ID code: '4NH5' 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' --------------------------------------------------------------------------------- 2189 C1' U B 1 2185 2188 2201 C1' U B 2 beta 2196 2202 2199 2221 C1' G B 3 beta 2216 2222 2219 2244 C1' C B 4 beta 2239 2245 2242 2264 C1' G B 5 beta 2259 2265 2262 2287 C1' A B 6 beta 2282 2288 2285 2309 C1' A B 7 beta 2304 2310 2307 2331 C1' U B 8 beta 2326 2332 2329 2351 C1' U B 9 beta 2346 2352 2349 2371 C1' C B 10 beta 2366 2372 2369 2391 C1' G B 11 beta 2386 2392 2389 2414 C1' C B 12 beta 2409 2415 2412 2434 C1' U B 13 beta 2429 2435 2432 2454 C1' U B 14 beta 2449 2455 2452 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2188 C2' U B 1 2189 2186 2199 C2' U B 2 OK 2201 2197 2200 2219 C2' G B 3 OK 2221 2217 2220 2242 C2' C B 4 OK 2244 2240 2243 2262 C2' G B 5 OK 2264 2260 2263 2285 C2' A B 6 OK 2287 2283 2286 2307 C2' A B 7 OK 2309 2305 2308 2329 C2' U B 8 OK 2331 2327 2330 2349 C2' U B 9 OK 2351 2347 2350 2369 C2' C B 10 OK 2371 2367 2370 2389 C2' G B 11 OK 2391 2387 2390 2412 C2' C B 12 OK 2414 2410 2413 2432 C2' U B 13 OK 2434 2430 2433 2452 C2' U B 14 OK 2454 2450 2453 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2186 C3' U B 1 OK 2184 2187 2188 2197 C3' U B 2 OK 2195 2198 2199 2217 C3' G B 3 OK 2215 2218 2219 2240 C3' C B 4 OK 2238 2241 2242 2260 C3' G B 5 OK 2258 2261 2262 2283 C3' A B 6 OK 2281 2284 2285 2305 C3' A B 7 OK 2303 2306 2307 2327 C3' U B 8 OK 2325 2328 2329 2347 C3' U B 9 OK 2345 2348 2349 2367 C3' C B 10 OK 2365 2368 2369 2387 C3' G B 11 OK 2385 2388 2389 2410 C3' C B 12 OK 2408 2411 2412 2430 C3' U B 13 OK 2428 2431 2432 2450 C3' U B 14 OK 2448 2451 2452 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2184 C4' U B 1 OK 2186 2183 2185 2195 C4' U B 2 OK 2197 2194 2196 2215 C4' G B 3 OK 2217 2214 2216 2238 C4' C B 4 OK 2240 2237 2239 2258 C4' G B 5 OK 2260 2257 2259 2281 C4' A B 6 OK 2283 2280 2282 2303 C4' A B 7 OK 2305 2302 2304 2325 C4' U B 8 OK 2327 2324 2326 2345 C4' U B 9 OK 2347 2344 2346 2365 C4' C B 10 OK 2367 2364 2366 2385 C4' G B 11 OK 2387 2384 2386 2408 C4' C B 12 OK 2410 2407 2409 2428 C4' U B 13 OK 2430 2427 2429 2448 C4' U B 14 OK 2450 2447 2449 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2183 C5' U B 1 2182 2184 2194 C5' U B 2 2193 2195 2214 C5' G B 3 2213 2215 2237 C5' C B 4 2236 2238 2257 C5' G B 5 2256 2258 2280 C5' A B 6 2279 2281 2302 C5' A B 7 2301 2303 2324 C5' U B 8 2323 2325 2344 C5' U B 9 2343 2345 2364 C5' C B 10 2363 2365 2384 C5' G B 11 2383 2385 2407 C5' C B 12 2406 2408 2427 C5' U B 13 2426 2428 2447 C5' U B 14 2446 2448 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2179 P U B 1 distorted distorted 2180 2181 2182 2190 P U B 2 distorted distorted 2187 2191 2192 2193 2210 P G B 3 distorted distorted 2198 2211 2212 2213 2233 P C B 4 distorted distorted 2218 2234 2235 2236 2253 P G B 5 distorted distorted 2241 2254 2255 2256 2276 P A B 6 distorted distorted 2261 2277 2278 2279 2298 P A B 7 distorted distorted 2284 2299 2300 2301 2320 P U B 8 distorted distorted 2306 2321 2322 2323 2340 P U B 9 distorted distorted 2328 2341 2342 2343 2360 P C B 10 distorted distorted 2348 2361 2362 2363 2380 P G B 11 distorted distorted 2368 2381 2382 2383 2403 P C B 12 distorted distorted 2388 2404 2405 2406 2423 P U B 13 distorted distorted 2411 2424 2425 2426 2443 P U B 14 distorted distorted 2431 2444 2445 2446 ---------------------------------------------------------------------------------