ID code: '2STW' 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' --------------------------------------------------------------------------------- 1603 C1' T B 1 beta 1599 1604 1602 1636 C1' C B 2 beta 1632 1637 1635 1666 C1' G B 3 beta 1662 1667 1665 1699 C1' A B 4 beta 1695 1700 1698 1731 C1' G B 5 beta 1727 1732 1730 1764 C1' C B 6 beta 1760 1765 1763 1794 C1' C B 7 beta 1790 1795 1793 1824 C1' G B 8 beta 1820 1825 1823 1857 C1' G B 9 beta 1853 1858 1856 1890 C1' A B 10 beta 1886 1891 1889 1922 C1' A B 11 beta 1918 1923 1921 1954 C1' G B 12 beta 1950 1955 1953 1987 C1' T B 13 beta 1983 1988 1986 2019 C1' T B 14 beta 2015 2020 2018 2051 C1' C B 15 beta 2047 2052 2050 2081 C1' G B 16 beta 2077 2082 2080 2114 C1' A B 17 beta 2110 2115 2113 2144 C1' T B 18 beta 2140 2145 2143 2177 C1' C B 19 beta 2173 2178 2176 2207 C1' G B 20 beta 2203 2208 2206 2240 C1' A B 21 beta 2236 2241 2239 2272 C1' A B 22 beta 2268 2273 2271 2304 C1' C B 23 beta 2300 2305 2303 2334 C1' T B 24 beta 2330 2335 2333 2366 C1' T B 25 beta 2362 2367 2365 2398 C1' C B 26 beta 2394 2399 2397 2428 C1' C B 27 beta 2424 2429 2427 2458 C1' G B 28 beta 2454 2459 2457 2491 C1' G B 29 beta 2487 2492 2490 2524 C1' C B 30 beta 2520 2525 2523 2554 C1' T B 31 beta 2550 2555 2553 2586 C1' C B 32 beta 2582 2587 2585 2616 C1' G B 33 beta 2612 2617 2615 2649 C1' A B 34 beta 2645 2650 2648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1602 C2' T B 1 1603 1600 1635 C2' C B 2 1636 1633 1665 C2' G B 3 1666 1663 1698 C2' A B 4 1699 1696 1730 C2' G B 5 1731 1728 1763 C2' C B 6 1764 1761 1793 C2' C B 7 1794 1791 1823 C2' G B 8 1824 1821 1856 C2' G B 9 1857 1854 1889 C2' A B 10 1890 1887 1921 C2' A B 11 1922 1919 1953 C2' G B 12 1954 1951 1986 C2' T B 13 1987 1984 2018 C2' T B 14 2019 2016 2050 C2' C B 15 2051 2048 2080 C2' G B 16 2081 2078 2113 C2' A B 17 2114 2111 2143 C2' T B 18 2144 2141 2176 C2' C B 19 2177 2174 2206 C2' G B 20 2207 2204 2239 C2' A B 21 2240 2237 2271 C2' A B 22 2272 2269 2303 C2' C B 23 2304 2301 2333 C2' T B 24 2334 2331 2365 C2' T B 25 2366 2363 2397 C2' C B 26 2398 2395 2427 C2' C B 27 2428 2425 2457 C2' G B 28 2458 2455 2490 C2' G B 29 2491 2488 2523 C2' C B 30 2524 2521 2553 C2' T B 31 2554 2551 2585 C2' C B 32 2586 2583 2615 C2' G B 33 2616 2613 2648 C2' A B 34 2649 2646 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1600 C3' T B 1 OK 1598 1601 1602 1633 C3' C B 2 OK 1631 1634 1635 1663 C3' G B 3 OK 1661 1664 1665 1696 C3' A B 4 OK 1694 1697 1698 1728 C3' G B 5 OK 1726 1729 1730 1761 C3' C B 6 OK 1759 1762 1763 1791 C3' C B 7 OK 1789 1792 1793 1821 C3' G B 8 OK 1819 1822 1823 1854 C3' G B 9 OK 1852 1855 1856 1887 C3' A B 10 OK 1885 1888 1889 1919 C3' A B 11 OK 1917 1920 1921 1951 C3' G B 12 OK 1949 1952 1953 1984 C3' T B 13 OK 1982 1985 1986 2016 C3' T B 14 OK 2014 2017 2018 2048 C3' C B 15 OK 2046 2049 2050 2078 C3' G B 16 OK 2076 2079 2080 2111 C3' A B 17 OK 2109 2112 2113 2141 C3' T B 18 OK 2139 2142 2143 2174 C3' C B 19 OK 2172 2175 2176 2204 C3' G B 20 OK 2202 2205 2206 2237 C3' A B 21 OK 2235 2238 2239 2269 C3' A B 22 OK 2267 2270 2271 2301 C3' C B 23 OK 2299 2302 2303 2331 C3' T B 24 OK 2329 2332 2333 2363 C3' T B 25 OK 2361 2364 2365 2395 C3' C B 26 OK 2393 2396 2397 2425 C3' C B 27 OK 2423 2426 2427 2455 C3' G B 28 OK 2453 2456 2457 2488 C3' G B 29 OK 2486 2489 2490 2521 C3' C B 30 OK 2519 2522 2523 2551 C3' T B 31 OK 2549 2552 2553 2583 C3' C B 32 OK 2581 2584 2585 2613 C3' G B 33 OK 2611 2614 2615 2646 C3' A B 34 OK 2644 2647 