ID code: '4NH3' 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' --------------------------------------------------------------------------------- 2142 C1' U B 1 beta 2137 2143 2140 2162 C1' G B 2 beta 2157 2163 2160 2185 C1' C B 3 beta 2180 2186 2183 2205 C1' G B 4 beta 2200 2206 2203 2228 C1' A B 5 beta 2223 2229 2226 2250 C1' A B 6 beta 2245 2251 2248 2272 C1' U B 7 beta 2267 2273 2270 2292 C1' U B 8 beta 2287 2293 2290 2312 C1' C B 9 beta 2307 2313 2310 2332 C1' G B 10 beta 2327 2333 2330 2355 C1' C B 11 beta 2350 2356 2353 2375 C1' U B 12 beta 2370 2376 2373 2395 C1' U B 13 beta 2390 2396 2393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2140 C2' U B 1 OK 2142 2138 2141 2160 C2' G B 2 OK 2162 2158 2161 2183 C2' C B 3 OK 2185 2181 2184 2203 C2' G B 4 OK 2205 2201 2204 2226 C2' A B 5 OK 2228 2224 2227 2248 C2' A B 6 OK 2250 2246 2249 2270 C2' U B 7 OK 2272 2268 2271 2290 C2' U B 8 OK 2292 2288 2291 2310 C2' C B 9 OK 2312 2308 2311 2330 C2' G B 10 OK 2332 2328 2331 2353 C2' C B 11 OK 2355 2351 2354 2373 C2' U B 12 OK 2375 2371 2374 2393 C2' U B 13 OK 2395 2391 2394 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2138 C3' U B 1 OK 2136 2139 2140 2158 C3' G B 2 OK 2156 2159 2160 2181 C3' C B 3 OK 2179 2182 2183 2201 C3' G B 4 OK 2199 2202 2203 2224 C3' A B 5 OK 2222 2225 2226 2246 C3' A B 6 OK 2244 2247 2248 2268 C3' U B 7 OK 2266 2269 2270 2288 C3' U B 8 OK 2286 2289 2290 2308 C3' C B 9 OK 2306 2309 2310 2328 C3' G B 10 OK 2326 2329 2330 2351 C3' C B 11 OK 2349 2352 2353 2371 C3' U B 12 OK 2369 2372 2373 2391 C3' U B 13 OK 2389 2392 2393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2136 C4' U B 1 OK 2138 2135 2137 2156 C4' G B 2 OK 2158 2155 2157 2179 C4' C B 3 OK 2181 2178 2180 2199 C4' G B 4 OK 2201 2198 2200 2222 C4' A B 5 OK 2224 2221 2223 2244 C4' A B 6 OK 2246 2243 2245 2266 C4' U B 7 OK 2268 2265 2267 2286 C4' U B 8 OK 2288 2285 2287 2306 C4' C B 9 OK 2308 2305 2307 2326 C4' G B 10 OK 2328 2325 2327 2349 C4' C B 11 OK 2351 2348 2350 2369 C4' U B 12 OK 2371 2368 2370 2389 C4' U B 13 OK 2391 2388 2390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2135 C5' U B 1 2134 2136 2155 C5' G B 2 2154 2156 2178 C5' C B 3 2177 2179 2198 C5' G B 4 2197 2199 2221 C5' A B 5 2220 2222 2243 C5' A B 6 2242 2244 2265 C5' U B 7 2264 2266 2285 C5' U B 8 2284 2286 2305 C5' C B 9 2304 2306 2325 C5' G B 10 2324 2326 2348 C5' C B 11 2347 2349 2368 C5' U B 12 2367 2369 2388 C5' U B 13 2387 2389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2131 P U B 1 OK OK 2132 2133 2134 2151 P G B 2 distorted distorted 2139 2152 2153 2154 2174 P C B 3 distorted distorted 2159 2175 2176 2177 2194 P G B 4 distorted distorted 2182 2195 2196 2197 2217 P A B 5 distorted distorted 2202 2218 2219 2220 2239 P A B 6 distorted distorted 2225 2240 2241 2242 2261 P U B 7 distorted distorted 2247 2262 2263 2264 2281 P U B 8 distorted distorted 2269 2282 2283 2284 2301 P C B 9 distorted distorted 2289 2302 2303 2304 2321 P G B 10 distorted distorted 2309 2322 2323 2324 2344 P C B 11 distorted distorted 2329 2345 2346 2347 2364 P U B 12 distorted distorted 2352 2365 2366 2367 2384 P U B 13 distorted distorted 2372 2385 2386 2387 ---------------------------------------------------------------------------------