ID code: '3VYY' 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' --------------------------------------------------------------------------------- 1367 C1' G C 1 beta 1362 1368 1365 1390 C1' C C 2 beta 1385 1391 1388 1410 C1' G C 3 beta 1405 1411 1408 1433 C1' C C 4 beta 1428 1434 1431 1453 C1' G C 5 beta 1448 1454 1451 1476 C1' C C 6 beta 1471 1477 1474 1496 C1' G C 7 beta 1491 1497 1494 1519 C1' C C 8 beta 1514 1520 1517 1539 C1' G C 9 beta 1534 1540 1537 1562 C1' C C 10 beta 1557 1563 1560 1580 C1' G D 1 beta 1575 1581 1578 1603 C1' C D 2 beta 1598 1604 1601 1623 C1' G D 3 beta 1618 1624 1621 1646 C1' C D 4 beta 1641 1647 1644 1666 C1' G D 5 beta 1661 1667 1664 1689 C1' C D 6 beta 1684 1690 1687 1709 C1' G D 7 beta 1704 1710 1707 1732 C1' C D 8 beta 1727 1733 1730 1752 C1' G D 9 beta 1747 1753 1750 1775 C1' C D 10 beta 1770 1776 1773 1793 C1' G E 1 beta 1788 1794 1791 1816 C1' C E 2 beta 1811 1817 1814 1836 C1' G E 3 beta 1831 1837 1834 1859 C1' C E 4 beta 1854 1860 1857 1879 C1' G E 5 beta 1874 1880 1877 1902 C1' C E 6 beta 1897 1903 1900 1922 C1' G E 7 beta 1917 1923 1920 1945 C1' C E 8 beta 1940 1946 1943 1965 C1' G E 9 beta 1960 1966 1963 1988 C1' C E 10 beta 1983 1989 1986 2006 C1' G F 1 beta 2001 2007 2004 2029 C1' C F 2 beta 2024 2030 2027 2049 C1' G F 3 beta 2044 2050 2047 2072 C1' C F 4 beta 2067 2073 2070 2092 C1' G F 5 beta 2087 2093 2090 2115 C1' C F 6 beta 2110 2116 2113 2135 C1' G F 7 beta 2130 2136 2133 2158 C1' C F 8 beta 2153 2159 2156 2178 C1' G F 9 beta 2173 2179 2176 2201 C1' C F 10 beta 2196 2202 2199 2219 C1' G G 1 beta 2214 2220 2217 2242 C1' C G 2 beta 2237 2243 2240 2262 C1' G G 3 beta 2257 2263 2260 2285 C1' C G 4 beta 2280 2286 2283 2305 C1' G G 5 beta 2300 2306 2303 2328 C1' C G 6 beta 2323 2329 2326 2348 C1' G G 7 beta 2343 2349 2346 2371 C1' C G 8 beta 2366 2372 2369 2391 C1' G G 9 beta 2386 2392 2389 2414 C1' C G 10 beta 2409 2415 2412 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1365 C2' G C 1 OK 1367 1363 1366 1388 C2' C C 2 OK 1390 1386 1389 1408 C2' G C 3 OK 1410 1406 1409 1431 C2' C C 4 OK 1433 1429 1432 1451 C2' G C 5 OK 1453 1449 1452 1474 C2' C C 6 OK 1476 1472 1475 1494 C2' G C 7 OK 1496 1492 1495 1517 C2' C C 8 OK 1519 1515 1518 1537 C2' G C 9 OK 1539 1535 1538 1560 C2' C C 10 OK 1562 1558 1561 1578 C2' G D 1 OK 1580 1576 1579 1601 C2' C D 2 OK 1603 1599 1602 1621 C2' G D 3 OK 1623 1619 1622 1644 C2' C D 4 OK 1646 1642 1645 1664 C2' G D 5 OK 1666 1662 1665 1687 C2' C D 6 OK 1689 1685 1688 1707 C2' G D 7 OK 1709 1705 1708 1730 C2' C D 8 OK 1732 1728 1731 1750 C2' G D 9 OK 1752 1748 1751 1773 C2' C D 10 OK 1775 1771 1774 1791 C2' G E 1 OK 1793 1789 1792 1814 C2' C E 2 OK 1816 1812 1815 1834 C2' G E 3 OK 1836 1832 