ID code: '4AL7' 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' --------------------------------------------------------------------------------- 2323 C1' C B 6 alpha beta 2318 2338 2324 2321 2355 C1' U B 7 alpha beta 2350 2370 2356 2353 2385 C1' G B 8 alpha beta 2380 2403 2386 2383 2419 C1' C B 9 alpha beta 2414 2434 2420 2417 2450 C1' C B 10 alpha beta 2445 2465 2451 2448 2481 C1' G B 11 alpha beta 2476 2499 2482 2479 2515 C1' U B 12 alpha beta 2510 2530 2516 2513 2545 C1' A B 13 alpha beta 2540 2562 2546 2543 2590 C1' A B 15 alpha beta 2585 2607 2591 2588 2623 C1' G B 16 alpha beta 2618 2641 2624 2621 2657 C1' G B 17 alpha beta 2652 2675 2658 2655 2691 C1' C B 18 alpha beta 2686 2706 2692 2689 2722 C1' A B 19 alpha beta 2717 2739 2723 2720 2755 C1' G B 20 alpha beta 2750 2774 2756 2753 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2321 C2' C B 6 OK OK 2323 2319 2336 2322 2353 C2' U B 7 OK OK 2355 2351 2368 2354 2383 C2' G B 8 OK OK 2385 2381 2401 2384 2417 C2' C B 9 OK OK 2419 2415 2432 2418 2448 C2' C B 10 OK OK 2450 2446 2463 2449 2479 C2' G B 11 OK OK 2481 2477 2497 2480 2513 C2' U B 12 OK OK 2515 2511 2528 2514 2543 C2' A B 13 OK OK 2545 2541 2560 2544 2588 C2' A B 15 OK OK 2590 2586 2605 2589 2621 C2' G B 16 OK OK 2623 2619 2639 2622 2655 C2' G B 17 OK OK 2657 2653 2673 2656 2689 C2' C B 18 OK OK 2691 2687 2704 2690 2720 C2' A B 19 OK OK 2722 2718 2737 2721 2753 C2' G B 20 OK OK 2755 2751 2772 2754 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2319 C3' C B 6 OK OK 2317 2335 2320 2321 2351 C3' U B 7 OK OK 2349 2367 2352 2353 2381 C3' G B 8 OK OK 2379 2400 2382 2383 2415 C3' C B 9 OK OK 2413 2431 2416 2417 2446 C3' C B 10 OK OK 2444 2462 2447 2448 2477 C3' G B 11 OK OK 2475 2496 2478 2479 2511 C3' U B 12 OK OK 2509 2527 2512 2513 2541 C3' A B 13 OK OK 2539 2559 2542 2543 2573 C3' U B 14 2572 2578 2574 2586 C3' A B 15 OK OK 2584 2604 2587 2588 2619 C3' G B 16 OK OK 2617 2638 2620 2621 2653 C3' G B 17 OK OK 2651 2672 2654 2655 2687 C3' C B 18 OK OK 2685 2703 2688 2689 2718 C3' A B 19 OK OK 2716 2736 2719 2720 2751 C3' G B 20 OK OK 2749 2770 2752 2753 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2317 C4' C B 6 OK OK 2319 2334 2316 2318 2349 C4' U B 7 OK OK 2351 2366 2348 2350 2379 C4' G B 8 OK OK 2381 2399 2378 2380 2413 C4' C B 9 OK OK 2415 2430 2412 2414 2444 C4' C B 10 OK OK 2446 2461 2443 2445 2475 C4' G B 11 OK OK 2477 2495 2474 2476 2509 C4' U B 12 OK OK 2511 2526 2508 2510 2539 C4' A B 13 OK OK 2541 2558 2538 2540 2572 C4' U B 14 2573 2577 2571 2584 C4' A B 15 OK OK 2586 2603 2583 2585 2617 C4' G B 16 OK OK 2619 2637 2616 2618 2651 C4' G B 17 OK OK 2653 2671 2650 2652 2685 C4' C B 18 OK OK 2687 2702 2684 2686 2716 C4' A B 19 OK OK 2718 2735 2715 2717 2749 C4' G B 20 OK OK 2751 2769 2748 2750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2316 C5' C B 6 OK OK 2315 2332 2333 2317 2348 C5' U B 7 OK OK 2347 2364 2365 2349 2378 C5' G B 8 OK OK 2377 2397 2398 2379 2412 C5' C B 9 OK OK 2411 2428 2429 2413 2443 C5' C B 10 OK OK 2442 2459 2460 2444 2474 C5' G B 11 OK OK 2473 2493 2494 2475 2508 C5' U B 12 OK OK 2507 2524 2525 2509 2538 C5' A B 13 OK OK 2537 2556 2557 2539 2571 C5' U B 14 OK OK 2570 2575 2576 2572 2583 C5' A B 15 distorted distorted 2582 2601 2602 2584 2616 C5' G B 16 OK OK 2615 2635 2636 2617 2650 C5' G B 17 OK OK 2649 2669 2670 2651 2684 C5' C B 18 OK OK 2683 2700 2701 2685 2715 C5' A B 19 OK OK 2714 2733 2734 2716 2748 C5' G B 20 OK OK 2747 2767 2768 2749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2344 P U B 7 distorted distorted 2320 2345 2346 2347 2374 P G B 8 distorted distorted 2352 2375 2376 2377 2408 P C B 9 distorted distorted 2382 2409 2410 2411 2439 P C B 10 distorted distorted 2416 2440 2441 2442 2470 P G B 11 distorted distorted 2447 2471 2472 2473 2504 P U B 12 OK OK 2478 2505 2506 2507 2534 P A B 13 OK OK 2512 2535 2536 2537 2567 P U B 14 OK OK 2542 2568 2569 2570 2579 P A B 15 distorted distorted 2574 2580 2581 2582 2612 P G B 16 distorted distorted 2587 2613 2614 2615 2646 P G B 17 OK OK 2620 2647 2648 2649 2680 P C B 18 distorted distorted 2654 2681 2682 2683 2711 P A B 19 distorted distorted 2688 2712 2713 2714 2744 P G B 20 distorted distorted 2719 2745 2746 2747 ---------------------------------------------------------------------------------