ID code: '3DD2' 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' --------------------------------------------------------------------------------- 2339 C1' G B 1 beta 2334 2340 2337 2362 C1' G B 2 beta 2357 2363 2360 2385 C1' G B 3 beta 2380 2386 2383 2408 C1' A B 4 beta 2403 2409 2406 2430 C1' A B 5 beta 2425 2431 2428 2451 C1' CFL B 6 beta 2447 2452 2450 2472 C1' A B 7 beta 2467 2473 2470 2494 C1' A B 8 beta 2489 2495 2492 2516 C1' A B 9 beta 2511 2517 2514 2538 C1' G B 10 beta 2533 2539 2536 2560 C1' CFL B 11 beta 2556 2561 2559 2587 C1' UFT B 12 beta 2586 2574 2583 2601 C1' G B 13 beta 2596 2602 2599 2624 C1' A B 14 beta 2619 2625 2622 2646 C1' A B 15 beta 2641 2647 2644 2668 C1' G B 16 beta 2663 2669 2666 2697 C1' UFT B 17 beta 2696 2684 2693 2711 C1' A B 18 beta 2706 2712 2709 2732 C1' CFL B 19 beta 2728 2733 2731 2759 C1' UFT B 20 beta 2758 2746 2755 2779 C1' UFT B 21 beta 2778 2766 2775 2793 C1' A B 22 beta 2788 2794 2791 2814 C1' CFL B 23 beta 2810 2815 2813 2834 C1' CFL B 24 beta 2830 2835 2833 2854 C1' CFL B 25 beta 2850 2855 2853 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2337 C2' G B 1 OK 2339 2335 2338 2360 C2' G B 2 OK 2362 2358 2361 2383 C2' G B 3 OK 2385 2381 2384 2406 C2' A B 4 OK 2408 2404 2407 2428 C2' A B 5 OK 2430 2426 2429 2450 C2' CFL B 6 2451 2448 2470 C2' A B 7 OK 2472 2468 2471 2492 C2' A B 8 OK 2494 2490 2493 2514 C2' A B 9 OK 2516 2512 2515 2536 C2' G B 10 OK 2538 2534 2537 2559 C2' CFL B 11 2560 2557 2583 C2' UFT B 12 2587 2588 2599 C2' G B 13 OK 2601 2597 2600 2622 C2' A B 14 OK 2624 2620 2623 2644 C2' A B 15 OK 2646 2642 2645 2666 C2' G B 16 OK 2668 2664 2667 2693 C2' UFT B 17 2697 2698 2709 C2' A B 18 OK 2711 2707 2710 2731 C2' CFL B 19 2732 2729 2755 C2' UFT B 20 2759 2760 2775 C2' UFT B 21 2779 2780 2791 C2' A B 22 OK 2793 2789 2792 2813 C2' CFL B 23 2814 2811 2833 C2' CFL B 24 2834 2831 2853 C2' CFL B 25 2854 2851 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2335 C3' G B 1 OK 2333 2336 2337 2358 C3' G B 2 OK 2356 2359 2360 2381 C3' G B 3 OK 2379 2382 2383 2404 C3' A B 4 OK 2402 2405 2406 2426 C3' A B 5 OK 2424 2427 2428 2448 C3' CFL B 6 OK 2446 2449 2450 2468 C3' A B 7 OK 2466 2469 2470 2490 C3' A B 8 OK 2488 2491 2492 2512 C3' A B 9 OK 2510 2513 2514 2534 C3' G B 10 OK 2532 2535 2536 2557 C3' CFL B 11 OK 2555 2558 2559 2588 C3' UFT B 12 OK 2585 2589 2583 2597 C3' G B 13 OK 2595 2598 2599 2620 C3' A B 14 OK 2618 2621 2622 2642 C3' A B 15 OK 2640 2643 2644 2664 C3' G B 16 OK 2662 2665 2666 2698 C3' UFT B 17 OK 2695 2699 2693 2707 C3' A B 18 OK 2705 2708 2709 2729 C3' CFL B 19 OK 2727 2730 2731 2760 C3' UFT B 20 OK 2757 2761 2755 2780 C3' UFT B 21 OK 2777 2781 2775 2789 C3' A B 22 OK 2787 2790 2791 2811 C3' CFL B 23 OK 2809 2812 2813 2831 C3' CFL B 24 OK 2829 2832 2833 2851 C3' CFL B 25 OK 2849 2852 2853 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2333 C4' G B 1 OK 2335 2332 2334 2356 C4' G B 2 OK 2358 2355 