ID code: '1L1C' 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' --------------------------------------------------------------------------------- 1757 C1' G C 1 alpha beta 1752 1775 1758 1755 1792 C1' G C 2 alpha beta 1787 1810 1793 1790 1826 C1' A C 3 alpha beta 1821 1843 1827 1824 1859 C1' U C 4 alpha beta 1854 1874 1860 1857 1889 C1' U C 5 alpha beta 1884 1904 1890 1887 1919 C1' G C 6 alpha beta 1914 1937 1920 1917 1953 C1' U C 7 alpha beta 1948 1968 1954 1951 1983 C1' U C 8 alpha beta 1978 1998 1984 1981 2013 C1' A C 9 alpha beta 2008 2030 2014 2011 2046 C1' C C 10 alpha beta 2041 2061 2047 2044 2077 C1' U C 11 alpha beta 2072 2092 2078 2075 2107 C1' G C 12 alpha beta 2102 2125 2108 2105 2141 C1' C C 13 alpha beta 2136 2156 2142 2139 2172 C1' U C 14 alpha beta 2167 2187 2173 2170 2202 C1' A C 15 alpha beta 2197 2219 2203 2200 2235 C1' C C 16 alpha beta 2230 2250 2236 2233 2266 C1' G C 17 alpha beta 2261 2284 2267 2264 2300 C1' G C 18 alpha beta 2295 2318 2301 2298 2334 C1' C C 19 alpha beta 2329 2349 2335 2332 2365 C1' A C 20 alpha beta 2360 2382 2366 2363 2398 C1' G C 21 alpha beta 2393 2416 2399 2396 2432 C1' G C 22 alpha beta 2427 2450 2433 2430 2466 C1' C C 23 alpha beta 2461 2481 2467 2464 2497 C1' A C 24 alpha beta 2492 2514 2498 2495 2530 C1' A C 25 alpha beta 2525 2547 2531 2528 2563 C1' A C 26 alpha beta 2558 2580 2564 2561 2596 C1' A C 27 alpha beta 2591 2613 2597 2594 2629 C1' C C 28 alpha beta 2624 2644 2630 2627 2660 C1' C C 29 alpha beta 2655 2676 2661 2658 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1755 C2' G C 1 OK OK 1757 1753 1773 1756 1790 C2' G C 2 OK OK 1792 1788 1808 1791 1824 C2' A C 3 OK OK 1826 1822 1841 1825 1857 C2' U C 4 OK OK 1859 1855 1872 1858 1887 C2' U C 5 OK OK 1889 1885 1902 1888 1917 C2' G C 6 OK OK 1919 1915 1935 1918 1951 C2' U C 7 OK OK 1953 1949 1966 1952 1981 C2' U C 8 OK OK 1983 1979 1996 1982 2011 C2' A C 9 OK OK 2013 2009 2028 2012 2044 C2' C C 10 OK OK 2046 2042 2059 2045 2075 C2' U C 11 OK OK 2077 2073 2090 2076 2105 C2' G C 12 OK OK 2107 2103 2123 2106 2139 C2' C C 13 OK OK 2141 2137 2154 2140 2170 C2' U C 14 OK OK 2172 2168 2185 2171 2200 C2' A C 15 OK OK 2202 2198 2217 2201 2233 C2' C C 16 OK OK 2235 2231 2248 2234 2264 C2' G C 17 OK OK 2266 2262 2282 2265 2298 C2' G C 18 OK OK 2300 2296 2316 2299 2332 C2' C C 19 OK OK 2334 2330 2347 2333 2363 C2' A C 20 OK OK 2365 2361 2380 2364 2396 C2' G C 21 OK OK 2398 2394 2414 2397 2430 C2' G C 22 OK OK 2432 2428 2448 2431 2464 C2' C C 23 OK OK 2466 2462 2479 2465 2495 C2' A C 24 OK OK 2497 2493 2512 2496 2528 C2' A C 25 OK OK 2530 2526 2545 2529 2561 C2' A C 26 OK OK 2563 2559 2578 2562 2594 C2' A C 27 OK OK 2596 2592 2611 2595 2627 C2' C C 28 OK OK 2629 2625 2642 2628 2658 