ID code: '1LYR' 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' --------------------------------------------------------------------------------- 2235 C1' G X 1 beta 2231 2236 2234 2257 C1' C X 2 beta 2253 2258 2256 2276 C1' G X 3 beta 2272 2277 2275 2298 C1' T X 4 beta 2294 2299 2297 2318 C1' C X 5 beta 2314 2319 2317 2337 C1' C X 6 alpha beta 2333 2350 2338 2336 2365 C1' 3DR X 7 2364 2361 2387 C1' C X 8 alpha beta 2383 2400 2388 2386 2417 C1' G X 9 beta 2413 2418 2416 2439 C1' A X 10 beta 2435 2440 2438 2460 C1' C X 11 beta 2456 2461 2459 2479 C1' G X 12 beta 2475 2480 2478 2501 C1' A X 13 beta 2497 2502 2500 2522 C1' C X 14 beta 2518 2523 2521 2541 C1' G X 15 beta 2537 2542 2540 2561 C1' G Y 17 beta 2557 2562 2560 2583 C1' T Y 18 beta 2579 2584 2582 2603 C1' C Y 19 beta 2599 2604 2602 2622 C1' G Y 20 beta 2618 2623 2621 2644 C1' T Y 21 beta 2640 2645 2643 2664 C1' C Y 22 beta 2660 2665 2663 2683 C1' G Y 23 beta 2679 2684 2682 2705 C1' G Y 24 beta 2701 2706 2704 2727 C1' G Y 25 beta 2723 2728 2726 2749 C1' G Y 26 beta 2745 2750 2748 2771 C1' A Y 27 beta 2767 2772 2770 2792 C1' C Y 28 beta 2788 2793 2791 2811 C1' G Y 29 beta 2807 2812 2810 2833 C1' C Y 30 beta 2829 2834 2832 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2234 C2' G X 1 2235 2232 2256 C2' C X 2 2257 2254 2275 C2' G X 3 2276 2273 2297 C2' T X 4 2298 2295 2317 C2' C X 5 2318 2315 2336 C2' C X 6 OK OK 2337 2334 2355 2356 2361 C2' 3DR X 7 OK OK 2365 2366 2369 2370 2386 C2' C X 8 OK OK 2387 2384 2405 2406 2416 C2' G X 9 2417 2414 2438 C2' A X 10 2439 2436 2459 C2' C X 11 2460 2457 2478 C2' G X 12 2479 2476 2500 C2' A X 13 2501 2498 2521 C2' C X 14 2522 2519 2540 C2' G X 15 2541 2538 2560 C2' G Y 17 2561 2558 2582 C2' T Y 18 2583 2580 2602 C2' C Y 19 2603 2600 2621 C2' G Y 20 2622 2619 2643 C2' T Y 21 2644 2641 2663 C2' C Y 22 2664 2661 2682 C2' G Y 23 2683 2680 2704 C2' G Y 24 2705 2702 2726 C2' G Y 25 2727 2724 2748 C2' G Y 26 2749 2746 2770 C2' A Y 27 2771 2768 2791 C2' C Y 28 2792 2789 2810 C2' G Y 29 2811 2808 2832 C2' C Y 30 2833 2830 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2232 C3' G X 1 OK 2230 2233 2234 2254 C3' C X 2 OK 2252 2255 2256 2273 C3' G X 3 OK 2271 2274 2275 2295 C3' T X 4 OK 2293 2296 2297 2315 C3' C X 5 OK 2313 2316 2317 2334 C3' C X 6 OK OK 2332 2349 2335 2336 2366 C3' 3DR X 7 OK OK 2363 2376 2367 2361 2384 C3' C X 8 OK OK 2382 2399 2385 2386 2414 C3' G X 9 OK 2412 2415 2416 2436 C3' A X 10 OK 2434 2437 2438 2457 C3' C X 11 OK 2455 2458 2459 2476 C3' G X 12 OK 2474 2477 2478 2498 C3' A X 13 OK 2496 2499 2500 2519 C3' C X 14 OK 2517 2520 2521 2538 C3' G X 15 OK 2536 2539 2540 2558 C3' G Y 17 OK 2556 2559 2560 2580 C3' T Y 18 OK 2578 2581 2582 2600 C3' C Y 19 OK 2598 2601 2602 2619 C3' G Y 20 OK 2617 2620 2621 2641 C3' T Y 21 OK 2639 2642 2643 2661 C3' C Y 22 OK 2659 2662 2663 2680 C3' G Y 23 OK 2678 2681 2682 2702 C3' G Y 24 OK 2700 2703 2704 2724 C3' G Y 25 OK 2722 2725 2726 2746 C3' G Y 26 OK 2744 2747 2748 2768 C3' A Y 27 OK 2766 2769 2770 2789 C3' C Y 28 OK 2787 2790 2791 2808 C3' G Y 29 OK 2806 2809 2810 2830 C3' C Y 30 OK 2828 2831 2832 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2230 C4' G X 1 OK 2232 2229 2231 2252 C4' C X 2 OK 2254 2251 2253 2271 C4' G X 3 OK 2273 2270 2272 2293 C4' T X 4 OK 2295 2292 2294 