ID code: '1XZT' 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' --------------------------------------------------------------------------------- 2224 C1' G X 1 beta 2220 2225 2223 2246 C1' C X 2 beta 2242 2247 2245 2265 C1' G X 3 beta 2261 2266 2264 2287 C1' T X 4 beta 2283 2288 2286 2307 C1' C X 5 beta 2303 2308 2306 2326 C1' C X 6 beta 2322 2327 2325 2343 C1' 3DR X 7 2342 2339 2365 C1' C X 8 beta 2361 2366 2364 2384 C1' G X 9 beta 2380 2385 2383 2406 C1' A X 10 beta 2402 2407 2405 2427 C1' C X 11 beta 2423 2428 2426 2446 C1' G X 12 beta 2442 2447 2445 2468 C1' A X 13 beta 2464 2469 2467 2489 C1' C X 14 beta 2485 2490 2488 2508 C1' G X 15 beta 2504 2509 2507 2528 C1' G Y 17 beta 2524 2529 2527 2550 C1' T Y 18 beta 2546 2551 2549 2570 C1' C Y 19 beta 2566 2571 2569 2589 C1' G Y 20 beta 2585 2590 2588 2611 C1' T Y 21 beta 2607 2612 2610 2631 C1' C Y 22 beta 2627 2632 2630 2650 C1' G Y 23 beta 2646 2651 2649 2672 C1' G Y 24 beta 2668 2673 2671 2694 C1' G Y 25 beta 2690 2695 2693 2716 C1' G Y 26 beta 2712 2717 2715 2738 C1' A Y 27 beta 2734 2739 2737 2759 C1' C Y 28 beta 2755 2760 2758 2778 C1' G Y 29 beta 2774 2779 2777 2800 C1' C Y 30 beta 2796 2801 2799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2223 C2' G X 1 2224 2221 2245 C2' C X 2 2246 2243 2264 C2' G X 3 2265 2262 2286 C2' T X 4 2287 2284 2306 C2' C X 5 2307 2304 2325 C2' C X 6 2326 2323 2339 C2' 3DR X 7 OK OK 2343 2344 2347 2348 2364 C2' C X 8 2365 2362 2383 C2' G X 9 2384 2381 2405 C2' A X 10 2406 2403 2426 C2' C X 11 2427 2424 2445 C2' G X 12 2446 2443 2467 C2' A X 13 2468 2465 2488 C2' C X 14 2489 2486 2507 C2' G X 15 2508 2505 2527 C2' G Y 17 2528 2525 2549 C2' T Y 18 2550 2547 2569 C2' C Y 19 2570 2567 2588 C2' G Y 20 2589 2586 2610 C2' T Y 21 2611 2608 2630 C2' C Y 22 2631 2628 2649 C2' G Y 23 2650 2647 2671 C2' G Y 24 2672 2669 2693 C2' G Y 25 2694 2691 2715 C2' G Y 26 2716 2713 2737 C2' A Y 27 2738 2735 2758 C2' C Y 28 2759 2756 2777 C2' G Y 29 2778 2775 2799 C2' C Y 30 2800 2797 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2221 C3' G X 1 OK 2219 2222 2223 2243 C3' C X 2 OK 2241 2244 2245 2262 C3' G X 3 OK 2260 2263 2264 2284 C3' T X 4 OK 2282 2285 2286 2304 C3' C X 5 OK 2302 2305 2306 2323 C3' C X 6 OK 2321 2324 2325 2344 C3' 3DR X 7 OK OK 2341 2354 2345 2339 2362 C3' C X 8 OK 2360 2363 2364 2381 C3' G X 9 OK 2379 2382 2383 2403 C3' A X 10 OK 2401 2404 2405 2424 C3' C X 11 OK 2422 2425 2426 2443 C3' G X 12 OK 2441 2444 2445 2465 C3' A X 13 OK 2463 2466 2467 2486 C3' C X 14 OK 2484 2487 2488 2505 C3' G X 15 OK 2503 2506 2507 2525 C3' G Y 17 OK 2523 2526 2527 2547 C3' T Y 18 OK 2545 2548 2549 2567 C3' C Y 19 OK 2565 2568 2569 2586 C3' G Y 20 OK 2584 2587 2588 2608 C3' T Y 21 OK 2606 2609 2610 2628 C3' C Y 22 OK 2626 2629 2630 2647 C3' G Y 23 OK 2645 2648 2649 2669 C3' G Y 24 OK 2667 2670 2671 2691 C3' G Y 25 OK 2689 2692 2693 2713 C3' G Y 26 OK 2711 2714 2715 2735 C3' A Y 27 OK 2733 2736 2737 2756 C3' C Y 28 OK 2754 2757 2758 2775 C3' G Y 29 OK 2773 2776 2777 2797 C3' C Y 30 OK 2795 2798 2799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2219 C4' G X 1 OK 2221 2218 2220 2241 C4' C X 2 OK 2243 2240 2242 2260 C4' G X 3 OK 2262 2259 2261 2282 C4' T X 4 OK 2284 2281 2283 2302 C4' C X 5 