ID code: '1D6K' 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' --------------------------------------------------------------------------------- 1543 C1' G B 267 alpha beta 1538 1561 1544 1541 1578 C1' G B 268 alpha beta 1573 1596 1579 1576 1612 C1' A B 269 alpha beta 1607 1629 1613 1610 1645 C1' C B 270 alpha beta 1640 1660 1646 1643 1676 C1' C B 271 alpha beta 1671 1691 1677 1674 1707 C1' G B 272 alpha beta 1702 1725 1708 1705 1741 C1' A B 273 alpha beta 1736 1758 1742 1739 1774 C1' U B 274 alpha beta 1769 1789 1775 1772 1804 C1' G B 275 alpha beta 1799 1822 1805 1802 1838 C1' G B 276 alpha beta 1833 1856 1839 1836 1872 C1' U B 277 alpha beta 1867 1887 1873 1870 1902 C1' A B 278 alpha beta 1897 1919 1903 1900 1935 C1' G B 279 alpha beta 1930 1953 1936 1933 1969 C1' U B 280 alpha beta 1964 1984 1970 1967 1999 C1' G B 281 alpha beta 1994 2017 2000 1997 2033 C1' U B 282 alpha beta 2028 2048 2034 2031 2063 C1' C B 283 alpha beta 2058 2078 2064 2061 2094 C1' U B 284 alpha beta 2089 2109 2095 2092 2124 C1' U B 285 alpha beta 2119 2139 2125 2122 2154 C1' C B 291 alpha beta 2149 2169 2155 2152 2185 C1' G B 292 alpha beta 2180 2203 2186 2183 2219 C1' G B 293 alpha beta 2214 2237 2220 2217 2253 C1' A B 294 alpha beta 2248 2270 2254 2251 2286 C1' U B 295 alpha beta 2281 2301 2287 2284 2316 C1' G B 296 alpha beta 2311 2334 2317 2314 2350 C1' C B 297 alpha beta 2345 2365 2351 2348 2381 C1' G B 298 alpha beta 2376 2399 2382 2379 2415 C1' A B 299 alpha beta 2410 2432 2416 2413 2448 C1' G B 300 alpha beta 2443 2466 2449 2446 2482 C1' A B 301 alpha beta 2477 2499 2483 2480 2515 C1' G B 302 alpha beta 2510 2533 2516 2513 2549 C1' U B 303 alpha beta 2544 2564 2550 2547 2579 C1' A B 304 alpha beta 2574 2596 2580 2577 2612 C1' G B 305 alpha beta 2607 2630 2613 2610 2646 C1' G B 306 alpha beta 2641 2664 2647 2644 2680 C1' U B 307 alpha beta 2675 2695 2681 2678 2710 C1' C B 308 alpha beta 2705 2726 2711 2708 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1541 C2' G B 267 OK OK 1543 1539 1559 1542 1576 C2' G B 268 OK OK 1578 1574 1594 1577 1610 C2' A B 269 OK OK 1612 1608 1627 1611 1643 C2' C B 270 OK OK 1645 1641 1658 1644 1674 C2' C B 271 OK OK 1676 1672 1689 1675 1705 C2' G B 272 OK OK 1707 1703 1723 1706 1739 C2' A B 273 OK OK 1741 1737 1756 1740 1772 C2' U B 274 OK OK 1774 1770 1787 1773 1802 C2' G B 275 OK OK 1804 1800 1820 1803 1836 C2' G B 276 OK OK 1838 1834 1854 1837 1870 C2' U B 277 OK OK 1872 1868 1885 1871 1900 C2' A B 278 OK OK 1902 1898 1917 1901 1933 C2' G B 279 OK OK 1935 1931 1951 1934 1967 C2' U B 280 OK OK 1969 1965 1982 1968 1997 C2' G B 281 OK OK 1999 1995 2015 1998 2031 C2' U B 282 OK OK 2033 