ID code: '4NH6' 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' --------------------------------------------------------------------------------- 2213 C1' U B 1 beta 2208 2214 2211 2233 C1' U B 2 beta 2228 2234 2231 2253 C1' U B 3 beta 2248 2254 2251 2266 C1' G B 4 beta 2261 2267 2264 2289 C1' C B 5 beta 2284 2290 2287 2309 C1' G B 6 beta 2304 2310 2307 2332 C1' A B 7 beta 2327 2333 2330 2354 C1' A B 8 beta 2349 2355 2352 2376 C1' U B 9 beta 2371 2377 2374 2396 C1' U B 10 beta 2391 2397 2394 2416 C1' C B 11 beta 2411 2417 2414 2436 C1' G B 12 beta 2431 2437 2434 2459 C1' C B 13 beta 2454 2460 2457 2479 C1' U B 14 beta 2474 2480 2477 2499 C1' U B 15 beta 2494 2500 2497 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2211 C2' U B 1 OK 2213 2209 2212 2231 C2' U B 2 OK 2233 2229 2232 2251 C2' U B 3 OK 2253 2249 2252 2264 C2' G B 4 OK 2266 2262 2265 2287 C2' C B 5 OK 2289 2285 2288 2307 C2' G B 6 OK 2309 2305 2308 2330 C2' A B 7 OK 2332 2328 2331 2352 C2' A B 8 OK 2354 2350 2353 2374 C2' U B 9 OK 2376 2372 2375 2394 C2' U B 10 OK 2396 2392 2395 2414 C2' C B 11 OK 2416 2412 2415 2434 C2' G B 12 OK 2436 2432 2435 2457 C2' C B 13 OK 2459 2455 2458 2477 C2' U B 14 OK 2479 2475 2478 2497 C2' U B 15 OK 2499 2495 2498 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2209 C3' U B 1 OK 2207 2210 2211 2229 C3' U B 2 OK 2227 2230 2231 2249 C3' U B 3 OK 2247 2250 2251 2262 C3' G B 4 OK 2260 2263 2264 2285 C3' C B 5 OK 2283 2286 2287 2305 C3' G B 6 OK 2303 2306 2307 2328 C3' A B 7 OK 2326 2329 2330 2350 C3' A B 8 OK 2348 2351 2352 2372 C3' U B 9 OK 2370 2373 2374 2392 C3' U B 10 OK 2390 2393 2394 2412 C3' C B 11 OK 2410 2413 2414 2432 C3' G B 12 OK 2430 2433 2434 2455 C3' C B 13 OK 2453 2456 2457 2475 C3' U B 14 OK 2473 2476 2477 2495 C3' U B 15 OK 2493 2496 2497 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2207 C4' U B 1 OK 2209 2206 2208 2227 C4' U B 2 OK 2229 2226 2228 2247 C4' U B 3 OK 2249 2246 2248 2260 C4' G B 4 OK 2262 2259 2261 2283 C4' C B 5 OK 2285 2282 2284 2303 C4' G B 6 OK 2305 2302 2304 2326 C4' A B 7 OK 2328 2325 2327 2348 C4' A B 8 OK 2350 2347 2349 2370 C4' U B 9 OK 2372 2369 2371 2390 C4' U B 10 OK 2392 2389 2391 2410 C4' C B 11 OK 2412 2409 2411 2430 C4' G B 12 OK 2432 2429 2431 2453 C4' C B 13 OK 2455 2452 2454 2473 C4' U B 14 OK 2475 2472 2474 2493 C4' U B 15 OK 2495 2492 2494 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2206 C5' U B 1 2205 2207 2226 C5' U B 2 2225 2227 2246 C5' U B 3 2245 2247 2259 C5' G B 4 2258 2260 2282 C5' C B 5 2281 2283 2302 C5' G B 6 2301 2303 2325 C5' A B 7 2324 2326 2347 C5' A B 8 2346 2348 2369 C5' U B 9 2368 2370 2389 C5' U B 10 2388 2390 2409 C5' C B 11 2408 2410 2429 C5' G B 12 2428 2430 2452 C5' C B 13 2451 2453 2472 C5' U B 14 2471 2473 2492 C5' U B 15 2491 2493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2202 P U B 1 OK OK 2203 2204 2205 2222 P U B 2 distorted distorted 2210 2223 2224 2225 2242 P U B 3 distorted distorted 2230 2243 2244 2245 2255 P G B 4 distorted distorted 2250 2256 2257 2258 2278 P C B 5 distorted distorted 2263 2279 2280 2281 2298 P G B 6 distorted distorted 2286 2299 2300 2301 2321 P A B 7 distorted distorted 2306 2322 2323 2324 2343 P A B 8 distorted distorted 2329 2344 2345 2346 2365 P U B 9 distorted distorted 2351 2366 2367 2368 2385 P U B 10 distorted distorted 2373 2386 2387 2388 2405 P C B 11 distorted distorted 2393 2406 2407 2408 2425 P G B 12 distorted distorted 2413 2426 2427 2428 2448 P C B 13 distorted distorted 2433 2449 2450 2451 2468 P U B 14 distorted distorted 2456 2469 2470 2471 2488 P U B 15 distorted distorted 2476 2489 2490 2491 ---------------------------------------------------------------------------------