ID code: '1QE4' 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' --------------------------------------------------------------------------------- 1609 C1' G E 2 beta 1605 1610 1608 1631 C1' C E 3 beta 1627 1632 1630 1650 C1' G E 4 beta 1646 1651 1649 1672 C1' G E 5 beta 1668 1673 1671 1694 C1' A E 6 beta 1690 1695 1693 1715 C1' A E 7 beta 1711 1716 1714 1736 C1' C E 8 beta 1732 1737 1735 1755 C1' T E 9 beta 1751 1756 1754 1775 C1' A E 10 beta 1771 1776 1774 1796 C1' C E 11 beta 1792 1797 1795 1815 C1' T E 12 beta 1811 1816 1814 1835 C1' G E 13 beta 1831 1836 1834 1857 C1' A E 14 beta 1853 1858 1856 1878 C1' C E 15 beta 1874 1879 1877 1897 C1' G E 16 beta 1893 1898 1896 1919 C1' A E 17 beta 1915 1920 1918 1940 C1' C E 18 beta 1936 1941 1939 1959 C1' G E 19 beta 1955 1960 1958 1981 C1' A E 20 beta 1977 1982 1980 2002 C1' C E 21 beta 1998 2003 2001 2021 C1' G E 22 beta 2017 2022 2020 2043 C1' A E 23 beta 2039 2044 2042 2065 C1' T D 23 beta 2061 2066 2064 2085 C1' C D 22 beta 2081 2086 2084 2104 C1' G D 21 beta 2100 2105 2103 2126 C1' T D 20 beta 2122 2127 2125 2146 C1' C D 19 beta 2142 2147 2145 2165 C1' G D 18 beta 2161 2166 2164 2187 C1' T D 17 beta 2183 2188 2186 2207 C1' C D 16 beta 2203 2208 2206 2226 C1' G D 15 beta 2222 2227 2225 2248 C1' T D 14 beta 2244 2249 2247 2268 C1' C D 13 beta 2264 2269 2267 2284 C1' A D 12 beta 2280 2285 2283 2305 C1' G D 11 beta 2301 2306 2304 2327 C1' T D 10 beta 2323 2328 2326 2347 C1' A D 9 beta 2343 2348 2346 2368 C1' G D 8 beta 2364 2369 2367 2390 C1' T D 7 beta 2386 2391 2389 2410 C1' T D 6 beta 2406 2411 2409 2430 C1' C D 5 beta 2426 2431 2429 2449 C1' C D 4 beta 2445 2450 2448 2468 C1' G D 3 beta 2464 2469 2467 2490 C1' C D 2 beta 2486 2491 2489 2509 C1' G D 1 beta 2505 2510 2508 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1608 C2' G E 2 1609 1606 1630 C2' C E 3 1631 1628 1649 C2' G E 4 1650 1647 1671 C2' G E 5 1672 1669 1693 C2' A E 6 1694 1691 1714 C2' A E 7 1715 1712 1735 C2' C E 8 1736 1733 1754 C2' T E 9 1755 1752 1774 C2' A E 10 1775 1772 1795 C2' C E 11 1796 1793 1814 C2' T E 12 1815 1812 1834 C2' G E 13 1835 1832 1856 C2' A E 14 1857 1854 1877 C2' C E 15 1878 1875 1896 C2' G E 16 1897 1894 1918 C2' A E 17 1919 1916 1939 C2' C E 18 1940 1937 1958 C2' G E 19 1959 1956 1980 C2' A E 20 1981 1978 2001 C2' C E 21 2002 1999 2020 C2' G E 22 2021 2018 2042 C2' A E 23 2043 2040 2064 C2' T D 23 2065 2062 2084 C2' C D 22 2085 2082 2103 C2' G D 21 2104 2101 2125 C2' T D 20 2126 2123 2145 C2' C D 19 2146 2143 2164 C2' G D 18 2165 2162 2186 C2' T D 17 2187 2184 2206 C2' C D 16 2207 2204 2225 C2' G D 15 2226 2223 2247 C2' T D 14 2248 2245 2267 C2' C D 13 2268 2265 2283 C2' A D 12 2284 2281 2304 C2' G D 11 2305 2302 2326 C2' T D 10 2327 2324 2346 C2' A D 9 2347 2344 2367 C2' G D 8 2368 2365 2389 C2' T D 7 2390 2387 2409 C2' T D 6 2410 2407 2429 C2' C D 5 2430 2427 2448 C2' C D 4 2449 2446 2467 C2' G D 3 2468 2465 2489 C2' C D 2 2490 2487 2508 C2' G D 1 2509 2506 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1606 C3' G E 2 OK 1604 1607 1608 1628 C3' C E 3 OK 1626 1629 1630 1647 C3' G E 4 OK 1645 1648 1649 1669 C3' G E 5 OK 1667 1670 1671 1691 C3' A E 6 OK 1689 1692 1693 1712 C3' A E 7 OK 1710 1713 1714 1733 C3' C E 8 OK 1731 