ID code: '3EQT' 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' --------------------------------------------------------------------------------- 2177 C1' G C 1 beta 2172 2178 2175 2200 C1' C C 2 beta 2195 2201 2198 2220 C1' G C 3 beta 2215 2221 2218 2243 C1' C C 4 beta 2238 2244 2241 2263 C1' G C 5 beta 2258 2264 2261 2286 C1' C C 6 beta 2281 2287 2284 2306 C1' G C 7 beta 2301 2307 2304 2329 C1' C C 8 beta 2324 2330 2327 2347 C1' G D 1 beta 2342 2348 2345 2370 C1' C D 2 beta 2365 2371 2368 2390 C1' G D 3 beta 2385 2391 2388 2413 C1' C D 4 beta 2408 2414 2411 2433 C1' G D 5 beta 2428 2434 2431 2456 C1' C D 6 beta 2451 2457 2454 2476 C1' G D 7 beta 2471 2477 2474 2499 C1' C D 8 beta 2494 2500 2497 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2175 C2' G C 1 OK 2177 2173 2176 2198 C2' C C 2 OK 2200 2196 2199 2218 C2' G C 3 OK 2220 2216 2219 2241 C2' C C 4 OK 2243 2239 2242 2261 C2' G C 5 OK 2263 2259 2262 2284 C2' C C 6 OK 2286 2282 2285 2304 C2' G C 7 OK 2306 2302 2305 2327 C2' C C 8 OK 2329 2325 2328 2345 C2' G D 1 OK 2347 2343 2346 2368 C2' C D 2 OK 2370 2366 2369 2388 C2' G D 3 OK 2390 2386 2389 2411 C2' C D 4 OK 2413 2409 2412 2431 C2' G D 5 OK 2433 2429 2432 2454 C2' C D 6 OK 2456 2452 2455 2474 C2' G D 7 OK 2476 2472 2475 2497 C2' C D 8 OK 2499 2495 2498 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2173 C3' G C 1 OK 2171 2174 2175 2196 C3' C C 2 OK 2194 2197 2198 2216 C3' G C 3 OK 2214 2217 2218 2239 C3' C C 4 OK 2237 2240 2241 2259 C3' G C 5 OK 2257 2260 2261 2282 C3' C C 6 OK 2280 2283 2284 2302 C3' G C 7 OK 2300 2303 2304 2325 C3' C C 8 OK 2323 2326 2327 2343 C3' G D 1 OK 2341 2344 2345 2366 C3' C D 2 OK 2364 2367 2368 2386 C3' G D 3 OK 2384 2387 2388 2409 C3' C D 4 OK 2407 2410 2411 2429 C3' G D 5 OK 2427 2430 2431 2452 C3' C D 6 OK 2450 2453 2454 2472 C3' G D 7 OK 2470 2473 2474 2495 C3' C D 8 OK 2493 2496 2497 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2171 C4' G C 1 OK 2173 2170 2172 2194 C4' C C 2 OK 2196 2193 2195 2214 C4' G C 3 OK 2216 2213 2215 2237 C4' C C 4 OK 2239 2236 2238 2257 C4' G C 5 OK 2259 2256 2258 2280 C4' C C 6 OK 2282 2279 2281 2300 C4' G C 7 OK 2302 2299 2301 2323 C4' C C 8 OK 2325 2322 2324 2341 C4' G D 1 OK 2343 2340 2342 2364 C4' C D 2 OK 2366 2363 2365 2384 C4' G D 3 OK 2386 2383 2385 2407 C4' C D 4 OK 2409 2406 2408 2427 C4' G D 5 OK 2429 2426 2428 2450 C4' C D 6 OK 2452 2449 2451 2470 C4' G D 7 OK 2472 2469 2471 2493 C4' C D 8 OK 2495 2492 2494 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2170 C5' G C 1 2169 2171 2193 C5' C C 2 2192 2194 2213 C5' G C 3 2212 2214 2236 C5' C C 4 2235 2237 2256 C5' G C 5 2255 2257 2279 C5' C C 6 2278 2280 2299 C5' G C 7 2298 2300 2322 C5' C C 8 2321 2323 2340 C5' G D 1 2339 2341 2363 C5' C D 2 2362 2364 2383 C5' G D 3 2382 2384 2406 C5' C D 4 2405 2407 2426 C5' G D 5 2425 2427 2449 C5' C D 6 2448 2450 2469 C5' G D 7 2468 2470 2492 C5' C D 8 2491 2493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2189 P C C 2 distorted distorted 2174 2190 2191 2192 2209 P G C 3 distorted distorted 2197 2210 2211 2212 2232 P C C 4 distorted distorted 2217 2233 2234 2235 2252 P G C 5 distorted distorted 2240 2253 2254 2255 2275 P C C 6 distorted distorted 2260 2276 2277 2278 2295 P G C 7 distorted distorted 2283 2296 2297 2298 2318 P C C 8 distorted distorted 2303 2319 2320 2321 2359 P C D 2 distorted distorted 2344 2360 2361 2362 2379 P G D 3 distorted distorted 2367 2380 2381 2382 2402 P C D 4 distorted distorted 2387 2403 2404 2405 2422 P G D 5 distorted distorted 2410 2423 2424 2425 2445 P C D 6 distorted distorted 2430 2446 2447 2448 2465 P G D 7 distorted distorted 2453 2466 2467 2468 2488 P C D 8 distorted distorted 2473 2489 2490 2491 ---------------------------------------------------------------------------------