1835 1857 C2' C E 4 OK 1859 1855 1858 1877 C2' G E 5 OK 1879 1875 1878 1900 C2' C E 6 OK 1902 1898 1901 1920 C2' G E 7 OK 1922 1918 1921 1943 C2' C E 8 OK 1945 1941 1944 1963 C2' G E 9 OK 1965 1961 1964 1986 C2' C E 10 OK 1988 1984 1987 2004 C2' G F 1 OK 2006 2002 2005 2027 C2' C F 2 OK 2029 2025 2028 2047 C2' G F 3 OK 2049 2045 2048 2070 C2' C F 4 OK 2072 2068 2071 2090 C2' G F 5 OK 2092 2088 2091 2113 C2' C F 6 OK 2115 2111 2114 2133 C2' G F 7 OK 2135 2131 2134 2156 C2' C F 8 OK 2158 2154 2157 2176 C2' G F 9 OK 2178 2174 2177 2199 C2' C F 10 OK 2201 2197 2200 2217 C2' G G 1 OK 2219 2215 2218 2240 C2' C G 2 OK 2242 2238 2241 2260 C2' G G 3 OK 2262 2258 2261 2283 C2' C G 4 OK 2285 2281 2284 2303 C2' G G 5 OK 2305 2301 2304 2326 C2' C G 6 OK 2328 2324 2327 2346 C2' G G 7 OK 2348 2344 2347 2369 C2' C G 8 OK 2371 2367 2370 2389 C2' G G 9 OK 2391 2387 2390 2412 C2' C G 10 OK 2414 2410 2413 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1363 C3' G C 1 OK 1361 1364 1365 1386 C3' C C 2 OK 1384 1387 1388 1406 C3' G C 3 OK 1404 1407 1408 1429 C3' C C 4 OK 1427 1430 1431 1449 C3' G C 5 OK 1447 1450 1451 1472 C3' C C 6 OK 1470 1473 1474 1492 C3' G C 7 OK 1490 1493 1494 1515 C3' C C 8 OK 1513 1516 1517 1535 C3' G C 9 OK 1533 1536 1537 1558 C3' C C 10 OK 1556 1559 1560 1576 C3' G D 1 OK 1574 1577 1578 1599 C3' C D 2 OK 1597 1600 1601 1619 C3' G D 3 OK 1617 1620 1621 1642 C3' C D 4 OK 1640 1643 1644 1662 C3' G D 5 OK 1660 1663 1664 1685 C3' C D 6 OK 1683 1686 1687 1705 C3' G D 7 OK 1703 1706 1707 1728 C3' C D 8 OK 1726 1729 1730 1748 C3' G D 9 OK 1746 1749 1750 1771 C3' C D 10 OK 1769 1772 1773 1789 C3' G E 1 OK 1787 1790 1791 1812 C3' C E 2 OK 1810 1813 1814 1832 C3' G E 3 OK 1830 1833 1834 1855 C3' C E 4 OK 1853 1856 1857 1875 C3' G E 5 OK 1873 1876 1877 1898 C3' C E 6 OK 1896 1899 1900 1918 C3' G E 7 OK 1916 1919 1920 1941 C3' C E 8 OK 1939 1942 1943 1961 C3' G E 9 OK 1959 1962 1963 1984 C3' C E 10 OK 1982 1985 1986 2002 C3' G F 1 OK 2000 2003 2004 2025 C3' C F 2 OK 2023 2026 2027 2045 C3' G F 3 OK 2043 2046 2047 2068 C3' C F 4 OK 2066 2069 2070 2088 C3' G F 5 OK 2086 2089 2090 2111 C3' C F 6 OK 2109 2112 2113 2131 C3' G F 7 OK 2129 2132 2133 2154 C3' C F 8 OK 2152 2155 2156 2174 C3' G F 9 OK 2172 2175 2176 2197 C3' C F 10 OK 2195 2198 2199 2215 C3' G G 1 OK 2213 2216 2217 2238 C3' C G 2 OK 2236 2239 2240 2258 C3' G G 3 OK 2256 2259 2260 2281 C3' C G 4 OK 2279 2282 2283 2301 C3' G G 5 OK 2299 2302 2303 2324 C3' C G 6 OK 2322 2325 2326 2344 C3' G G 7 OK 2342 2345 2346 2367 C3' C G 8 OK 2365 2368 2369 2387 C3' G G 9 OK 2385 2388 2389 2410 C3' C G 10 OK 2408 2411 2412 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1361 C4' G C 1 OK 1363 1360 1362 1384 C4' C C 2 OK 1386 