1734 1735 1752 C3' T E 9 OK 1750 1753 1754 1772 C3' A E 10 OK 1770 1773 1774 1793 C3' C E 11 OK 1791 1794 1795 1812 C3' T E 12 OK 1810 1813 1814 1832 C3' G E 13 OK 1830 1833 1834 1854 C3' A E 14 distorted 1852 1855 1856 1875 C3' C E 15 OK 1873 1876 1877 1894 C3' G E 16 OK 1892 1895 1896 1916 C3' A E 17 distorted 1914 1917 1918 1937 C3' C E 18 OK 1935 1938 1939 1956 C3' G E 19 OK 1954 1957 1958 1978 C3' A E 20 distorted 1976 1979 1980 1999 C3' C E 21 OK 1997 2000 2001 2018 C3' G E 22 OK 2016 2019 2020 2040 C3' A E 23 distorted 2038 2041 2042 2062 C3' T D 23 OK 2060 2063 2064 2082 C3' C D 22 2080 2084 2101 C3' G D 21 distorted 2099 2102 2103 2123 C3' T D 20 OK 2121 2124 2125 2143 C3' C D 19 2141 2145 2162 C3' G D 18 distorted 2160 2163 2164 2184 C3' T D 17 OK 2182 2185 2186 2204 C3' C D 16 2202 2206 2223 C3' G D 15 distorted 2221 2224 2225 2245 C3' T D 14 OK 2243 2246 2247 2265 C3' C D 13 2263 2267 2281 C3' A D 12 OK 2279 2282 2283 2302 C3' G D 11 OK 2300 2303 2304 2324 C3' T D 10 OK 2322 2325 2326 2344 C3' A D 9 OK 2342 2345 2346 2365 C3' G D 8 OK 2363 2366 2367 2387 C3' T D 7 OK 2385 2388 2389 2407 C3' T D 6 OK 2405 2408 2409 2427 C3' C D 5 OK 2425 2428 2429 2446 C3' C D 4 OK 2444 2447 2448 2465 C3' G D 3 OK 2463 2466 2467 2487 C3' C D 2 OK 2485 2488 2489 2506 C3' G D 1 OK 2504 2507 2508 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1604 C4' G E 2 OK 1606 1603 1605 1626 C4' C E 3 OK 1628 1625 1627 1645 C4' G E 4 OK 1647 1644 1646 1667 C4' G E 5 OK 1669 1666 1668 1689 C4' A E 6 OK 1691 1688 1690 1710 C4' A E 7 OK 1712 1709 1711 1731 C4' C E 8 OK 1733 1730 1732 1750 C4' T E 9 OK 1752 1749 1751 1770 C4' A E 10 OK 1772 1769 1771 1791 C4' C E 11 OK 1793 1790 1792 1810 C4' T E 12 OK 1812 1809 1811 1830 C4' G E 13 OK 1832 1829 1831 1852 C4' A E 14 OK 1854 1851 1853 1873 C4' C E 15 OK 1875 1872 1874 1892 C4' G E 16 OK 1894 1891 1893 1914 C4' A E 17 OK 1916 1913 1915 1935 C4' C E 18 OK 1937 1934 1936 1954 C4' G E 19 OK 1956 1953 1955 1976 C4' A E 20 OK 1978 1975 1977 1997 C4' C E 21 OK 1999 1996 1998 2016 C4' G E 22 OK 2018 2015 2017 2038 C4' A E 23 OK 2040 2037 2039 2060 C4' T D 23 OK 2062 2059 2061 2080 C4' C D 22 OK 2082 2079 2081 2099 C4' G D 21 OK 2101 2098 2100 2121 C4' T D 20 OK 2123 2120 2122 2141 C4' C D 19 OK 2143 2140 2142 2160 C4' G D 18 OK 2162 2159 2161 2182 C4' T D 17 OK 2184 2181 2183 2202 C4' C D 16 OK 2204 2201 2203 2221 C4' G D 15 OK 2223 2220 2222 2243 C4' T D 14 OK 2245 2242 2244 2263 C4' C D 13 OK 2265 2262 2264 2279 C4' A D 12 OK 2281 2278 2280 2300 C4' G D 11 OK 2302 2299 2301 2322 C4' T D 10 OK 2324 2321 2323 2342 C4' A D 9 OK 2344 2341 2343 2363 C4' G D 8 OK 2365 2362 2364 2385 C4' T D 7 OK 2387 2384 2386 2405 C4' T D 6 OK 2407 2404 2406 2425 C4' C D 5 OK 2427 2424 2426 2444 C4' C D 4 OK 2446 2443 2445 2463 C4' G D 3 OK 2465 2462 2464 2485 C4' C D 2 OK 2487 2484 2486 2504 C4' G D 1 OK 2506 2503 2505 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1603 C5' G E 2 1602 1604 1625 C5' C E 3 1624 1626 1644 C5' G E 4 1643 1645 1666 C5' G E 5 1665 1667 1688 C5' A E 6 1687 1689 1709 C5' A E 7 1708 1710 1730 C5' C E 8 1729 1731 1749 C5' T E 9 1748 1750 1769 C5' A E 10 1768 1770 1790 C5' C E 11 1789 1791 1809 C5' T E 12 1808 1810 1829 C5' G E 13 1828 1830 1851 