ID code: '5ELT' 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' --------------------------------------------------------------------------------- 2432 C1' U E 0 beta 2427 2433 2430 2452 C1' A E 1 beta 2447 2453 2450 2474 C1' A E 2 beta 2469 2475 2472 2496 C1' U E 3 beta 2491 2497 2494 2517 C1' U F 1 beta 2512 2518 2515 2537 C1' A F 2 beta 2532 2538 2535 2559 C1' A F 3 beta 2554 2560 2557 2581 C1' U F 4 beta 2576 2582 2579 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2430 C2' U E 0 OK 2432 2428 2431 2450 C2' A E 1 OK 2452 2448 2451 2472 C2' A E 2 OK 2474 2470 2473 2494 C2' U E 3 OK 2496 2492 2495 2515 C2' U F 1 OK 2517 2513 2516 2535 C2' A F 2 OK 2537 2533 2536 2557 C2' A F 3 OK 2559 2555 2558 2579 C2' U F 4 OK 2581 2577 2580 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2428 C3' U E 0 OK 2426 2429 2430 2448 C3' A E 1 OK 2446 2449 2450 2470 C3' A E 2 OK 2468 2471 2472 2492 C3' U E 3 OK 2490 2493 2494 2513 C3' U F 1 OK 2511 2514 2515 2533 C3' A F 2 OK 2531 2534 2535 2555 C3' A F 3 OK 2553 2556 2557 2577 C3' U F 4 OK 2575 2578 2579 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2426 C4' U E 0 OK 2428 2425 2427 2446 C4' A E 1 OK 2448 2445 2447 2468 C4' A E 2 OK 2470 2467 2469 2490 C4' U E 3 OK 2492 2489 2491 2511 C4' U F 1 OK 2513 2510 2512 2531 C4' A F 2 OK 2533 2530 2532 2553 C4' A F 3 OK 2555 2552 2554 2575 C4' U F 4 OK 2577 2574 2576 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2425 C5' U E 0 2424 2426 2445 C5' A E 1 2444 2446 2467 C5' A E 2 2466 2468 2489 C5' U E 3 2488 2490 2510 C5' U F 1 2509 2511 2530 C5' A F 2 2529 2531 2552 C5' A F 3 2551 2553 2574 C5' U F 4 2573 2575 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2421 P U E 0 distorted distorted 2422 2423 2424 2441 P A E 1 distorted distorted 2429 2442 2443 2444 2463 P A E 2 distorted distorted 2449 2464 2465 2466 2485 P U E 3 distorted distorted 2471 2486 2487 2488 2506 P U F 1 OK OK 2507 2508 2509 2526 P A F 2 distorted distorted 2514 2527 2528 2529 2548 P A F 3 distorted distorted 2534 2549 2550 2551 2570 P U F 4 distorted distorted 2556 2571 2572 2573 ---------------------------------------------------------------------------------