2029 2046 2032 2061 C2' C B 283 OK OK 2063 2059 2076 2062 2092 C2' U B 284 OK OK 2094 2090 2107 2093 2122 C2' U B 285 OK OK 2124 2120 2137 2123 2152 C2' C B 291 OK OK 2154 2150 2167 2153 2183 C2' G B 292 OK OK 2185 2181 2201 2184 2217 C2' G B 293 OK OK 2219 2215 2235 2218 2251 C2' A B 294 OK OK 2253 2249 2268 2252 2284 C2' U B 295 OK OK 2286 2282 2299 2285 2314 C2' G B 296 OK OK 2316 2312 2332 2315 2348 C2' C B 297 OK OK 2350 2346 2363 2349 2379 C2' G B 298 OK OK 2381 2377 2397 2380 2413 C2' A B 299 OK OK 2415 2411 2430 2414 2446 C2' G B 300 OK OK 2448 2444 2464 2447 2480 C2' A B 301 OK OK 2482 2478 2497 2481 2513 C2' G B 302 OK OK 2515 2511 2531 2514 2547 C2' U B 303 OK OK 2549 2545 2562 2548 2577 C2' A B 304 OK OK 2579 2575 2594 2578 2610 C2' G B 305 OK OK 2612 2608 2628 2611 2644 C2' G B 306 OK OK 2646 2642 2662 2645 2678 C2' U B 307 OK OK 2680 2676 2693 2679 2708 C2' C B 308 OK OK 2710 2706 2724 2709 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1539 C3' G B 267 OK OK 1537 1558 1540 1541 1574 C3' G B 268 OK OK 1572 1593 1575 1576 1608 C3' A B 269 OK OK 1606 1626 1609 1610 1641 C3' C B 270 OK OK 1639 1657 1642 1643 1672 C3' C B 271 OK OK 1670 1688 1673 1674 1703 C3' G B 272 OK OK 1701 1722 1704 1705 1737 C3' A B 273 OK OK 1735 1755 1738 1739 1770 C3' U B 274 OK OK 1768 1786 1771 1772 1800 C3' G B 275 OK OK 1798 1819 1801 1802 1834 C3' G B 276 OK OK 1832 1853 1835 1836 1868 C3' U B 277 OK OK 1866 1884 1869 1870 1898 C3' A B 278 OK OK 1896 1916 1899 1900 1931 C3' G B 279 OK OK 1929 1950 1932 1933 1965 C3' U B 280 OK OK 1963 1981 1966 1967 1995 C3' G B 281 OK OK 1993 2014 1996 1997 2029 C3' U B 282 OK OK 2027 2045 2030 2031 2059 C3' C B 283 OK OK 2057 2075 2060 2061 2090 C3' U B 284 OK OK 2088 2106 2091 2092 2120 C3' U B 285 OK OK 2118 2136 2121 2122 2150 C3' C B 291 OK OK 2148 2166 2151 2152 2181 C3' G B 292 OK OK 2179 2200 2182 2183 2215 C3' G B 293 OK OK 2213 2234 2216 2217 2249 C3' A B 294 OK OK 2247 2267 2250 2251 2282 C3' U B 295 OK OK 2280 2298 2283 2284 2312 C3' G B 296 OK OK 2310 2331 2313 2314 2346 C3' C B 297 OK OK 2344 2362 2347 2348 2377 C3' G B 298 OK OK 2375 2396 2378 2379 2411 C3' A B 299 OK OK 2409 2429 2412 2413 2444 C3' G B 300 OK OK 2442 2463 2445 2446 2478 C3' A B 301 OK OK 2476 2496 2479 2480 2511 C3' G B 302 OK OK 2509 2530 2512 2513 2545 C3' U B 303 OK OK 2543 2561 2546 2547 2575 C3' A B 304 OK OK 2573 2593 2576 2577 2608 C3' G B 305 OK OK 2606 2627 2609 2610 2642 C3' G B 306 OK OK 2640 2661 2643 2644 2676 C3' U B 307 OK OK 2674 2692 2677 2678 2706 C3' C B 308 OK OK 2704 2722 2707 2708 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1537 C4' G B 267 OK OK 1539 1557 1536 