ID code: '3OH6' 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' --------------------------------------------------------------------------------- 2263 C1' DG B 15 beta 2259 2264 2262 2285 C1' DC B 16 beta 2281 2286 2284 2304 C1' DA B 17 beta 2300 2305 2303 2325 C1' DT B 18 beta 2321 2326 2324 2345 C1' DT B 19 beta 2341 2346 2344 2365 C1' DC B 20 beta 2361 2366 2364 2384 C1' DA B 21 beta 2380 2385 2383 2405 C1' DT B 22 beta 2401 2406 2404 2425 C1' DG B 23 beta 2421 2426 2424 2447 C1' DT B 24 beta 2443 2448 2446 2467 C1' DC B 25 beta 2463 2468 2466 2484 C1' DG C 1 beta 2480 2485 2483 2506 C1' DA C 2 beta 2502 2507 2505 2527 C1' DC C 3 beta 2523 2528 2526 2546 C1' DA C 4 beta 2542 2547 2545 2566 C1' BRU C 5 beta 2571 2557 2567 2587 C1' DG C 6 beta 2583 2588 2586 2609 C1' DA C 7 beta 2605 2610 2608 2630 C1' DA C 8 beta 2626 2631 2629 2650 C1' BRU C 9 beta 2655 2641 2651 2671 C1' DG C 10 beta 2667 2672 2670 2693 C1' DC C 11 beta 2689 2694 2692 2712 C1' DC C 12 beta 2708 2713 2711 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2262 C2' DG B 15 2263 2260 2284 C2' DC B 16 2285 2282 2303 C2' DA B 17 2304 2301 2324 C2' DT B 18 2325 2322 2344 C2' DT B 19 2345 2342 2364 C2' DC B 20 2365 2362 2383 C2' DA B 21 2384 2381 2404 C2' DT B 22 2405 2402 2424 C2' DG B 23 2425 2422 2446 C2' DT B 24 2447 2444 2466 C2' DC B 25 2467 2464 2483 C2' DG C 1 2484 2481 2505 C2' DA C 2 2506 2503 2526 C2' DC C 3 2527 2524 2545 C2' DA C 4 2546 2543 2567 C2' BRU C 5 2566 2568 2586 C2' DG C 6 2587 2584 2608 C2' DA C 7 2609 2606 2629 C2' DA C 8 2630 2627 2651 C2' BRU C 9 2650 2652 2670 C2' DG C 10 2671 2668 2692 C2' DC C 11 2693 2690 2711 C2' DC C 12 2712 2709 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2260 C3' DG B 15 OK 2258 2261 2262 2282 C3' DC B 16 OK 2280 2283 2284 2301 C3' DA B 17 OK 2299 2302 2303 2322 C3' DT B 18 OK 2320 2323 2324 2342 C3' DT B 19 OK 2340 2343 2344 2362 C3' DC B 20 OK 2360 2363 2364 2381 C3' DA B 21 OK 2379 2382 2383 2402 C3' DT B 22 OK 2400 2403 2404 2422 C3' DG B 23 OK 2420 2423 2424 2444 C3' DT B 24 OK 2442 2445 2446 2464 C3' DC B 25 OK 2462 2465 2466 2481 C3' DG C 1 OK 2479 2482 2483 2503 C3' DA C 2 OK 2501 2504 2505 2524 C3' DC C 3 OK 2522 2525 2526 2543 C3' DA C 4 OK 2541 2544 2545 2568 C3' BRU C 5 OK 2569 2570 2567 2584 C3' DG C 6 OK 2582 2585 2586 2606 C3' DA C 7 OK 2604 2607 2608 2627 C3' DA C 8 OK 2625 2628 2629 2652 C3' BRU C 9 OK 2653 2654 2651 2668 C3' DG C 10 OK 2666 2669 2670 2690 C3' DC C 11 OK 2688 2691 2692 2709 C3' DC C 12 OK 2707 2710 2711 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2258 C4' DG B 15 OK 2260 2257 2259 2280 C4' DC B 16 OK 2282 2279 2281 2299 C4' DA B 17 OK 