ID code: '1BDT' 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' --------------------------------------------------------------------------------- 1729 C1' A E 2 beta 1725 1730 1728 1750 C1' T E 3 beta 1746 1751 1749 1770 C1' A E 4 beta 1766 1771 1769 1791 C1' G E 5 beta 1787 1792 1790 1813 C1' T E 6 beta 1809 1814 1812 1833 C1' A E 7 beta 1829 1834 1832 1854 C1' G E 8 beta 1850 1855 1853 1876 C1' A E 9 beta 1872 1877 1875 1897 C1' G E 10 beta 1893 1898 1896 1919 C1' T E 11 beta 1915 1920 1918 1939 C1' G E 12 beta 1935 1940 1938 1961 C1' C E 13 beta 1957 1962 1960 1980 C1' T E 14 beta 1976 1981 1979 2000 C1' T E 15 beta 1996 2001 1999 2020 C1' C E 16 beta 2016 2021 2019 2039 C1' T E 17 beta 2035 2040 2038 2059 C1' A E 18 beta 2055 2060 2058 2080 C1' T E 19 beta 2076 2081 2079 2100 C1' C E 20 beta 2096 2101 2099 2119 C1' A E 21 beta 2115 2120 2118 2140 C1' T E 22 beta 2136 2141 2139 2179 C1' A F 2 beta 2175 2180 2178 2200 C1' T F 3 beta 2196 2201 2199 2220 C1' G F 4 beta 2216 2221 2219 2242 C1' A F 5 beta 2238 2243 2241 2263 C1' T F 6 beta 2259 2264 2262 2283 C1' A F 7 beta 2279 2284 2282 2304 C1' G F 8 beta 2300 2305 2303 2326 C1' A F 9 beta 2322 2327 2325 2347 C1' A F 10 beta 2343 2348 2346 2368 C1' G F 11 beta 2364 2369 2367 2390 C1' C F 12 beta 2386 2391 2389 2409 C1' A F 13 beta 2405 2410 2408 2430 C1' C F 14 beta 2426 2431 2429 2449 C1' T F 15 beta 2445 2450 2448 2469 C1' C F 16 beta 2465 2470 2468 2488 C1' T F 17 beta 2484 2489 2487 2508 C1' A F 18 beta 2504 2509 2507 2529 C1' C F 19 beta 2525 2530 2528 2548 C1' T F 20 beta 2544 2549 2547 2568 C1' A F 21 beta 2564 2569 2567 2589 C1' T F 22 beta 2585 2590 2588 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1728 C2' A E 2 1729 1726 1749 C2' T E 3 1750 1747 1769 C2' A E 4 1770 1767 1790 C2' G E 5 1791 1788 1812 C2' T E 6 1813 1810 1832 C2' A E 7 1833 1830 1853 C2' G E 8 1854 1851 1875 C2' A E 9 1876 1873 1896 C2' G E 10 1897 1894 1918 C2' T E 11 1919 1916 1938 C2' G E 12 1939 1936 1960 C2' C E 13 1961 1958 1979 C2' T E 14 1980 1977 1999 C2' T E 15 2000 1997 2019 C2' C E 16 2020 2017 2038 C2' T E 17 2039 2036 2058 C2' A E 18 2059 2056 2079 C2' T E 19 2080 2077 2099 C2' C E 20 2100 2097 2118 C2' A E 21 2119 2116 2139 C2' T E 22 2140 2137 2178 C2' A F 2 2179 2176 2199 C2' T F 3 2200 2197 2219 C2' G F 4 2220 2217 2241 C2' A F 5 2242 2239 2262 C2' T F 6 2263 2260 2282 C2' A F 7 2283 2280 2303 C2' G F 8 2304 2301 2325 C2' A F 9 2326 2323 2346 C2' A F 10 2347 2344 2367 C2' G F 11 2368 2365 2389 C2' C F 12 2390 2387 2408 C2' A F 13 2409 2406 2429 C2' C F 14 2430 2427 2448 C2' T F 15 2449 2446 2468 C2' C F 16 2469 2466 2487 C2' T F 17 2488 2485 2507 C2' A F 18 2508 2505 2528 C2' C F 19 2529 2526 2547 C2' T F 20 2548 2545 2567 C2' A F 21 2568 2565 2588 C2' T F 22 2589 2586 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1726 C3' A E 2 OK 1724 1727 1728 1747 C3' T E 3 OK 1745 1748 1749 