C2' C C 29 OK OK 2660 2656 2674 2659 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1753 C3' G C 1 OK OK 1751 1772 1754 1755 1788 C3' G C 2 OK OK 1786 1807 1789 1790 1822 C3' A C 3 OK OK 1820 1840 1823 1824 1855 C3' U C 4 OK OK 1853 1871 1856 1857 1885 C3' U C 5 OK OK 1883 1901 1886 1887 1915 C3' G C 6 OK OK 1913 1934 1916 1917 1949 C3' U C 7 OK OK 1947 1965 1950 1951 1979 C3' U C 8 OK OK 1977 1995 1980 1981 2009 C3' A C 9 OK OK 2007 2027 2010 2011 2042 C3' C C 10 OK OK 2040 2058 2043 2044 2073 C3' U C 11 OK OK 2071 2089 2074 2075 2103 C3' G C 12 OK OK 2101 2122 2104 2105 2137 C3' C C 13 OK OK 2135 2153 2138 2139 2168 C3' U C 14 OK OK 2166 2184 2169 2170 2198 C3' A C 15 OK OK 2196 2216 2199 2200 2231 C3' C C 16 OK OK 2229 2247 2232 2233 2262 C3' G C 17 OK OK 2260 2281 2263 2264 2296 C3' G C 18 OK OK 2294 2315 2297 2298 2330 C3' C C 19 OK OK 2328 2346 2331 2332 2361 C3' A C 20 OK OK 2359 2379 2362 2363 2394 C3' G C 21 OK OK 2392 2413 2395 2396 2428 C3' G C 22 OK OK 2426 2447 2429 2430 2462 C3' C C 23 OK OK 2460 2478 2463 2464 2493 C3' A C 24 OK OK 2491 2511 2494 2495 2526 C3' A C 25 OK OK 2524 2544 2527 2528 2559 C3' A C 26 OK OK 2557 2577 2560 2561 2592 C3' A C 27 OK OK 2590 2610 2593 2594 2625 C3' C C 28 OK OK 2623 2641 2626 2627 2656 C3' C C 29 OK OK 2654 2672 2657 2658 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1751 C4' G C 1 OK OK 1753 1771 1750 1752 1786 C4' G C 2 OK OK 1788 1806 1785 1787 1820 C4' A C 3 OK OK 1822 1839 1819 1821 1853 C4' U C 4 OK OK 1855 1870 1852 1854 1883 C4' U C 5 OK OK 1885 1900 1882 1884 1913 C4' G C 6 OK OK 1915 1933 1912 1914 1947 C4' U C 7 OK OK 1949 1964 1946 1948 1977 C4' U C 8 OK OK 1979 1994 1976 1978 2007 C4' A C 9 OK OK 2009 2026 2006 2008 2040 C4' C C 10 OK OK 2042 2057 2039 2041 2071 C4' U C 11 OK OK 2073 2088 2070 2072 2101 C4' G C 12 OK OK 2103 2121 2100 2102 2135 C4' C C 13 OK OK 2137 2152 2134 2136 2166 C4' U C 14 OK OK 2168 2183 2165 2167 2196 C4' A C 15 OK OK 2198 2215 2195 2197 2229 C4' C C 16 OK OK 2231 2246 2228 2230 2260 C4' G C 17 OK OK 2262 2280 2259 2261 2294 C4' G C 18 OK OK 2296 2314 2293 2295 2328 C4' C C 19 OK OK 2330 2345 2327 2329 2359 C4' A C 20 OK OK 2361 2378 2358 2360 2392 C4' G C 21 OK OK 2394 2412 2391 2393 2426 C4' G C 22 OK OK 2428 2446 2425 2427 2460 C4' C C 23 OK OK 2462 2477 2459 2461 2491 C4' A C 24 OK OK 2493 2510 2490 2492 2524 C4' A C 25 OK OK 2526 2543 2523 2525 2557 C4' A C 26 OK OK 2559 2576 2556 2558 2590 C4' A C 27 OK OK 2592 2609 2589 2591 2623 C4' C C 28 OK OK 2625 2640 2622 2624 2654 C4' C C 29 OK OK 2656 2671 2653 2655 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1750 C5' G C 1 OK OK 1749 1769 1770 1751 1785 C5' G C 2 OK OK 1784 1804 1805 1786 1819 C5' A C 3 OK OK 1818 1837 1838 