OK 2304 2301 2303 2321 C4' C X 6 OK 2323 2320 2322 2341 C4' 3DR X 7 OK 2344 2340 2342 2360 C4' C X 8 OK 2362 2359 2361 2379 C4' G X 9 OK 2381 2378 2380 2401 C4' A X 10 OK 2403 2400 2402 2422 C4' C X 11 OK 2424 2421 2423 2441 C4' G X 12 OK 2443 2440 2442 2463 C4' A X 13 OK 2465 2462 2464 2484 C4' C X 14 OK 2486 2483 2485 2503 C4' G X 15 OK 2505 2502 2504 2523 C4' G Y 17 OK 2525 2522 2524 2545 C4' T Y 18 OK 2547 2544 2546 2565 C4' C Y 19 OK 2567 2564 2566 2584 C4' G Y 20 OK 2586 2583 2585 2606 C4' T Y 21 OK 2608 2605 2607 2626 C4' C Y 22 OK 2628 2625 2627 2645 C4' G Y 23 OK 2647 2644 2646 2667 C4' G Y 24 OK 2669 2666 2668 2689 C4' G Y 25 OK 2691 2688 2690 2711 C4' G Y 26 OK 2713 2710 2712 2733 C4' A Y 27 OK 2735 2732 2734 2754 C4' C Y 28 OK 2756 2753 2755 2773 C4' G Y 29 OK 2775 2772 2774 2795 C4' C Y 30 OK 2797 2794 2796 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2218 C5' G X 1 2217 2219 2240 C5' C X 2 2239 2241 2259 C5' G X 3 2258 2260 2281 C5' T X 4 2280 2282 2301 C5' C X 5 2300 2302 2320 C5' C X 6 2319 2321 2340 C5' 3DR X 7 OK OK 2335 2349 2350 2341 2359 C5' C X 8 2358 2360 2378 C5' G X 9 2377 2379 2400 C5' A X 10 2399 2401 2421 C5' C X 11 2420 2422 2440 C5' G X 12 2439 2441 2462 C5' A X 13 2461 2463 2483 C5' C X 14 2482 2484 2502 C5' G X 15 2501 2503 2522 C5' G Y 17 2521 2523 2544 C5' T Y 18 2543 2545 2564 C5' C Y 19 2563 2565 2583 C5' G Y 20 2582 2584 2605 C5' T Y 21 2604 2606 2625 C5' C Y 22 2624 2626 2644 C5' G Y 23 2643 2645 2666 C5' G Y 24 2665 2667 2688 C5' G Y 25 2687 2689 2710 C5' G Y 26 2709 2711 2732 C5' A Y 27 2731 2733 2753 C5' C Y 28 2752 2754 2772 C5' G Y 29 2771 2773 2794 C5' C Y 30 2793 2795 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2236 P C X 2 distorted distorted 2222 2237 2238 2239 2255 P G X 3 distorted distorted 2244 2256 2257 2258 2277 P T X 4 distorted distorted 2263 2278 2279 2280 2297 P C X 5 distorted distorted 2285 2298 2299 2300 2316 P C X 6 distorted distorted 2305 2317 2318 2319 2336 P 3DR X 7 distorted distorted 2324 2337 2338 2335 2355 P C X 8 distorted distorted 2345 2356 2357 2358 2374 P G X 9 distorted distorted 2363 2375 2376 2377 2396 P A X 10 distorted distorted 2382 2397 2398 2399 2417 P C X 11 distorted distorted 2404 2418 2419 2420 2436 P G X 12 distorted distorted 2425 2437 2438 2439 2458 P A X 13 distorted distorted 2444 2459 2460 2461 2479 P C X 14 distorted distorted 2466 2480 2481 2482 2498 P G X 15 distorted distorted 2487 2499 2500 2501 2540 P T Y 18 distorted distorted 2526 2541 2542 2543 2560 P C Y 19 distorted distorted 2548 2561 2562 2563 2579 P G Y 20 distorted distorted 2568 2580 2581 2582 2601 P T Y 21 distorted distorted 2587 2602 2603 2604 2621 P C Y 22 distorted distorted 2609 2622 2623 2624 2640 P G Y 23 distorted distorted 2629 2641 2642 2643 2662 P G Y 24 distorted distorted 2648 2663 2664 2665 2684 P G Y 25 distorted distorted 2670 2685 2686 2687 2706 P G Y 26 distorted distorted 2692 2707 2708 2709 2728 P A Y 27 distorted distorted 2714 2729 2730 2731 2749 P C Y 28 distorted distorted 2736 2750 2751 2752 2768 P G Y 29 distorted distorted 2757 2769 2770 2771 2790 P C Y 30 distorted distorted 2776 2791 2792 2793 ---------------------------------------------------------------------------------