1383 1385 1404 C4' G C 3 OK 1406 1403 1405 1427 C4' C C 4 OK 1429 1426 1428 1447 C4' G C 5 OK 1449 1446 1448 1470 C4' C C 6 OK 1472 1469 1471 1490 C4' G C 7 OK 1492 1489 1491 1513 C4' C C 8 OK 1515 1512 1514 1533 C4' G C 9 OK 1535 1532 1534 1556 C4' C C 10 OK 1558 1555 1557 1574 C4' G D 1 OK 1576 1573 1575 1597 C4' C D 2 OK 1599 1596 1598 1617 C4' G D 3 OK 1619 1616 1618 1640 C4' C D 4 OK 1642 1639 1641 1660 C4' G D 5 OK 1662 1659 1661 1683 C4' C D 6 OK 1685 1682 1684 1703 C4' G D 7 OK 1705 1702 1704 1726 C4' C D 8 OK 1728 1725 1727 1746 C4' G D 9 OK 1748 1745 1747 1769 C4' C D 10 OK 1771 1768 1770 1787 C4' G E 1 OK 1789 1786 1788 1810 C4' C E 2 OK 1812 1809 1811 1830 C4' G E 3 OK 1832 1829 1831 1853 C4' C E 4 OK 1855 1852 1854 1873 C4' G E 5 OK 1875 1872 1874 1896 C4' C E 6 OK 1898 1895 1897 1916 C4' G E 7 OK 1918 1915 1917 1939 C4' C E 8 OK 1941 1938 1940 1959 C4' G E 9 OK 1961 1958 1960 1982 C4' C E 10 OK 1984 1981 1983 2000 C4' G F 1 OK 2002 1999 2001 2023 C4' C F 2 OK 2025 2022 2024 2043 C4' G F 3 OK 2045 2042 2044 2066 C4' C F 4 OK 2068 2065 2067 2086 C4' G F 5 OK 2088 2085 2087 2109 C4' C F 6 OK 2111 2108 2110 2129 C4' G F 7 OK 2131 2128 2130 2152 C4' C F 8 OK 2154 2151 2153 2172 C4' G F 9 OK 2174 2171 2173 2195 C4' C F 10 OK 2197 2194 2196 2213 C4' G G 1 OK 2215 2212 2214 2236 C4' C G 2 OK 2238 2235 2237 2256 C4' G G 3 OK 2258 2255 2257 2279 C4' C G 4 OK 2281 2278 2280 2299 C4' G G 5 OK 2301 2298 2300 2322 C4' C G 6 OK 2324 2321 2323 2342 C4' G G 7 OK 2344 2341 2343 2365 C4' C G 8 OK 2367 2364 2366 2385 C4' G G 9 OK 2387 2384 2386 2408 C4' C G 10 OK 2410 2407 2409 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1360 C5' G C 1 1359 1361 1383 C5' C C 2 1382 1384 1403 C5' G C 3 1402 1404 1426 C5' C C 4 1425 1427 1446 C5' G C 5 1445 1447 1469 C5' C C 6 1468 1470 1489 C5' G C 7 1488 1490 1512 C5' C C 8 1511 1513 1532 C5' G C 9 1531 1533 1555 C5' C C 10 1554 1556 1573 C5' G D 1 1572 1574 1596 C5' C D 2 1595 1597 1616 C5' G D 3 1615 1617 1639 C5' C D 4 1638 1640 1659 C5' G D 5 1658 1660 1682 C5' C D 6 1681 1683 1702 C5' G D 7 1701 1703 1725 C5' C D 8 1724 1726 1745 C5' G D 9 1744 1746 1768 C5' C D 10 1767 1769 1786 C5' G E 1 1785 1787 1809 C5' C E 2 1808 1810 1829 C5' G E 3 1828 1830 1852 C5' C E 4 1851 1853 1872 C5' G E 5 1871 1873 1895 C5' C E 6 1894 1896 1915 C5' G E 7 1914 1916 1938 C5' C E 8 1937 1939 1958 C5' G E 9 1957 1959 1981 C5' C E 10 1980 1982 1999 C5' G F 1 1998 2000 2022 C5' C F 2 2021 2023 2042 C5' G F 3 2041 2043 2065 C5' C F 4 2064 2066 2085 C5' G F 5 2084 2086 2108 C5' C F 6 2107 2109 2128 C5' G F 7 2127 2129 2151 C5' C F 8 2150 2152 2171 C5' G F 9 2170 2172 2194 C5' C F 10 2193 2195 2212 C5' G G 1 2211 2213 2235 C5' C G 2 2234 2236 2255 C5' G