ID code: '2N3O' 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' --------------------------------------------------------------------------------- 1902 C1' G B 1 alpha beta 1897 1920 1903 1900 1936 C1' G B 2 alpha beta 1931 1954 1937 1934 1970 C1' G B 3 alpha beta 1965 1988 1971 1968 2004 C1' A B 4 alpha beta 1999 2021 2005 2002 2037 C1' C B 5 alpha beta 2032 2052 2038 2035 2068 C1' C B 6 alpha beta 2063 2083 2069 2066 2099 C1' U B 7 alpha beta 2094 2114 2100 2097 2129 C1' G B 8 alpha beta 2124 2147 2130 2127 2163 C1' G B 9 alpha beta 2158 2181 2164 2161 2197 C1' U B 10 alpha beta 2192 2212 2198 2195 2227 C1' C B 11 alpha beta 2222 2242 2228 2225 2258 C1' U B 12 alpha beta 2253 2273 2259 2256 2288 C1' U B 13 alpha beta 2283 2303 2289 2286 2318 C1' U B 14 alpha beta 2313 2333 2319 2316 2348 C1' C B 15 alpha beta 2343 2363 2349 2346 2379 C1' C B 16 alpha beta 2374 2394 2380 2377 2410 C1' A B 17 alpha beta 2405 2427 2411 2408 2443 C1' G B 18 alpha beta 2438 2461 2444 2441 2477 C1' G B 19 alpha beta 2472 2495 2478 2475 2511 C1' U B 20 alpha beta 2506 2526 2512 2509 2541 C1' C B 21 alpha beta 2536 2556 2542 2539 2572 C1' C B 22 alpha beta 2567 2587 2573 2570 2603 C1' C B 23 alpha beta 2598 2618 2604 2601 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1900 C2' G B 1 OK OK 1902 1898 1918 1901 1934 C2' G B 2 OK OK 1936 1932 1952 1935 1968 C2' G B 3 OK OK 1970 1966 1986 1969 2002 C2' A B 4 OK OK 2004 2000 2019 2003 2035 C2' C B 5 OK OK 2037 2033 2050 2036 2066 C2' C B 6 OK OK 2068 2064 2081 2067 2097 C2' U B 7 OK OK 2099 2095 2112 2098 2127 C2' G B 8 OK OK 2129 2125 2145 2128 2161 C2' G B 9 OK OK 2163 2159 2179 2162 2195 C2' U B 10 OK OK 2197 2193 2210 2196 2225 C2' C B 11 OK OK 2227 2223 2240 2226 2256 C2' U B 12 OK OK 2258 2254 2271 2257 2286 C2' U B 13 OK OK 2288 2284 2301 2287 2316 C2' U B 14 OK OK 2318 2314 2331 2317 2346 C2' C B 15 OK OK 2348 2344 2361 2347 2377 C2' C B 16 OK OK 2379 2375 2392 2378 2408 C2' A B 17 OK OK 2410 2406 2425 2409 2441 C2' G B 18 OK OK 2443 2439 2459 2442 2475 C2' G B 19 OK OK 2477 2473 2493 2476 2509 C2' U B 20 OK OK 2511 2507 2524 2510 2539 C2' C B 21 OK OK 2541 2537 2554 2540 2570 C2' C B 22 OK OK 2572 2568 2585 2571 2601 C2' C B 23 OK OK 2603 2599 2616 2602 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1898 C3' G B 1 OK OK 1896 1917 1899 1900 1932 C3' G B 2 OK OK 1930 1951 1933 1934 1966 C3' G B 3 OK OK 1964 1985 1967 1968 2000 C3' A B 4 OK OK 1998 2018 2001 2002 2033 C3' C B 5 OK OK 2031 2049 2034 2035 2064 C3' C B 6 OK OK 2062 2080 2065 2066 2095 C3' U B 7 OK OK 2093 2111 2096 2097 2125 C3' G B 8 OK OK 2123 2144 2126 2127 2159 C3' G B 9 OK OK 2157 2178 2160 2161 2193 C3' U B 10 OK OK 2191 2209 2194 2195 2223 C3' C B 11 OK OK 2221 2239 2224 2225 2254 C3' U B 12 OK OK 2252 2270 2255 2256 2284 C3' U B 13 OK OK 2282 2300 2285 2286 2314 C3' U B 14 OK OK 2312 2330 2315 2316 2344 C3' C B 15 OK OK 2342 2360 2345 2346 2375 C3' C B 16 OK OK 2373 2391 2376 2377 2406 C3' A B 17 OK OK 2404 2424 2407 2408 2439 C3' G B 18 OK OK 2437 2458 2440 2441 2473 C3' G B 19 OK OK 2471 2492 2474 2475 2507 C3' U B 20 OK OK 2505 2523 2508 2509 2537 C3' C B 21 OK OK 2535 2553 2538 2539 2568 C3' C B 22 OK OK 2566 2584 2569 2570 2599 C3' C B 23 OK OK 2597 2615 2600 2601 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1896 