ID code: '4NGG' 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' --------------------------------------------------------------------------------- 2165 C1' A B 1 beta 2160 2166 2163 2187 C1' G B 2 beta 2182 2188 2185 2210 C1' C B 3 beta 2205 2211 2208 2230 C1' G B 4 beta 2225 2231 2228 2253 C1' A B 5 beta 2248 2254 2251 2275 C1' A B 6 beta 2270 2276 2273 2297 C1' U B 7 beta 2292 2298 2295 2317 C1' U B 8 beta 2312 2318 2315 2337 C1' C B 9 beta 2332 2338 2335 2357 C1' G B 10 beta 2352 2358 2355 2380 C1' C B 11 beta 2375 2381 2378 2400 C1' U B 12 beta 2395 2401 2398 2420 C1' U B 13 beta 2415 2421 2418 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2163 C2' A B 1 OK 2165 2161 2164 2185 C2' G B 2 OK 2187 2183 2186 2208 C2' C B 3 OK 2210 2206 2209 2228 C2' G B 4 OK 2230 2226 2229 2251 C2' A B 5 OK 2253 2249 2252 2273 C2' A B 6 OK 2275 2271 2274 2295 C2' U B 7 OK 2297 2293 2296 2315 C2' U B 8 OK 2317 2313 2316 2335 C2' C B 9 OK 2337 2333 2336 2355 C2' G B 10 OK 2357 2353 2356 2378 C2' C B 11 OK 2380 2376 2379 2398 C2' U B 12 OK 2400 2396 2399 2418 C2' U B 13 OK 2420 2416 2419 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2161 C3' A B 1 OK 2159 2162 2163 2183 C3' G B 2 OK 2181 2184 2185 2206 C3' C B 3 OK 2204 2207 2208 2226 C3' G B 4 OK 2224 2227 2228 2249 C3' A B 5 OK 2247 2250 2251 2271 C3' A B 6 OK 2269 2272 2273 2293 C3' U B 7 OK 2291 2294 2295 2313 C3' U B 8 OK 2311 2314 2315 2333 C3' C B 9 OK 2331 2334 2335 2353 C3' G B 10 OK 2351 2354 2355 2376 C3' C B 11 OK 2374 2377 2378 2396 C3' U B 12 OK 2394 2397 2398 2416 C3' U B 13 OK 2414 2417 2418 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2159 C4' A B 1 2161 2160 2181 C4' G B 2 OK 2183 2180 2182 2204 C4' C B 3 OK 2206 2203 2205 2224 C4' G B 4 OK 2226 2223 2225 2247 C4' A B 5 OK 2249 2246 2248 2269 C4' A B 6 OK 2271 2268 2270 2291 C4' U B 7 OK 2293 2290 2292 2311 C4' U B 8 OK 2313 2310 2312 2331 C4' C B 9 OK 2333 2330 2332 2351 C4' G B 10 OK 2353 2350 2352 2374 C4' C B 11 OK 2376 2373 2375 2394 C4' U B 12 OK 2396 2393 2395 2414 C4' U B 13 OK 2416 2413 2415 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2180 C5' G B 2 2179 2181 2203 C5' C B 3 2202 2204 2223 C5' G B 4 2222 2224 2246 C5' A B 5 2245 2247 2268 C5' A B 6 2267 2269 2290 C5' U B 7 2289 2291 2310 C5' U B 8 2309 2311 2330 C5' C B 9 2329 2331 2350 C5' G B 10 2349 2351 2373 C5' C B 11 2372 2374 2393 C5' U B 12 2392 2394 2413 C5' U B 13 2412 2414 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2176 P G B 2 distorted distorted 2162 2177 2178 2179 2199 P C B 3 distorted distorted 2184 2200 2201 2202 2219 P G B 4 distorted distorted 2207 2220 2221 2222 2242 P A B 5 distorted distorted 2227 2243 2244 2245 2264 P A B 6 distorted distorted 2250 2265 2266 2267 2286 P U B 7 distorted distorted 2272 2287 2288 2289 2306 P U B 8 distorted distorted 2294 2307 2308 2309 2326 P C B 9 distorted distorted 2314 2327 2328 2329 2346 P G B 10 distorted distorted 2334 2347 2348 2349 2369 P C B 11 distorted distorted 2354 2370 2371 2372 2389 P U B 12 distorted distorted 2377 2390 2391 2392 2409 P U B 13 distorted distorted 2397 2410 2411 2412 2430 P PO4 A1101 ---------------------------------------------------------------------------------