ID code: '4FO6' 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' --------------------------------------------------------------------------------- 2399 C1' DC T 1 beta 2395 2400 2398 2418 C1' DG T 2 beta 2414 2419 2417 2440 C1' DG T 3 beta 2436 2441 2439 2462 C1' DC T 4 beta 2458 2463 2461 2481 C1' DT T 5 beta 2477 2482 2480 2501 C1' DG T 6 beta 2497 2502 2500 2523 C1' DT T 7 beta 2519 2524 2522 2543 C1' DA T 8 beta 2539 2544 2542 2564 C1' DC T 9 beta 2560 2565 2563 2583 C1' DT T 10 beta 2579 2584 2582 2603 C1' DG T 11 beta 2599 2604 2602 2623 C1' DC P 1 beta 2619 2624 2622 2642 C1' DA P 2 beta 2638 2643 2641 2663 C1' DG P 3 beta 2659 2664 2662 2685 C1' DT P 4 beta 2681 2686 2684 2705 C1' DA P 5 beta 2701 2706 2704 2727 C1' C P 6 beta 2722 2728 2725 2748 C1' DG D 1 beta 2744 2749 2747 2770 C1' DC D 2 beta 2766 2771 2769 2789 C1' DC D 3 beta 2785 2790 2788 2808 C1' DG D 4 beta 2804 2809 2807 2831 C1' DT H 7 beta 2827 2832 2830 2851 C1' DA H 8 beta 2847 2852 2850 2872 C1' DC H 9 beta 2868 2873 2871 2891 C1' DT H 10 beta 2887 2892 2890 2911 C1' DG H 11 beta 2907 2912 2910 2929 C1' DC I 1 beta 2925 2930 2928 2948 C1' DA I 2 beta 2944 2949 2947 2969 C1' DG I 3 beta 2965 2970 2968 2991 C1' DT I 4 beta 2987 2992 2990 3011 C1' DA I 5 beta 3007 3012 3010 3044 C1' F2A A 606 beta 3043 3045 3055 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2398 C2' DC T 1 2399 2396 2417 C2' DG T 2 2418 2415 2439 C2' DG T 3 2440 2437 2461 C2' DC T 4 2462 2459 2480 C2' DT T 5 2481 2478 2500 C2' DG T 6 2501 2498 2522 C2' DT T 7 2523 2520 2542 C2' DA T 8 2543 2540 2563 C2' DC T 9 2564 2561 2582 C2' DT T 10 2583 2580 2602 C2' DG T 11 2603 2600 2622 C2' DC P 1 2623 2620 2641 C2' DA P 2 2642 2639 2662 C2' DG P 3 2663 2660 2684 C2' DT P 4 2685 2682 2704 C2' DA P 5 2705 2702 2725 C2' C P 6 OK 2727 2723 2726 2747 C2' DG D 1 2748 2745 2769 C2' DC D 2 2770 2767 2788 C2' DC D 3 2789 2786 2807 C2' DG D 4 2808 2805 2830 C2' DT H 7 2831 2828 2850 C2' DA H 8 2851 2848 2871 C2' DC H 9 2872 2869 2890 C2' DT H 10 2891 2888 2910 C2' DG H 11 2911 2908 2928 C2' DC I 1 2929 2926 2947 C2' DA I 2 2948 2945 2968 C2' DG I 3 2969 2966 2990 C2' DT I 4 2991 2988 3010 C2' DA I 5 3011 3008 3055 C2' F2A A 606 3044 3056 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2396 C3' DC T 1 OK 2394 2397 2398 2415 C3' DG T 2 OK 2413 2416 2417 2437 C3' DG T 3 OK 2435 2438 2439 2459 C3' DC T 4 OK 2457 2460 2461 2478 C3' DT T 5 OK 2476 2479 2480 2498 C3' DG T 6 OK 2496 2499 2500 2520 C3' DT T 7 OK 2518 2521 2522 2540 C3' DA T 8 OK 2538 2541 2542 2561 C3' DC T 9 OK 2559 2562 2563 2580 C3' DT T 10 OK 2578 2581 2582 2600 C3' DG T 11 OK 2598 2601 2602 2620 C3' DC P 1 OK 2618 2621 2622 2639 C3' DA P 2 OK 2637 2640 2641 2660 C3' DG P 3 OK 2658 2661 2662 2682 C3' DT P 4 OK 2680 2683 2684 2702 C3' DA P 5 OK 2700 2703 2704 2723 C3' C P 6 OK 2721 2724 2725 2745 C3' DG D 1 OK 2743 2746 2747 2767 C3' DC D 2 OK 2765 2768 2769 2786 C3' DC D 3 OK 2784 2787 2788 2805 C3' DG D 4 OK 2803 2806 2807 2828 C3' DT H 7 OK 2826 2829 2830 2848 C3' DA H 8 OK 2846 2849 2850 2869 C3' DC H 9 OK 2867 2870 2871 2888 C3' DT H 10 OK 2886 2889 2890 2908 C3' DG H 11 OK 2906 2909 2910 2926 C3' DC I 1 OK 2924 2927 2928 2945 C3' DA I 2 OK 2943 2946 2947 2966 C3' DG I 3 OK 2964 2967 2968 2988 C3' DT I 4 OK 2986 2989 2990 3008 C3' DA I 5 OK 3006 3009 3010 3056 C3' F2A A 606 OK 3042 3057 3055 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2394 C4' DC T 1 OK 2396 2393 2395 2413 C4' DG T 2 OK 2415 2412 2414 2435 C4' DG T 