G 3 2254 2256 2278 C5' C G 4 2277 2279 2298 C5' G G 5 2297 2299 2321 C5' C G 6 2320 2322 2341 C5' G G 7 2340 2342 2364 C5' C G 8 2363 2365 2384 C5' G G 9 2383 2385 2407 C5' C G 10 2406 2408 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1379 P C C 2 distorted distorted 1364 1380 1381 1382 1399 P G C 3 distorted distorted 1387 1400 1401 1402 1422 P C C 4 distorted distorted 1407 1423 1424 1425 1442 P G C 5 distorted distorted 1430 1443 1444 1445 1465 P C C 6 distorted distorted 1450 1466 1467 1468 1485 P G C 7 distorted distorted 1473 1486 1487 1488 1508 P C C 8 distorted distorted 1493 1509 1510 1511 1528 P G C 9 distorted distorted 1516 1529 1530 1531 1551 P C C 10 distorted distorted 1536 1552 1553 1554 1592 P C D 2 distorted distorted 1577 1593 1594 1595 1612 P G D 3 distorted distorted 1600 1613 1614 1615 1635 P C D 4 distorted distorted 1620 1636 1637 1638 1655 P G D 5 distorted distorted 1643 1656 1657 1658 1678 P C D 6 distorted distorted 1663 1679 1680 1681 1698 P G D 7 distorted distorted 1686 1699 1700 1701 1721 P C D 8 distorted distorted 1706 1722 1723 1724 1741 P G D 9 distorted distorted 1729 1742 1743 1744 1764 P C D 10 distorted distorted 1749 1765 1766 1767 1805 P C E 2 distorted distorted 1790 1806 1807 1808 1825 P G E 3 distorted distorted 1813 1826 1827 1828 1848 P C E 4 distorted distorted 1833 1849 1850 1851 1868 P G E 5 distorted distorted 1856 1869 1870 1871 1891 P C E 6 distorted distorted 1876 1892 1893 1894 1911 P G E 7 distorted distorted 1899 1912 1913 1914 1934 P C E 8 distorted distorted 1919 1935 1936 1937 1954 P G E 9 distorted distorted 1942 1955 1956 1957 1977 P C E 10 distorted distorted 1962 1978 1979 1980 2018 P C F 2 distorted distorted 2003 2019 2020 2021 2038 P G F 3 distorted distorted 2026 2039 2040 2041 2061 P C F 4 distorted distorted 2046 2062 2063 2064 2081 P G F 5 distorted distorted 2069 2082 2083 2084 2104 P C F 6 distorted distorted 2089 2105 2106 2107 2124 P G F 7 distorted distorted 2112 2125 2126 2127 2147 P C F 8 distorted distorted 2132 2148 2149 2150 2167 P G F 9 distorted distorted 2155 2168 2169 2170 2190 P C F 10 distorted distorted 2175 2191 2192 2193 2231 P C G 2 distorted distorted 2216 2232 2233 2234 2251 P G G 3 distorted distorted 2239 2252 2253 2254 2274 P C G 4 distorted distorted 2259 2275 2276 2277 2294 P G G 5 distorted distorted 2282 2295 2296 2297 2317 P C G 6 distorted distorted 2302 2318 2319 2320 2337 P G G 7 distorted distorted 2325 2338 2339 2340 2360 P C G 8 distorted distorted 2345 2361 2362 2363 2380 P G G 9 distorted distorted 2368 2381 2382 2383 2403 P C G 10 distorted distorted 2388 2404 2405 2406 ---------------------------------------------------------------------------------