ID code: '3D2S' 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' --------------------------------------------------------------------------------- 2197 C1' G E 2 beta 2192 2198 2195 2220 C1' C E 3 beta 2215 2221 2218 2240 C1' U E 4 beta 2235 2241 2238 2260 C1' G E 5 beta 2255 2261 2258 2283 C1' U E 6 beta 2278 2284 2281 2301 C1' C F 1 beta 2296 2302 2299 2321 C1' G F 2 beta 2316 2322 2319 2344 C1' C F 3 beta 2339 2345 2342 2381 C1' G G 2 beta 2376 2382 2379 2404 C1' C G 3 beta 2399 2405 2402 2424 C1' U G 4 beta 2419 2425 2422 2444 C1' G G 5 beta 2439 2445 2442 2467 C1' U G 6 beta 2462 2468 2465 2485 C1' C H 1 beta 2480 2486 2483 2505 C1' G H 2 beta 2500 2506 2503 2528 C1' C H 3 beta 2523 2529 2526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2195 C2' G E 2 OK 2197 2193 2196 2218 C2' C E 3 OK 2220 2216 2219 2238 C2' U E 4 OK 2240 2236 2239 2258 C2' G E 5 OK 2260 2256 2259 2281 C2' U E 6 OK 2283 2279 2282 2299 C2' C F 1 OK 2301 2297 2300 2319 C2' G F 2 OK 2321 2317 2320 2342 C2' C F 3 OK 2344 2340 2343 2379 C2' G G 2 OK 2381 2377 2380 2402 C2' C G 3 OK 2404 2400 2403 2422 C2' U G 4 OK 2424 2420 2423 2442 C2' G G 5 OK 2444 2440 2443 2465 C2' U G 6 OK 2467 2463 2466 2483 C2' C H 1 OK 2485 2481 2484 2503 C2' G H 2 OK 2505 2501 2504 2526 C2' C H 3 OK 2528 2524 2527 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2193 C3' G E 2 OK 2191 2194 2195 2216 C3' C E 3 OK 2214 2217 2218 2236 C3' U E 4 OK 2234 2237 2238 2256 C3' G E 5 OK 2254 2257 2258 2279 C3' U E 6 OK 2277 2280 2281 2297 C3' C F 1 OK 2295 2298 2299 2317 C3' G F 2 OK 2315 2318 2319 2340 C3' C F 3 OK 2338 2341 2342 2377 C3' G G 2 OK 2375 2378 2379 2400 C3' C G 3 OK 2398 2401 2402 2420 C3' U G 4 OK 2418 2421 2422 2440 C3' G G 5 OK 2438 2441 2442 2463 C3' U G 6 OK 2461 2464 2465 2481 C3' C H 1 OK 2479 2482 2483 2501 C3' G H 2 OK 2499 2502 2503 2524 C3' C H 3 OK 2522 2525 2526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2191 C4' G E 2 OK 2193 2190 2192 2214 C4' C E 3 OK 2216 2213 2215 2234 C4' U E 4 OK 2236 2233 2235 2254 C4' G E 5 OK 2256 2253 2255 2277 C4' U E 6 OK 2279 2276 2278 2295 C4' C F 1 OK 2297 2294 2296 2315 C4' G F 2 OK 2317 2314 2316 2338 C4' C F 3 OK 2340 2337 2339 2375 C4' G G 2 OK 2377 2374 2376 2398 C4' C G 3 OK 2400 2397 2399 2418 C4' U G 4 OK 2420 2417 2419 2438 C4' G G 5 OK 2440 2437 2439 2461 C4' U G 6 OK 2463 2460 2462 2479 C4' C H 1 OK 2481 2478 2480 2499 C4' G H 2 OK 2501 2498 2500 2522 C4' C H 3 OK 2524 2521 2523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2190 C5' G E 2 2189 2191 2213 C5' C E 3 2212 2214 2233 C5' U E 4 2232 2234 2253 C5' G E 5 2252 2254 2276 C5' U E 6 2275 2277 2294 C5' C F 1 2293 2295 2314 C5' G F 2 2313 2315 2337 C5' C F 3 2336 2338 2374 C5' G G 2 2373 2375 2397 C5' C G 3 2396 2398 2417 C5' U G 4 2416 2418 2437 C5' G G 5 2436 2438 2460 C5' U G 6 2459 2461 2478 C5' C H 1 2477 2479 2498 C5' G H 2 2497 2499 2521 C5' C H 3 2520 2522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2186 P G E 2 distorted distorted 2185 2187 2188 2189 2209 P C E 3 distorted distorted 2194 2210 2211 2212 2229 P U E 4 distorted distorted 2217 2230 2231 2232 2249 P G E 5 distorted distorted 2237 2250 2251 2252 2272 P U E 6 distorted distorted 2257 2273 2274 2275 2310 P G F 2 distorted distorted 2298 2311 2312 2313 2333 P C F 3 distorted distorted 2318 2334 2335 2336 2353 P U F 4 distorted distorted 2341 2354 2355 2356 2370 P G G 2 distorted distorted 2369 2371 2372 2373 2393 P C G 3 distorted distorted 2378 2394 2395 2396 2413 P U G 4 distorted distorted 2401 2414 2415 2416 2433 P G G 5 distorted distorted 2421 2434 2435 2436 2456 P U G 6 distorted distorted 2441 2457 2458 2459 2494 P G H 2 distorted distorted 2482 2495 2496 2497 2517 P C H 3 distorted distorted 2502 2518 2519 2520 2537 P U H 4 distorted distorted 2525 2538 2539 2540 ---------------------------------------------------------------------------------