1820 1852 C5' U C 4 OK OK 1851 1868 1869 1853 1882 C5' U C 5 OK OK 1881 1898 1899 1883 1912 C5' G C 6 OK OK 1911 1931 1932 1913 1946 C5' U C 7 OK OK 1945 1962 1963 1947 1976 C5' U C 8 OK OK 1975 1992 1993 1977 2006 C5' A C 9 OK OK 2005 2024 2025 2007 2039 C5' C C 10 OK OK 2038 2055 2056 2040 2070 C5' U C 11 OK OK 2069 2086 2087 2071 2100 C5' G C 12 OK OK 2099 2119 2120 2101 2134 C5' C C 13 OK OK 2133 2150 2151 2135 2165 C5' U C 14 OK OK 2164 2181 2182 2166 2195 C5' A C 15 OK OK 2194 2213 2214 2196 2228 C5' C C 16 OK OK 2227 2244 2245 2229 2259 C5' G C 17 OK OK 2258 2278 2279 2260 2293 C5' G C 18 OK OK 2292 2312 2313 2294 2327 C5' C C 19 OK OK 2326 2343 2344 2328 2358 C5' A C 20 OK OK 2357 2376 2377 2359 2391 C5' G C 21 OK OK 2390 2410 2411 2392 2425 C5' G C 22 OK OK 2424 2444 2445 2426 2459 C5' C C 23 OK OK 2458 2475 2476 2460 2490 C5' A C 24 OK OK 2489 2508 2509 2491 2523 C5' A C 25 OK OK 2522 2541 2542 2524 2556 C5' A C 26 OK OK 2555 2574 2575 2557 2589 C5' A C 27 OK OK 2588 2607 2608 2590 2622 C5' C C 28 OK OK 2621 2638 2639 2623 2653 C5' C C 29 OK OK 2652 2669 2670 2654 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1781 P G C 2 distorted distorted 1754 1782 1783 1784 1815 P A C 3 distorted distorted 1789 1816 1817 1818 1848 P U C 4 distorted distorted 1823 1849 1850 1851 1878 P U C 5 distorted distorted 1856 1879 1880 1881 1908 P G C 6 distorted distorted 1886 1909 1910 1911 1942 P U C 7 distorted distorted 1916 1943 1944 1945 1972 P U C 8 distorted distorted 1950 1973 1974 1975 2002 P A C 9 distorted distorted 1980 2003 2004 2005 2035 P C C 10 distorted distorted 2010 2036 2037 2038 2066 P U C 11 distorted distorted 2043 2067 2068 2069 2096 P G C 12 distorted distorted 2074 2097 2098 2099 2130 P C C 13 distorted distorted 2104 2131 2132 2133 2161 P U C 14 distorted distorted 2138 2162 2163 2164 2191 P A C 15 distorted distorted 2169 2192 2193 2194 2224 P C C 16 distorted distorted 2199 2225 2226 2227 2255 P G C 17 distorted distorted 2232 2256 2257 2258 2289 P G C 18 distorted distorted 2263 2290 2291 2292 2323 P C C 19 distorted distorted 2297 2324 2325 2326 2354 P A C 20 distorted distorted 2331 2355 2356 2357 2387 P G C 21 distorted distorted 2362 2388 2389 2390 2421 P G C 22 distorted distorted 2395 2422 2423 2424 2455 P C C 23 distorted distorted 2429 2456 2457 2458 2486 P A C 24 distorted distorted 2463 2487 2488 2489 2519 P A C 25 distorted distorted 2494 2520 2521 2522 2552 P A C 26 distorted distorted 2527 2553 2554 2555 2585 P A C 27 distorted distorted 2560 2586 2587 2588 2618 P C C 28 distorted distorted 2593 2619 2620 2621 2649 P C C 29 distorted distorted 2626 2650 2651 2652 ---------------------------------------------------------------------------------