3 OK 2437 2434 2436 2457 C4' DC T 4 OK 2459 2456 2458 2476 C4' DT T 5 OK 2478 2475 2477 2496 C4' DG T 6 OK 2498 2495 2497 2518 C4' DT T 7 OK 2520 2517 2519 2538 C4' DA T 8 OK 2540 2537 2539 2559 C4' DC T 9 OK 2561 2558 2560 2578 C4' DT T 10 OK 2580 2577 2579 2598 C4' DG T 11 OK 2600 2597 2599 2618 C4' DC P 1 OK 2620 2617 2619 2637 C4' DA P 2 OK 2639 2636 2638 2658 C4' DG P 3 OK 2660 2657 2659 2680 C4' DT P 4 OK 2682 2679 2681 2700 C4' DA P 5 OK 2702 2699 2701 2721 C4' C P 6 OK 2723 2720 2722 2743 C4' DG D 1 OK 2745 2742 2744 2765 C4' DC D 2 OK 2767 2764 2766 2784 C4' DC D 3 OK 2786 2783 2785 2803 C4' DG D 4 OK 2805 2802 2804 2826 C4' DT H 7 OK 2828 2825 2827 2846 C4' DA H 8 OK 2848 2845 2847 2867 C4' DC H 9 OK 2869 2866 2868 2886 C4' DT H 10 OK 2888 2885 2887 2906 C4' DG H 11 OK 2908 2905 2907 2924 C4' DC I 1 2926 2925 2943 C4' DA I 2 OK 2945 2942 2944 2964 C4' DG I 3 OK 2966 2963 2965 2986 C4' DT I 4 OK 2988 2985 2987 3006 C4' DA I 5 OK 3008 3005 3007 3042 C4' F2A A 606 OK 3056 3041 3043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2393 C5' DC T 1 2392 2394 2412 C5' DG T 2 2411 2413 2434 C5' DG T 3 2433 2435 2456 C5' DC T 4 2455 2457 2475 C5' DT T 5 2474 2476 2495 C5' DG T 6 2494 2496 2517 C5' DT T 7 2516 2518 2537 C5' DA T 8 2536 2538 2558 C5' DC T 9 2557 2559 2577 C5' DT T 10 2576 2578 2597 C5' DG T 11 2596 2598 2617 C5' DC P 1 2616 2618 2636 C5' DA P 2 2635 2637 2657 C5' DG P 3 2656 2658 2679 C5' DT P 4 2678 2680 2699 C5' DA P 5 2698 2700 2720 C5' C P 6 2719 2721 2742 C5' DG D 1 2741 2743 2764 C5' DC D 2 2763 2765 2783 C5' DC D 3 2782 2784 2802 C5' DG D 4 2801 2803 2825 C5' DT H 7 2824 2826 2845 C5' DA H 8 2844 2846 2866 C5' DC H 9 2865 2867 2885 C5' DT H 10 2884 2886 2905 C5' DG H 11 2904 2906 2942 C5' DA I 2 2941 2943 2963 C5' DG I 3 2962 2964 2985 C5' DT I 4 2984 2986 3005 C5' DA I 5 3004 3006 3041 C5' F2A A 606 3032 3042 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2408 P DG T 2 distorted distorted 2397 2409 2410 2411 2430 P DG T 3 distorted distorted 2416 2431 2432 2433 2452 P DC T 4 distorted distorted 2438 2453 2454 2455 2471 P DT T 5 distorted distorted 2460 2472 2473 2474 2491 P DG T 6 distorted distorted 2479 2492 2493 2494 2513 P DT T 7 distorted distorted 2499 2514 2515 2516 2533 P DA T 8 distorted distorted 2521 2534 2535 2536 2554 P DC T 9 distorted distorted 2541 2555 2556 2557 2573 P DT T 10 distorted distorted 2562 2574 2575 2576 2593 P DG T 11 distorted distorted 2581 2594 2595 2596 2632 P DA P 2 distorted distorted 2621 2633 2634 2635 2653 P DG P 3 distorted distorted 2640 2654 2655 2656 2675 P DT P 4 distorted distorted 2661 2676 2677 2678 2695 P DA P 5 distorted distorted 2683 2696 2697 2698 2716 P C P 6 distorted distorted 2703 2717 2718 2719 2738 P DG D 1 OK OK 2739 2740 2741 2760 P DC D 2 distorted distorted 2746 2761 2762 2763 2779 P DC D 3 distorted distorted 2768 2780 2781 2782 2798 P DG D 4 distorted distorted 2787 2799 2800 2801 2821 P DT H 7 distorted distorted 2822 2823 2824 2841 P DA H 8 distorted distorted 2829 2842 2843 2844 2862 P DC H 9 distorted distorted 2849 2863 2864 2865 2881 P DT H 10 distorted distorted 2870 2882 2883 2884 2901 P DG H 11 distorted distorted 2889 2902 2903 2904 2938 P DA I 2 distorted distorted 2927 2939 2940 2941 2959 P DG I 3 distorted distorted 2946 2960 2961 2962 2981 P DT I 4 distorted distorted 2967 2982 2983 2984 3001 P DA I 5 distorted distorted 2989 3002 3003 3004 ---------------------------------------------------------------------------------