2357 2379 C4' G B 3 OK 2381 2378 2380 2402 C4' A B 4 OK 2404 2401 2403 2424 C4' A B 5 OK 2426 2423 2425 2446 C4' CFL B 6 OK 2448 2445 2447 2466 C4' A B 7 OK 2468 2465 2467 2488 C4' A B 8 OK 2490 2487 2489 2510 C4' A B 9 OK 2512 2509 2511 2532 C4' G B 10 OK 2534 2531 2533 2555 C4' CFL B 11 OK 2557 2554 2556 2585 C4' UFT B 12 OK 2588 2584 2586 2595 C4' G B 13 OK 2597 2594 2596 2618 C4' A B 14 OK 2620 2617 2619 2640 C4' A B 15 OK 2642 2639 2641 2662 C4' G B 16 OK 2664 2661 2663 2695 C4' UFT B 17 OK 2698 2694 2696 2705 C4' A B 18 OK 2707 2704 2706 2727 C4' CFL B 19 OK 2729 2726 2728 2757 C4' UFT B 20 OK 2760 2756 2758 2777 C4' UFT B 21 OK 2780 2776 2778 2787 C4' A B 22 OK 2789 2786 2788 2809 C4' CFL B 23 OK 2811 2808 2810 2829 C4' CFL B 24 OK 2831 2828 2830 2849 C4' CFL B 25 OK 2851 2848 2850 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2332 C5' G B 1 2331 2333 2355 C5' G B 2 2354 2356 2378 C5' G B 3 2377 2379 2401 C5' A B 4 2400 2402 2423 C5' A B 5 2422 2424 2445 C5' CFL B 6 2444 2446 2465 C5' A B 7 2464 2466 2487 C5' A B 8 2486 2488 2509 C5' A B 9 2508 2510 2531 C5' G B 10 2530 2532 2554 C5' CFL B 11 2553 2555 2584 C5' UFT B 12 2573 2585 2594 C5' G B 13 2593 2595 2617 C5' A B 14 2616 2618 2639 C5' A B 15 2638 2640 2661 C5' G B 16 2660 2662 2694 C5' UFT B 17 2683 2695 2704 C5' A B 18 2703 2705 2726 C5' CFL B 19 2725 2727 2756 C5' UFT B 20 2745 2757 2776 C5' UFT B 21 2765 2777 2786 C5' A B 22 2785 2787 2808 C5' CFL B 23 2807 2809 2828 C5' CFL B 24 2827 2829 2848 C5' CFL B 25 2847 2849 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2351 P G B 2 distorted distorted 2336 2352 2353 2354 2374 P G B 3 distorted distorted 2359 2375 2376 2377 2397 P A B 4 distorted distorted 2382 2398 2399 2400 2419 P A B 5 distorted distorted 2405 2420 2421 2422 2441 P CFL B 6 OK OK 2427 2442 2443 2444 2461 P A B 7 distorted distorted 2449 2462 2463 2464 2483 P A B 8 distorted distorted 2469 2484 2485 2486 2505 P A B 9 distorted distorted 2491 2506 2507 2508 2527 P G B 10 distorted distorted 2513 2528 2529 2530 2550 P CFL B 11 OK OK 2535 2551 2552 2553 2570 P UFT B 12 distorted distorted 2558 2571 2572 2573 2590 P G B 13 distorted distorted 2589 2591 2592 2593 2613 P A B 14 distorted distorted 2598 2614 2615 2616 2635 P A B 15 distorted distorted 2621 2636 2637 2638 2657 P G B 16 distorted distorted 2643 2658 2659 2660 2680 P UFT B 17 distorted distorted 2665 2681 2682 2683 2700 P A B 18 distorted distorted 2699 2701 2702 2703 2722 P CFL B 19 OK OK 2708 2723 2724 2725 2742 P UFT B 20 distorted distorted 2730 2743 2744 2745 2762 P UFT B 21 distorted distorted 2761 2763 2764 2765 2782 P A B 22 distorted distorted 2781 2783 2784 2785 2804 P CFL B 23 OK OK 2790 2805 2806 2807 2824 P CFL B 24 OK OK 2812 2825 2826 2827 2844 P CFL B 25 OK OK 2832 2845 2846 2847 2864 P DT B 26 distorted distorted 2852 2865 2866 2867 ---------------------------------------------------------------------------------