2313 C4' C X 5 OK 2315 2312 2314 2332 C4' C X 6 OK OK 2334 2348 2331 2333 2363 C4' 3DR X 7 OK 2366 2362 2364 2382 C4' C X 8 OK OK 2384 2398 2381 2383 2412 C4' G X 9 OK 2414 2411 2413 2434 C4' A X 10 OK 2436 2433 2435 2455 C4' C X 11 OK 2457 2454 2456 2474 C4' G X 12 OK 2476 2473 2475 2496 C4' A X 13 OK 2498 2495 2497 2517 C4' C X 14 OK 2519 2516 2518 2536 C4' G X 15 OK 2538 2535 2537 2556 C4' G Y 17 OK 2558 2555 2557 2578 C4' T Y 18 OK 2580 2577 2579 2598 C4' C Y 19 OK 2600 2597 2599 2617 C4' G Y 20 OK 2619 2616 2618 2639 C4' T Y 21 OK 2641 2638 2640 2659 C4' C Y 22 OK 2661 2658 2660 2678 C4' G Y 23 OK 2680 2677 2679 2700 C4' G Y 24 OK 2702 2699 2701 2722 C4' G Y 25 OK 2724 2721 2723 2744 C4' G Y 26 OK 2746 2743 2745 2766 C4' A Y 27 OK 2768 2765 2767 2787 C4' C Y 28 OK 2789 2786 2788 2806 C4' G Y 29 OK 2808 2805 2807 2828 C4' C Y 30 OK 2830 2827 2829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2229 C5' G X 1 2228 2230 2251 C5' C X 2 2250 2252 2270 C5' G X 3 2269 2271 2292 C5' T X 4 2291 2293 2312 C5' C X 5 2311 2313 2331 C5' C X 6 OK OK 2330 2346 2347 2332 2362 C5' 3DR X 7 OK OK 2357 2371 2372 2363 2381 C5' C X 8 OK OK 2380 2396 2397 2382 2411 C5' G X 9 2410 2412 2433 C5' A X 10 2432 2434 2454 C5' C X 11 2453 2455 2473 C5' G X 12 2472 2474 2495 C5' A X 13 2494 2496 2516 C5' C X 14 2515 2517 2535 C5' G X 15 2534 2536 2555 C5' G Y 17 2554 2556 2577 C5' T Y 18 2576 2578 2597 C5' C Y 19 2596 2598 2616 C5' G Y 20 2615 2617 2638 C5' T Y 21 2637 2639 2658 C5' C Y 22 2657 2659 2677 C5' G Y 23 2676 2678 2699 C5' G Y 24 2698 2700 2721 C5' G Y 25 2720 2722 2743 C5' G Y 26 2742 2744 2765 C5' A Y 27 2764 2766 2786 C5' C Y 28 2785 2787 2805 C5' G Y 29 2804 2806 2827 C5' C Y 30 2826 2828 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2247 P C X 2 distorted distorted 2233 2248 2249 2250 2266 P G X 3 distorted distorted 2255 2267 2268 2269 2288 P T X 4 distorted distorted 2274 2289 2290 2291 2308 P C X 5 distorted distorted 2296 2309 2310 2311 2327 P C X 6 distorted distorted 2316 2328 2329 2330 2358 P 3DR X 7 distorted distorted 2335 2359 2360 2357 2377 P C X 8 distorted distorted 2367 2378 2379 2380 2407 P G X 9 distorted distorted 2385 2408 2409 2410 2429 P A X 10 distorted distorted 2415 2430 2431 2432 2450 P C X 11 distorted distorted 2437 2451 2452 2453 2469 P G X 12 distorted distorted 2458 2470 2471 2472 2491 P A X 13 distorted distorted 2477 2492 2493 2494 2512 P C X 14 distorted distorted 2499 2513 2514 2515 2531 P G X 15 distorted distorted 2520 2532 2533 2534 2573 P T Y 18 distorted distorted 2559 2574 2575 2576 2593 P C Y 19 distorted distorted 2581 2594 2595 2596 2612 P G Y 20 distorted distorted 2601 2613 2614 2615 2634 P T Y 21 distorted distorted 2620 2635 2636 2637 2654 P C Y 22 distorted distorted 2642 2655 2656 2657 2673 P G Y 23 distorted distorted 2662 2674 2675 2676 2695 P G Y 24 distorted distorted 2681 2696 2697 2698 2717 P G Y 25 distorted distorted 2703 2718 2719 2720 2739 P G Y 26 distorted distorted 2725 2740 2741 2742 2761 P A Y 27 distorted distorted 2747 2762 2763 2764 2782 P C Y 28 distorted distorted 2769 2783 2784 2785 2801 P G Y 29 distorted distorted 2790 2802 2803 2804 2823 P C Y 30 distorted distorted 2809 2824 2825 2826 ---------------------------------------------------------------------------------