2648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1598 C4' T B 1 OK 1600 1597 1599 1631 C4' C B 2 OK 1633 1630 1632 1661 C4' G B 3 OK 1663 1660 1662 1694 C4' A B 4 OK 1696 1693 1695 1726 C4' G B 5 OK 1728 1725 1727 1759 C4' C B 6 OK 1761 1758 1760 1789 C4' C B 7 OK 1791 1788 1790 1819 C4' G B 8 OK 1821 1818 1820 1852 C4' G B 9 OK 1854 1851 1853 1885 C4' A B 10 OK 1887 1884 1886 1917 C4' A B 11 OK 1919 1916 1918 1949 C4' G B 12 OK 1951 1948 1950 1982 C4' T B 13 OK 1984 1981 1983 2014 C4' T B 14 OK 2016 2013 2015 2046 C4' C B 15 OK 2048 2045 2047 2076 C4' G B 16 OK 2078 2075 2077 2109 C4' A B 17 OK 2111 2108 2110 2139 C4' T B 18 OK 2141 2138 2140 2172 C4' C B 19 OK 2174 2171 2173 2202 C4' G B 20 OK 2204 2201 2203 2235 C4' A B 21 OK 2237 2234 2236 2267 C4' A B 22 OK 2269 2266 2268 2299 C4' C B 23 OK 2301 2298 2300 2329 C4' T B 24 OK 2331 2328 2330 2361 C4' T B 25 OK 2363 2360 2362 2393 C4' C B 26 OK 2395 2392 2394 2423 C4' C B 27 OK 2425 2422 2424 2453 C4' G B 28 OK 2455 2452 2454 2486 C4' G B 29 OK 2488 2485 2487 2519 C4' C B 30 OK 2521 2518 2520 2549 C4' T B 31 OK 2551 2548 2550 2581 C4' C B 32 OK 2583 2580 2582 2611 C4' G B 33 OK 2613 2610 2612 2644 C4' A B 34 OK 2646 2643 2645 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1597 C5' T B 1 1596 1598 1630 C5' C B 2 1629 1631 1660 C5' G B 3 1659 1661 1693 C5' A B 4 1692 1694 1725 C5' G B 5 1724 1726 1758 C5' C B 6 1757 1759 1788 C5' C B 7 1787 1789 1818 C5' G B 8 1817 1819 1851 C5' G B 9 1850 1852 1884 C5' A B 10 1883 1885 1916 C5' A B 11 1915 1917 1948 C5' G B 12 1947 1949 1981 C5' T B 13 1980 1982 2013 C5' T B 14 2012 2014 2045 C5' C B 15 2044 2046 2075 C5' G B 16 2074 2076 2108 C5' A B 17 2107 2109 2138 C5' T B 18 2137 2139 2171 C5' C B 19 2170 2172 2201 C5' G B 20 2200 2202 2234 C5' A B 21 2233 2235 2266 C5' A B 22 2265 2267 2298 C5' C B 23 2297 2299 2328 C5' T B 24 2327 2329 2360 C5' T B 25 2359 2361 2392 C5' C B 26 2391 2393 2422 C5' C B 27 2421 2423 2452 C5' G B 28 2451 2453 2485 C5' G B 29 2484 2486 2518 C5' C B 30 2517 2519 2548 C5' T B 31 2547 2549 2580 C5' C B 32 2579 2581 2610 C5' G B 33 2609 2611 2643 C5' A B 34 2642 2644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1626 P C B 2 OK OK 1601 1627 1628 1629 1656 P G B 3 OK OK 1634 1657 1658 1659 1689 P A B 4 OK OK 1664 1690 1691 1692 1721 P G B 5 OK OK 1697 1722 1723 1724 1754 P C B 6 OK OK 1729 1755 1756 1757 1784 P C B 7 OK OK 1762 1785 1786 1787 1814 P G B 8 OK OK 1792 1815 1816 1817 1847 P G B 9 OK OK 1822 1848 1849 1850 1880 P A B 10 OK OK 1855 1881 1882 1883 1912 P A B 11 OK OK 1888 1913 1914 1915 1944 P G B 12 OK OK 1920 1945 1946 1947 1977 P T B 13 OK OK 1952 1978 1979 1980 2009 P T B 14 OK OK 1985 2010 2011 2012 2041 P C B 15 OK OK 2017 2042 2043 2044 2071 P G B 16 OK OK 2049 2072 2073 2074 2104 P A B 17 OK OK 2079 2105 2106 2107 2167 P C B 19 OK OK 2142 2168 2169 2170 2197 P G B 20 OK OK 2175 2198 2199 2200 2230 P A B 21 OK OK 2205 2231 2232 2233 2262 P A B 22 OK OK 2238 2263 2264 2265 2294 P C B 23 OK OK 2270 2295 2296 2297 2324 P T B 24 OK OK 2302 2325 2326 2327 2356 P T B 25 OK OK 2332 2357 2358 2359 2388 P C B 26 OK OK 2364 2389 2390 2391 2418 P C B 27 OK OK 2396 2419 2420 2421 2448 P G B 28 OK OK 2426 2449 2450 2451 2481 P G B 29 OK OK 2456 2482 2483 2484 2514 P C B 30 OK OK 2489 2515 2516 2517 2544 P T B 31 OK OK 2522 2545 2546 2547 2576 P C B 32 OK OK 2552 2577 2578 2579 2606 P G B 33 OK OK 2584 2607 2608 2609 2639 P A B 34 OK OK 2614 2640 2641 2642 ---------------------------------------------------------------------------------