C5' A E 14 1850 1852 1872 C5' C E 15 1871 1873 1891 C5' G E 16 1890 1892 1913 C5' A E 17 1912 1914 1934 C5' C E 18 1933 1935 1953 C5' G E 19 1952 1954 1975 C5' A E 20 1974 1976 1996 C5' C E 21 1995 1997 2015 C5' G E 22 2014 2016 2037 C5' A E 23 2036 2038 2059 C5' T D 23 2058 2060 2079 C5' C D 22 2078 2080 2098 C5' G D 21 2097 2099 2120 C5' T D 20 2119 2121 2140 C5' C D 19 2139 2141 2159 C5' G D 18 2158 2160 2181 C5' T D 17 2180 2182 2201 C5' C D 16 2200 2202 2220 C5' G D 15 2219 2221 2242 C5' T D 14 2241 2243 2262 C5' C D 13 2261 2263 2278 C5' A D 12 2277 2279 2299 C5' G D 11 2298 2300 2321 C5' T D 10 2320 2322 2341 C5' A D 9 2340 2342 2362 C5' G D 8 2361 2363 2384 C5' T D 7 2383 2385 2404 C5' T D 6 2403 2405 2424 C5' C D 5 2423 2425 2443 C5' C D 4 2442 2444 2462 C5' G D 3 2461 2463 2484 C5' C D 2 2483 2485 2503 C5' G D 1 2502 2504 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1621 P C E 3 distorted distorted 1607 1622 1623 1624 1640 P G E 4 distorted distorted 1629 1641 1642 1643 1662 P G E 5 distorted distorted 1648 1663 1664 1665 1684 P A E 6 distorted distorted 1670 1685 1686 1687 1705 P A E 7 distorted distorted 1692 1706 1707 1708 1726 P C E 8 distorted distorted 1713 1727 1728 1729 1745 P T E 9 distorted distorted 1734 1746 1747 1748 1765 P A E 10 distorted distorted 1753 1766 1767 1768 1786 P C E 11 distorted distorted 1773 1787 1788 1789 1805 P T E 12 distorted distorted 1794 1806 1807 1808 1825 P G E 13 distorted distorted 1826 1827 1828 1847 P A E 14 distorted distorted 1833 1848 1849 1850 1868 P C E 15 distorted distorted 1869 1870 1871 1887 P G E 16 distorted distorted 1888 1889 1890 1909 P A E 17 distorted distorted 1895 1910 1911 1912 1930 P C E 18 distorted distorted 1931 1932 1933 1949 P G E 19 distorted distorted 1950 1951 1952 1971 P A E 20 distorted distorted 1957 1972 1973 1974 1992 P C E 21 distorted distorted 1993 1994 1995 2011 P G E 22 distorted distorted 2012 2013 2014 2033 P A E 23 distorted distorted 2019 2034 2035 2036 2055 P T D 23 distorted distorted 2056 2057 2058 2075 P C D 22 distorted distorted 2063 2076 2077 2078 2094 P G D 21 distorted distorted 2083 2095 2096 2097 2116 P T D 20 distorted distorted 2117 2118 2119 2136 P C D 19 distorted distorted 2124 2137 2138 2139 2155 P G D 18 distorted distorted 2144 2156 2157 2158 2177 P T D 17 distorted distorted 2163 2178 2179 2180 2197 P C D 16 distorted distorted 2185 2198 2199 2200 2216 P G D 15 distorted distorted 2205 2217 2218 2219 2238 P T D 14 distorted distorted 2239 2240 2241 2258 P C D 13 distorted distorted 2246 2259 2260 2261 2295 P G D 11 distorted distorted 2282 2296 2297 2298 2317 P T D 10 distorted distorted 2303 2318 2319 2320 2337 P A D 9 distorted distorted 2325 2338 2339 2340 2358 P G D 8 distorted distorted 2345 2359 2360 2361 2380 P T D 7 distorted distorted 2366 2381 2382 2383 2400 P T D 6 distorted distorted 2388 2401 2402 2403 2420 P C D 5 distorted distorted 2408 2421 2422 2423 2439 P C D 4 distorted distorted 2428 2440 2441 2442 2458 P G D 3 distorted distorted 2447 2459 2460 2461 2480 P C D 2 distorted distorted 2466 2481 2482 2483 2499 P G D 1 distorted distorted 2488 2500 2501 2502 ---------------------------------------------------------------------------------