ID code: '4AL6' 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' --------------------------------------------------------------------------------- 2279 C1' C B 6 alpha beta 2274 2295 2280 2277 2312 C1' U B 7 alpha beta 2307 2327 2313 2310 2342 C1' G B 8 alpha beta 2337 2360 2343 2340 2376 C1' C B 9 alpha beta 2371 2391 2377 2374 2407 C1' C B 10 alpha beta 2402 2422 2408 2405 2438 C1' G B 11 alpha beta 2433 2456 2439 2436 2472 C1' U B 12 alpha beta 2467 2487 2473 2470 2502 C1' A B 13 alpha beta 2497 2519 2503 2500 2535 C1' U B 14 2530 2533 2553 C1' A B 15 alpha beta 2548 2570 2554 2551 2586 C1' G B 16 alpha beta 2581 2604 2587 2584 2620 C1' G B 17 alpha beta 2615 2638 2621 2618 2654 C1' C B 18 alpha beta 2649 2669 2655 2652 2685 C1' A B 19 alpha beta 2680 2702 2686 2683 2718 C1' G B 20 alpha beta 2713 2736 2719 2716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2277 C2' C B 6 OK OK 2279 2275 2293 2278 2310 C2' U B 7 OK OK 2312 2308 2325 2311 2340 C2' G B 8 OK OK 2342 2338 2358 2341 2374 C2' C B 9 OK OK 2376 2372 2389 2375 2405 C2' C B 10 OK OK 2407 2403 2420 2406 2436 C2' G B 11 OK OK 2438 2434 2454 2437 2470 C2' U B 12 OK OK 2472 2468 2485 2471 2500 C2' A B 13 OK OK 2502 2498 2517 2501 2533 C2' U B 14 OK OK 2535 2531 2540 2534 2551 C2' A B 15 OK OK 2553 2549 2568 2552 2584 C2' G B 16 OK OK 2586 2582 2602 2585 2618 C2' G B 17 OK OK 2620 2616 2636 2619 2652 C2' C B 18 OK OK 2654 2650 2667 2653 2683 C2' A B 19 OK OK 2685 2681 2700 2684 2716 C2' G B 20 OK OK 2718 2714 2734 2717 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2275 C3' C B 6 OK OK 2273 2291 2276 2277 2308 C3' U B 7 OK OK 2306 2324 2309 2310 2338 C3' G B 8 OK OK 2336 2357 2339 2340 2372 C3' C B 9 OK OK 2370 2388 2373 2374 2403 C3' C B 10 OK OK 2401 2419 2404 2405 2434 C3' G B 11 OK OK 2432 2453 2435 2436 2468 C3' U B 12 OK OK 2466 2484 2469 2470 2498 C3' A B 13 OK OK 2496 2516 2499 2500 2531 C3' U B 14 OK OK 2529 2539 2532 2533 2549 C3' A B 15 OK OK 2547 2567 2550 2551 2582 C3' G B 16 OK OK 2580 2601 2583 2584 2616 C3' G B 17 OK OK 2614 2635 2617 2618 2650 C3' C B 18 OK OK 2648 2666 2651 2652 2681 C3' A B 19 OK OK 2679 2699 2682 2683 2714 C3' G B 20 OK OK 2712 2733 2715 2716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2273 C4' C B 6 OK OK 2275 2290 2272 2274 2306 C4' U B 7 OK OK 2308 2323 2305 2307 2336 C4' G B 8 OK OK 2338 2356 2335 2337 2370 C4' C B 9 OK OK 2372 2387 2369 2371 2401 C4' C B 10 OK OK 2403 2418 2400 2402 2432 C4' G B 11 OK OK 2434 2452 2431 2433 2466 C4' U B 12 OK OK 2468 2483 2465 2467 2496 C4' A B 13 OK OK 2498 2515 2495 2497 2529 C4' U B 14 OK OK 2531 2538 2528 2530 2547 C4' A B 15 OK OK 2549 2566 2546 2548 2580 C4' G B 16 OK OK 2582 2600 2579 2581 2614 C4' G B 17 OK OK 2616 2634 2613 2615 2648 C4' C B 18 OK OK 2650 2665 2647 2649 2679 C4' A B 19 OK OK 2681 2698 2678 2680 2712 C4' G B 20 OK OK 2714 2732 2711 2713 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2272 C5' C B 6 OK OK 2271 2288 2289 2273 2305 C5' U B 7 OK OK 2304 2321 2322 2306 2335 C5' G B 8 OK OK 2334 2354 2355 2336 2369 C5' C B 9 OK OK 2368 2385 2386 2370 2400 C5' C B 10 OK OK 2399 2416 2417 2401 2431 C5' G B 11 OK OK 2430 2450 2451 2432 2465 C5' U B 12 OK OK 2464 2481 2482 2466 2495 C5' A B 13 OK OK 2494 2513 2514 2496 2528 C5' U B 14 OK OK 2527 2536 2537 2529 2546 C5' A B 15 OK OK 2545 2564 2565 2547 2579 C5' G B 16 OK OK 2578 2598 2599 2580 2613 C5' G B 17 OK OK 2612 2632 2633 2614 2647 C5' C B 18 OK OK 2646 2663 2664 2648 2678 C5' A B 19 OK OK 2677 2696 2697 2679 2711 C5' G B 20 OK OK 2710 2730 2731 2712 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2301 P U B 7 distorted distorted 2276 2302 2303 2304 2331 P G B 8 distorted distorted 2309 2332 2333 2334 2365 P C B 9 distorted distorted 2339 2366 2367 2368 2396 P C B 10 distorted distorted 2373 2397 2398 2399 2427 P G B 11 distorted distorted 2404 2428 2429 2430 2461 P U B 12 OK OK 2435 2462 2463 2464 2491 P A B 13 distorted distorted 2469 2492 2493 2494 2524 P U B 14 distorted distorted 2499 2525 2526 2527 2542 P A B 15 OK OK 2532 2543 2544 2545 2575 P G B 16 distorted distorted 2550 2576 2577 2578 2609 P G B 17 OK OK 2583 2610 2611 2612 2643 P C B 18 distorted distorted 2617 2644 2645 2646 2674 P A B 19 distorted distorted 2651 2675 2676 2677 2707 P G B 20 distorted distorted 2682 2708 2709 2710 2741 P C B 21 distorted distorted 2715 2742 2743 2744 ---------------------------------------------------------------------------------