2301 2298 2300 2320 C4' DT B 18 OK 2322 2319 2321 2340 C4' DT B 19 OK 2342 2339 2341 2360 C4' DC B 20 OK 2362 2359 2361 2379 C4' DA B 21 OK 2381 2378 2380 2400 C4' DT B 22 OK 2402 2399 2401 2420 C4' DG B 23 OK 2422 2419 2421 2442 C4' DT B 24 OK 2444 2441 2443 2462 C4' DC B 25 OK 2464 2461 2463 2479 C4' DG C 1 OK 2481 2478 2480 2501 C4' DA C 2 OK 2503 2500 2502 2522 C4' DC C 3 OK 2524 2521 2523 2541 C4' DA C 4 OK 2543 2540 2542 2569 C4' BRU C 5 OK 2568 2572 2571 2582 C4' DG C 6 OK 2584 2581 2583 2604 C4' DA C 7 OK 2606 2603 2605 2625 C4' DA C 8 OK 2627 2624 2626 2653 C4' BRU C 9 OK 2652 2656 2655 2666 C4' DG C 10 OK 2668 2665 2667 2688 C4' DC C 11 OK 2690 2687 2689 2707 C4' DC C 12 OK 2709 2706 2708 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2257 C5' DG B 15 2256 2258 2279 C5' DC B 16 2278 2280 2298 C5' DA B 17 2297 2299 2319 C5' DT B 18 2318 2320 2339 C5' DT B 19 2338 2340 2359 C5' DC B 20 2358 2360 2378 C5' DA B 21 2377 2379 2399 C5' DT B 22 2398 2400 2419 C5' DG B 23 2418 2420 2441 C5' DT B 24 2440 2442 2461 C5' DC B 25 2460 2462 2478 C5' DG C 1 2477 2479 2500 C5' DA C 2 2499 2501 2521 C5' DC C 3 2520 2522 2540 C5' DA C 4 2539 2541 2572 C5' BRU C 5 2573 2569 2581 C5' DG C 6 2580 2582 2603 C5' DA C 7 2602 2604 2624 C5' DA C 8 2623 2625 2656 C5' BRU C 9 2657 2653 2665 C5' DG C 10 2664 2666 2687 C5' DC C 11 2686 2688 2706 C5' DC C 12 2705 2707 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2275 P DC B 16 distorted distorted 2261 2276 2277 2278 2294 P DA B 17 distorted distorted 2283 2295 2296 2297 2315 P DT B 18 distorted distorted 2302 2316 2317 2318 2335 P DT B 19 distorted distorted 2323 2336 2337 2338 2355 P DC B 20 distorted distorted 2343 2356 2357 2358 2374 P DA B 21 distorted distorted 2363 2375 2376 2377 2395 P DT B 22 distorted distorted 2382 2396 2397 2398 2415 P DG B 23 distorted distorted 2403 2416 2417 2418 2437 P DT B 24 distorted distorted 2423 2438 2439 2440 2457 P DC B 25 distorted distorted 2445 2458 2459 2460 2496 P DA C 2 distorted distorted 2482 2497 2498 2499 2517 P DC C 3 distorted distorted 2504 2518 2519 2520 2536 P DA C 4 distorted distorted 2525 2537 2538 2539 2574 P BRU C 5 distorted distorted 2544 2575 2576 2573 2577 P DG C 6 distorted distorted 2570 2578 2579 2580 2599 P DA C 7 distorted distorted 2585 2600 2601 2602 2620 P DA C 8 distorted distorted 2607 2621 2622 2623 2658 P BRU C 9 distorted distorted 2628 2659 2660 2657 2661 P DG C 10 distorted distorted 2654 2662 2663 2664 2683 P DC C 11 distorted distorted 2669 2684 2685 2686 2702 P DC C 12 distorted distorted 2691 2703 2704 2705 ---------------------------------------------------------------------------------