ID code: '4NGC' 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' --------------------------------------------------------------------------------- 2294 C1' G B 1 beta 2289 2295 2292 2317 C1' C B 2 beta 2312 2318 2315 2337 C1' G B 3 beta 2332 2338 2335 2360 C1' A B 4 beta 2355 2361 2358 2382 C1' A B 5 beta 2377 2383 2380 2404 C1' U B 6 beta 2399 2405 2402 2424 C1' U B 7 beta 2419 2425 2422 2444 C1' C B 8 beta 2439 2445 2442 2464 C1' G B 9 beta 2459 2465 2462 2487 C1' C B 10 beta 2482 2488 2485 2507 C1' U B 11 beta 2502 2508 2505 2527 C1' A B 12 beta 2522 2528 2525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2292 C2' G B 1 OK 2294 2290 2293 2315 C2' C B 2 OK 2317 2313 2316 2335 C2' G B 3 OK 2337 2333 2336 2358 C2' A B 4 OK 2360 2356 2359 2380 C2' A B 5 OK 2382 2378 2381 2402 C2' U B 6 OK 2404 2400 2403 2422 C2' U B 7 OK 2424 2420 2423 2442 C2' C B 8 OK 2444 2440 2443 2462 C2' G B 9 OK 2464 2460 2463 2485 C2' C B 10 OK 2487 2483 2486 2505 C2' U B 11 OK 2507 2503 2506 2525 C2' A B 12 OK 2527 2523 2526 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2290 C3' G B 1 OK 2288 2291 2292 2313 C3' C B 2 OK 2311 2314 2315 2333 C3' G B 3 OK 2331 2334 2335 2356 C3' A B 4 OK 2354 2357 2358 2378 C3' A B 5 OK 2376 2379 2380 2400 C3' U B 6 OK 2398 2401 2402 2420 C3' U B 7 OK 2418 2421 2422 2440 C3' C B 8 OK 2438 2441 2442 2460 C3' G B 9 OK 2458 2461 2462 2483 C3' C B 10 OK 2481 2484 2485 2503 C3' U B 11 OK 2501 2504 2505 2523 C3' A B 12 OK 2521 2524 2525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2288 C4' G B 1 OK 2290 2287 2289 2311 C4' C B 2 OK 2313 2310 2312 2331 C4' G B 3 OK 2333 2330 2332 2354 C4' A B 4 OK 2356 2353 2355 2376 C4' A B 5 OK 2378 2375 2377 2398 C4' U B 6 OK 2400 2397 2399 2418 C4' U B 7 OK 2420 2417 2419 2438 C4' C B 8 OK 2440 2437 2439 2458 C4' G B 9 OK 2460 2457 2459 2481 C4' C B 10 OK 2483 2480 2482 2501 C4' U B 11 OK 2503 2500 2502 2521 C4' A B 12 OK 2523 2520 2522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2287 C5' G B 1 2286 2288 2310 C5' C B 2 2309 2311 2330 C5' G B 3 2329 2331 2353 C5' A B 4 2352 2354 2375 C5' A B 5 2374 2376 2397 C5' U B 6 2396 2398 2417 C5' U B 7 2416 2418 2437 C5' C B 8 2436 2438 2457 C5' G B 9 2456 2458 2480 C5' C B 10 2479 2481 2500 C5' U B 11 2499 2501 2520 C5' A B 12 2519 2521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2306 P C B 2 distorted distorted 2291 2307 2308 2309 2326 P G B 3 distorted distorted 2314 2327 2328 2329 2349 P A B 4 distorted distorted 2334 2350 2351 2352 2371 P A B 5 distorted distorted 2357 2372 2373 2374 2393 P U B 6 distorted distorted 2379 2394 2395 2396 2413 P U B 7 distorted distorted 2401 2414 2415 2416 2433 P C B 8 distorted distorted 2421 2434 2435 2436 2453 P G B 9 distorted distorted 2441 2454 2455 2456 2476 P C B 10 distorted distorted 2461 2477 2478 2479 2496 P U B 11 distorted distorted 2484 2497 2498 2499 2516 P A B 12 distorted distorted 2504 2517 2518 2519 ---------------------------------------------------------------------------------