 2452 2453 2454 2490 P DA P 2 distorted distorted 2479 2491 2492 2493 2511 P DG P 3 distorted distorted 2498 2512 2513 2514 2533 P DT P 4 distorted distorted 2519 2534 2535 2536 2553 P DA P 5 distorted distorted 2541 2554 2555 2556 2589 P DOC P 6 distorted distorted 2561 2590 2591 2588 2609 P DG T 2 distorted distorted 2598 2610 2611 2612 2631 P DG T 3 distorted distorted 2617 2632 2633 2634 2653 P DC T 4 distorted distorted 2639 2654 2655 2656 2672 P 8OG T 5 distorted distorted 2661 2673 2674 2675 2695 P DG T 6 distorted distorted 2680 2696 2697 2698 2717 P DT T 7 distorted distorted 2703 2718 2719 2720 2737 P DA T 8 distorted distorted 2725 2738 2739 2740 2758 P DC T 9 distorted distorted 2745 2759 2760 2761 2777 P DT T 10 distorted distorted 2766 2778 2779 2780 2797 P DG T 11 distorted distorted 2785 2798 2799 2800 ---------------------------------------------------------------------------------