1767 C3' A E 4 OK 1765 1768 1769 1788 C3' G E 5 OK 1786 1789 1790 1810 C3' T E 6 OK 1808 1811 1812 1830 C3' A E 7 OK 1828 1831 1832 1851 C3' G E 8 OK 1849 1852 1853 1873 C3' A E 9 OK 1871 1874 1875 1894 C3' G E 10 OK 1892 1895 1896 1916 C3' T E 11 OK 1914 1917 1918 1936 C3' G E 12 OK 1934 1937 1938 1958 C3' C E 13 OK 1956 1959 1960 1977 C3' T E 14 OK 1975 1978 1979 1997 C3' T E 15 OK 1995 1998 1999 2017 C3' C E 16 OK 2015 2018 2019 2036 C3' T E 17 OK 2034 2037 2038 2056 C3' A E 18 OK 2054 2057 2058 2077 C3' T E 19 OK 2075 2078 2079 2097 C3' C E 20 OK 2095 2098 2099 2116 C3' A E 21 OK 2114 2117 2118 2137 C3' T E 22 OK 2135 2138 2139 2176 C3' A F 2 OK 2174 2177 2178 2197 C3' T F 3 OK 2195 2198 2199 2217 C3' G F 4 OK 2215 2218 2219 2239 C3' A F 5 OK 2237 2240 2241 2260 C3' T F 6 OK 2258 2261 2262 2280 C3' A F 7 OK 2278 2281 2282 2301 C3' G F 8 OK 2299 2302 2303 2323 C3' A F 9 OK 2321 2324 2325 2344 C3' A F 10 OK 2342 2345 2346 2365 C3' G F 11 OK 2363 2366 2367 2387 C3' C F 12 OK 2385 2388 2389 2406 C3' A F 13 OK 2404 2407 2408 2427 C3' C F 14 OK 2425 2428 2429 2446 C3' T F 15 OK 2444 2447 2448 2466 C3' C F 16 OK 2464 2467 2468 2485 C3' T F 17 OK 2483 2486 2487 2505 C3' A F 18 OK 2503 2506 2507 2526 C3' C F 19 OK 2524 2527 2528 2545 C3' T F 20 OK 2543 2546 2547 2565 C3' A F 21 OK 2563 2566 2567 2586 C3' T F 22 OK 2584 2587 2588 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1724 C4' A E 2 OK 1726 1723 1725 1745 C4' T E 3 OK 1747 1744 1746 1765 C4' A E 4 OK 1767 1764 1766 1786 C4' G E 5 OK 1788 1785 1787 1808 C4' T E 6 OK 1810 1807 1809 1828 C4' A E 7 OK 1830 1827 1829 1849 C4' G E 8 OK 1851 1848 1850 1871 C4' A E 9 OK 1873 1870 1872 1892 C4' G E 10 OK 1894 1891 1893 1914 C4' T E 11 OK 1916 1913 1915 1934 C4' G E 12 OK 1936 1933 1935 1956 C4' C E 13 OK 1958 1955 1957 1975 C4' T E 14 OK 1977 1974 1976 1995 C4' T E 15 OK 1997 1994 1996 2015 C4' C E 16 OK 2017 2014 2016 2034 C4' T E 17 OK 2036 2033 2035 2054 C4' A E 18 OK 2056 2053 2055 2075 C4' T E 19 OK 2077 2074 2076 2095 C4' C E 20 OK 2097 2094 2096 2114 C4' A E 21 OK 2116 2113 2115 2135 C4' T E 22 OK 2137 2134 2136 2174 C4' A F 2 OK 2176 2173 2175 2195 C4' T F 3 OK 2197 2194 2196 2215 C4' G F 4 OK 2217 2214 2216 2237 C4' A F 5 OK 2239 2236 2238 2258 C4' T F 6 OK 2260 2257 2259 2278 C4' A F 7 OK 2280 2277 2279 2299 C4' G F 8 OK 2301 2298 2300 2321 C4' A F 9 OK 2323 2320 2322 2342 C4' A F 10 OK 2344 2341 2343 2363 C4' G F 11 OK 2365 2362 2364 2385 C4' C F 12 OK 2387 2384 2386 2404 C4' A F 13 OK 2406 2403 2405 2425 C4' C F 14 OK 2427 2424 2426 2444 C4' T F 15 OK 2446 2443 2445 2464 C4' C F 16 OK 2466 2463 2465 2483 C4' T F 17 OK 2485 2482 2484 2503 C4' A F 18 OK 2505 2502 2504 2524 C4' C F 19 OK 2526 2523 2525 2543 C4' T F 20 OK 2545 2542 2544 2563 C4' A F 21 OK 2565 2562 2564 2584 C4' T F 22 OK 2586 2583 2585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1723 C5' A E 2 1722 1724 1744 C5' T E 