C4' G B 1 OK OK 1898 1916 1895 1897 1930 C4' G B 2 OK OK 1932 1950 1929 1931 1964 C4' G B 3 OK OK 1966 1984 1963 1965 1998 C4' A B 4 OK OK 2000 2017 1997 1999 2031 C4' C B 5 OK OK 2033 2048 2030 2032 2062 C4' C B 6 OK OK 2064 2079 2061 2063 2093 C4' U B 7 OK OK 2095 2110 2092 2094 2123 C4' G B 8 OK OK 2125 2143 2122 2124 2157 C4' G B 9 OK OK 2159 2177 2156 2158 2191 C4' U B 10 OK OK 2193 2208 2190 2192 2221 C4' C B 11 OK OK 2223 2238 2220 2222 2252 C4' U B 12 OK OK 2254 2269 2251 2253 2282 C4' U B 13 OK OK 2284 2299 2281 2283 2312 C4' U B 14 OK OK 2314 2329 2311 2313 2342 C4' C B 15 OK OK 2344 2359 2341 2343 2373 C4' C B 16 OK OK 2375 2390 2372 2374 2404 C4' A B 17 OK OK 2406 2423 2403 2405 2437 C4' G B 18 OK OK 2439 2457 2436 2438 2471 C4' G B 19 OK OK 2473 2491 2470 2472 2505 C4' U B 20 OK OK 2507 2522 2504 2506 2535 C4' C B 21 OK OK 2537 2552 2534 2536 2566 C4' C B 22 OK OK 2568 2583 2565 2567 2597 C4' C B 23 OK OK 2599 2614 2596 2598 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1895 C5' G B 1 OK OK 1894 1914 1915 1896 1929 C5' G B 2 OK OK 1928 1948 1949 1930 1963 C5' G B 3 OK OK 1962 1982 1983 1964 1997 C5' A B 4 OK OK 1996 2015 2016 1998 2030 C5' C B 5 OK OK 2029 2046 2047 2031 2061 C5' C B 6 OK OK 2060 2077 2078 2062 2092 C5' U B 7 OK OK 2091 2108 2109 2093 2122 C5' G B 8 OK OK 2121 2141 2142 2123 2156 C5' G B 9 OK OK 2155 2175 2176 2157 2190 C5' U B 10 OK OK 2189 2206 2207 2191 2220 C5' C B 11 OK OK 2219 2236 2237 2221 2251 C5' U B 12 OK OK 2250 2267 2268 2252 2281 C5' U B 13 OK OK 2280 2297 2298 2282 2311 C5' U B 14 OK OK 2310 2327 2328 2312 2341 C5' C B 15 OK OK 2340 2357 2358 2342 2372 C5' C B 16 OK OK 2371 2388 2389 2373 2403 C5' A B 17 OK OK 2402 2421 2422 2404 2436 C5' G B 18 OK OK 2435 2455 2456 2437 2470 C5' G B 19 OK OK 2469 2489 2490 2471 2504 C5' U B 20 OK OK 2503 2520 2521 2505 2534 C5' C B 21 OK OK 2533 2550 2551 2535 2565 C5' C B 22 OK OK 2564 2581 2582 2566 2596 C5' C B 23 OK OK 2595 2612 2613 2597 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1925 P G B 2 distorted distorted 1899 1926 1927 1928 1959 P G B 3 distorted distorted 1933 1960 1961 1962 1993 P A B 4 distorted distorted 1967 1994 1995 1996 2026 P C B 5 distorted distorted 2001 2027 2028 2029 2057 P C B 6 distorted distorted 2034 2058 2059 2060 2088 P U B 7 distorted distorted 2065 2089 2090 2091 2118 P G B 8 distorted distorted 2096 2119 2120 2121 2152 P G B 9 distorted distorted 2126 2153 2154 2155 2186 P U B 10 distorted distorted 2160 2187 2188 2189 2216 P C B 11 distorted distorted 2194 2217 2218 2219 2247 P U B 12 distorted distorted 2224 2248 2249 2250 2277 P U B 13 distorted distorted 2255 2278 2279 2280 2307 P U B 14 distorted distorted 2285 2308 2309 2310 2337 P C B 15 distorted distorted 2315 2338 2339 2340 2368 P C B 16 distorted distorted 2345 2369 2370 2371 2399 P A B 17 distorted distorted 2376 2400 2401 2402 2432 P G B 18 distorted distorted 2407 2433 2434 2435 2466 P G B 19 distorted distorted 2440 2467 2468 2469 2500 P U B 20 distorted distorted 2474 2501 2502 2503 2530 P C B 21 distorted distorted 2508 2531 2532 2533 2561 P C B 22 distorted distorted 2538 2562 2563 2564 2592 P C B 23 distorted distorted 2569 2593 2594 2595 ---------------------------------------------------------------------------------