1538 1572 C4' G B 268 OK OK 1574 1592 1571 1573 1606 C4' A B 269 OK OK 1608 1625 1605 1607 1639 C4' C B 270 OK OK 1641 1656 1638 1640 1670 C4' C B 271 OK OK 1672 1687 1669 1671 1701 C4' G B 272 OK OK 1703 1721 1700 1702 1735 C4' A B 273 OK OK 1737 1754 1734 1736 1768 C4' U B 274 OK OK 1770 1785 1767 1769 1798 C4' G B 275 OK OK 1800 1818 1797 1799 1832 C4' G B 276 OK OK 1834 1852 1831 1833 1866 C4' U B 277 OK OK 1868 1883 1865 1867 1896 C4' A B 278 OK OK 1898 1915 1895 1897 1929 C4' G B 279 OK OK 1931 1949 1928 1930 1963 C4' U B 280 OK OK 1965 1980 1962 1964 1993 C4' G B 281 OK OK 1995 2013 1992 1994 2027 C4' U B 282 OK OK 2029 2044 2026 2028 2057 C4' C B 283 OK OK 2059 2074 2056 2058 2088 C4' U B 284 OK OK 2090 2105 2087 2089 2118 C4' U B 285 OK OK 2120 2135 2117 2119 2148 C4' C B 291 OK OK 2150 2165 2147 2149 2179 C4' G B 292 OK OK 2181 2199 2178 2180 2213 C4' G B 293 OK OK 2215 2233 2212 2214 2247 C4' A B 294 OK OK 2249 2266 2246 2248 2280 C4' U B 295 OK OK 2282 2297 2279 2281 2310 C4' G B 296 OK OK 2312 2330 2309 2311 2344 C4' C B 297 OK OK 2346 2361 2343 2345 2375 C4' G B 298 OK OK 2377 2395 2374 2376 2409 C4' A B 299 OK OK 2411 2428 2408 2410 2442 C4' G B 300 OK OK 2444 2462 2441 2443 2476 C4' A B 301 OK OK 2478 2495 2475 2477 2509 C4' G B 302 OK OK 2511 2529 2508 2510 2543 C4' U B 303 OK OK 2545 2560 2542 2544 2573 C4' A B 304 OK OK 2575 2592 2572 2574 2606 C4' G B 305 OK OK 2608 2626 2605 2607 2640 C4' G B 306 OK OK 2642 2660 2639 2641 2674 C4' U B 307 OK OK 2676 2691 2673 2675 2704 C4' C B 308 OK OK 2706 2721 2703 2705 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1536 C5' G B 267 OK OK 1535 1555 1556 1537 1571 C5' G B 268 OK OK 1570 1590 1591 1572 1605 C5' A B 269 OK OK 1604 1623 1624 1606 1638 C5' C B 270 OK OK 1637 1654 1655 1639 1669 C5' C B 271 OK OK 1668 1685 1686 1670 1700 C5' G B 272 OK OK 1699 1719 1720 1701 1734 C5' A B 273 OK OK 1733 1752 1753 1735 1767 C5' U B 274 OK OK 1766 1783 1784 1768 1797 C5' G B 275 OK OK 1796 1816 1817 1798 1831 C5' G B 276 OK OK 1830 1850 1851 1832 1865 C5' U B 277 OK OK 1864 1881 1882 1866 1895 C5' A B 278 OK OK 1894 1913 1914 1896 1928 C5' G B 279 OK OK 1927 1947 1948 1929 1962 C5' U B 280 OK OK 1961 1978 1979 1963 1992 C5' G B 281 OK OK 1991 2011 2012 1993 2026 C5' U B 282 OK OK 2025 2042 2043 2027 2056 C5' C B 283 OK OK 2055 2072 2073 2057 2087 C5' U B 284 OK OK 2086 2103 2104 2088 2117 C5' U B 285 OK OK 2116 2133 2134 2118 2147 C5' C B 291 OK OK 2146 2163 2164 2148 2178 C5' G B 292 OK OK 2177 2197 2198 2179 2212 C5' G B 293 OK OK 2211 2231 2232 2213 2246 C5' A B 294 OK OK 2245 2264 2265 2247 2279 C5' U B 295 OK OK 2278 2295 2296 2280 2309 C5' G B 296 