3 1743 1745 1764 C5' A E 4 1763 1765 1785 C5' G E 5 1784 1786 1807 C5' T E 6 1806 1808 1827 C5' A E 7 1826 1828 1848 C5' G E 8 1847 1849 1870 C5' A E 9 1869 1871 1891 C5' G E 10 1890 1892 1913 C5' T E 11 1912 1914 1933 C5' G E 12 1932 1934 1955 C5' C E 13 1954 1956 1974 C5' T E 14 1973 1975 1994 C5' T E 15 1993 1995 2014 C5' C E 16 2013 2015 2033 C5' T E 17 2032 2034 2053 C5' A E 18 2052 2054 2074 C5' T E 19 2073 2075 2094 C5' C E 20 2093 2095 2113 C5' A E 21 2112 2114 2134 C5' T E 22 2133 2135 2173 C5' A F 2 2172 2174 2194 C5' T F 3 2193 2195 2214 C5' G F 4 2213 2215 2236 C5' A F 5 2235 2237 2257 C5' T F 6 2256 2258 2277 C5' A F 7 2276 2278 2298 C5' G F 8 2297 2299 2320 C5' A F 9 2319 2321 2341 C5' A F 10 2340 2342 2362 C5' G F 11 2361 2363 2384 C5' C F 12 2383 2385 2403 C5' A F 13 2402 2404 2424 C5' C F 14 2423 2425 2443 C5' T F 15 2442 2444 2463 C5' C F 16 2462 2464 2482 C5' T F 17 2481 2483 2502 C5' A F 18 2501 2503 2523 C5' C F 19 2522 2524 2542 C5' T F 20 2541 2543 2562 C5' A F 21 2561 2563 2583 C5' T F 22 2582 2584 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1740 P T E 3 OK OK 1727 1741 1742 1743 1760 P A E 4 OK OK 1748 1761 1762 1763 1781 P G E 5 OK OK 1768 1782 1783 1784 1803 P T E 6 OK OK 1789 1804 1805 1806 1823 P A E 7 OK OK 1811 1824 1825 1826 1844 P G E 8 OK OK 1831 1845 1846 1847 1866 P A E 9 OK OK 1852 1867 1868 1869 1887 P G E 10 OK OK 1874 1888 1889 1890 1909 P T E 11 OK OK 1895 1910 1911 1912 1929 P G E 12 OK OK 1917 1930 1931 1932 1951 P C E 13 OK OK 1937 1952 1953 1954 1970 P T E 14 OK OK 1959 1971 1972 1973 1990 P T E 15 OK OK 1978 1991 1992 1993 2010 P C E 16 OK OK 1998 2011 2012 2013 2029 P T E 17 OK OK 2018 2030 2031 2032 2049 P A E 18 OK OK 2037 2050 2051 2052 2070 P T E 19 OK OK 2057 2071 2072 2073 2090 P C E 20 OK OK 2078 2091 2092 2093 2109 P A E 21 OK OK 2098 2110 2111 2112 2130 P T E 22 OK OK 2117 2131 2132 2133 2190 P T F 3 distorted distorted 2177 2191 2192 2193 2210 P G F 4 distorted distorted 2198 2211 2212 2213 2232 P A F 5 OK OK 2218 2233 2234 2235 2253 P T F 6 OK OK 2240 2254 2255 2256 2273 P A F 7 OK OK 2261 2274 2275 2276 2294 P G F 8 OK OK 2281 2295 2296 2297 2316 P A F 9 distorted distorted 2302 2317 2318 2319 2337 P A F 10 distorted distorted 2324 2338 2339 2340 2358 P G F 11 OK OK 2345 2359 2360 2361 2380 P C F 12 OK OK 2366 2381 2382 2383 2399 P A F 13 distorted distorted 2388 2400 2401 2402 2420 P C F 14 distorted distorted 2407 2421 2422 2423 2439 P T F 15 distorted distorted 2428 2440 2441 2442 2459 P C F 16 OK OK 2447 2460 2461 2462 2478 P T F 17 OK OK 2467 2479 2480 2481 2498 P A F 18 OK OK 2486 2499 2500 2501 2519 P C F 19 OK OK 2506 2520 2521 2522 2538 P T F 20 distorted distorted 2527 2539 2540 2541 2558 P A F 21 distorted distorted 2546 2559 2560 2561 2579 P T F 22 distorted distorted 2566 2580 2581 2582 ---------------------------------------------------------------------------------