ID code: '2L5D' 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' --------------------------------------------------------------------------------- 2205 C1' U B 501 alpha beta 2200 2220 2206 2203 2236 C1' G B 502 alpha beta 2231 2254 2237 2234 2270 C1' A B 503 alpha beta 2265 2287 2271 2268 2303 C1' C B 504 alpha beta 2298 2318 2304 2301 2334 C1' A B 505 alpha beta 2329 2352 2335 2332 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2203 C2' U B 501 OK OK 2205 2201 2218 2204 2234 C2' G B 502 OK OK 2236 2232 2252 2235 2268 C2' A B 503 OK OK 2270 2266 2285 2269 2301 C2' C B 504 OK OK 2303 2299 2316 2302 2332 C2' A B 505 OK OK 2334 2330 2350 2333 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2201 C3' U B 501 OK OK 2199 2217 2202 2203 2232 C3' G B 502 OK OK 2230 2251 2233 2234 2266 C3' A B 503 OK OK 2264 2284 2267 2268 2299 C3' C B 504 OK OK 2297 2315 2300 2301 2330 C3' A B 505 OK OK 2328 2348 2331 2332 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2199 C4' U B 501 OK OK 2201 2216 2198 2200 2230 C4' G B 502 OK OK 2232 2250 2229 2231 2264 C4' A B 503 OK OK 2266 2283 2263 2265 2297 C4' C B 504 OK OK 2299 2314 2296 2298 2328 C4' A B 505 OK OK 2330 2347 2327 2329 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2198 C5' U B 501 OK OK 2197 2214 2215 2199 2229 C5' G B 502 OK OK 2228 2248 2249 2230 2263 C5' A B 503 OK OK 2262 2281 2282 2264 2296 C5' C B 504 OK OK 2295 2312 2313 2297 2327 C5' A B 505 OK OK 2326 2345 2346 2328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2225 P G B 502 distorted distorted 2202 2226 2227 2228 2259 P A B 503 distorted distorted 2233 2260 2261 2262 2292 P C B 504 distorted distorted 2267 2293 2294 2295 2323 P A B 505 distorted distorted 2300 2324 2325 2326 ---------------------------------------------------------------------------------