ID code: '3T5N' 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' U C 2 beta 2192 2198 2195 2217 C1' A C 3 beta 2212 2218 2215 2239 C1' U C 4 beta 2234 2240 2237 2259 C1' C C 5 beta 2254 2260 2257 2279 C1' U C 6 beta 2274 2280 2277 2299 C1' C C 7 beta 2294 2300 2297 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2195 C2' U C 2 OK 2197 2193 2196 2215 C2' A C 3 OK 2217 2213 2216 2237 C2' U C 4 OK 2239 2235 2238 2257 C2' C C 5 OK 2259 2255 2258 2277 C2' U C 6 OK 2279 2275 2278 2297 C2' C C 7 OK 2299 2295 2298 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2193 C3' U C 2 OK 2191 2194 2195 2213 C3' A C 3 OK 2211 2214 2215 2235 C3' U C 4 OK 2233 2236 2237 2255 C3' C C 5 OK 2253 2256 2257 2275 C3' U C 6 OK 2273 2276 2277 2295 C3' C C 7 OK 2293 2296 2297 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2191 C4' U C 2 OK 2193 2190 2192 2211 C4' A C 3 OK 2213 2210 2212 2233 C4' U C 4 OK 2235 2232 2234 2253 C4' C C 5 OK 2255 2252 2254 2273 C4' U C 6 OK 2275 2272 2274 2293 C4' C C 7 OK 2295 2292 2294 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2190 C5' U C 2 2189 2191 2210 C5' A C 3 2209 2211 2232 C5' U C 4 2231 2233 2252 C5' C C 5 2251 2253 2272 C5' U C 6 2271 2273 2292 C5' C C 7 2291 2293 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2186 P U C 2 distorted distorted 2187 2188 2189 2206 P A C 3 distorted distorted 2194 2207 2208 2209 2228 P U C 4 distorted distorted 2214 2229 2230 2231 2248 P C C 5 distorted distorted 2236 2249 2250 2251 2268 P U C 6 distorted distorted 2256 2269 2270 2271 2288 P C C 7 distorted distorted 2276 2289 2290 2291 ---------------------------------------------------------------------------------