OK OK 2308 2328 2329 2310 2343 C5' C B 297 OK OK 2342 2359 2360 2344 2374 C5' G B 298 OK OK 2373 2393 2394 2375 2408 C5' A B 299 OK OK 2407 2426 2427 2409 2441 C5' G B 300 OK OK 2440 2460 2461 2442 2475 C5' A B 301 OK OK 2474 2493 2494 2476 2508 C5' G B 302 OK OK 2507 2527 2528 2509 2542 C5' U B 303 OK OK 2541 2558 2559 2543 2572 C5' A B 304 OK OK 2571 2590 2591 2573 2605 C5' G B 305 OK OK 2604 2624 2625 2606 2639 C5' G B 306 OK OK 2638 2658 2659 2640 2673 C5' U B 307 OK OK 2672 2689 2690 2674 2703 C5' C B 308 OK OK 2702 2719 2720 2704 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1567 P G B 268 distorted distorted 1540 1568 1569 1570 1601 P A B 269 distorted distorted 1575 1602 1603 1604 1634 P C B 270 distorted distorted 1609 1635 1636 1637 1665 P C B 271 distorted distorted 1642 1666 1667 1668 1696 P G B 272 distorted distorted 1673 1697 1698 1699 1730 P A B 273 distorted distorted 1704 1731 1732 1733 1763 P U B 274 distorted distorted 1738 1764 1765 1766 1793 P G B 275 distorted distorted 1771 1794 1795 1796 1827 P G B 276 distorted distorted 1801 1828 1829 1830 1861 P U B 277 distorted distorted 1835 1862 1863 1864 1891 P A B 278 distorted distorted 1869 1892 1893 1894 1924 P G B 279 distorted distorted 1899 1925 1926 1927 1958 P U B 280 distorted distorted 1932 1959 1960 1961 1988 P G B 281 distorted distorted 1966 1989 1990 1991 2022 P U B 282 distorted distorted 1996 2023 2024 2025 2052 P C B 283 distorted distorted 2030 2053 2054 2055 2083 P U B 284 distorted distorted 2060 2084 2085 2086 2113 P U B 285 distorted distorted 2091 2114 2115 2116 2143 P C B 291 distorted distorted 2121 2144 2145 2146 2174 P G B 292 distorted distorted 2151 2175 2176 2177 2208 P G B 293 distorted distorted 2182 2209 2210 2211 2242 P A B 294 distorted distorted 2216 2243 2244 2245 2275 P U B 295 distorted distorted 2250 2276 2277 2278 2305 P G B 296 distorted distorted 2283 2306 2307 2308 2339 P C B 297 distorted distorted 2313 2340 2341 2342 2370 P G B 298 distorted distorted 2347 2371 2372 2373 2404 P A B 299 distorted distorted 2378 2405 2406 2407 2437 P G B 300 distorted distorted 2412 2438 2439 2440 2471 P A B 301 distorted distorted 2445 2472 2473 2474 2504 P G B 302 distorted distorted 2479 2505 2506 2507 2538 P U B 303 distorted distorted 2512 2539 2540 2541 2568 P A B 304 distorted distorted 2546 2569 2570 2571 2601 P G B 305 distorted distorted 2576 2602 2603 2604 2635 P G B 306 distorted distorted 2609 2636 2637 2638 2669 P U B 307 distorted distorted 2643 2670 2671 2672 2699 P C B 308 distorted distorted 2677 2700 2701 2702 ---------------------------------------------------------------------------------