ID code: '4TUW' 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' --------------------------------------------------------------------------------- 1168 C1' G D 1 beta 1163 1169 1166 1191 C1' G D 2 beta 1186 1192 1189 1214 C1' C D 3 beta 1209 1215 1212 1234 C1' C D 4 beta 1229 1235 1232 1254 C1' A D 5 beta 1249 1255 1252 1276 C1' A D 6 beta 1271 1277 1274 1298 C1' A D 7 beta 1293 1299 1296 1320 C1' G D 8 beta 1315 1321 1318 1343 C1' G D 9 beta 1338 1344 1341 1366 C1' C D 10 beta 1361 1367 1364 1386 C1' C D 11 beta 1381 1387 1384 1406 C1' C D 12 beta 1401 1407 1404 1426 C1' U D 13 beta 1421 1427 1424 1446 C1' U D 14 beta 1441 1447 1444 1466 C1' U D 15 beta 1461 1467 1464 1486 C1' U D 16 beta 1481 1487 1484 1506 C1' C D 17 beta 1501 1507 1504 1526 C1' A D 18 beta 1521 1527 1524 1548 C1' G D 19 beta 1543 1549 1546 1571 C1' G D 20 beta 1566 1572 1569 1594 C1' G D 21 beta 1589 1595 1592 1617 C1' C D 22 beta 1612 1618 1615 1637 C1' C D 23 beta 1632 1638 1635 1657 C1' A D 24 beta 1652 1658 1655 1679 C1' C D 25 beta 1674 1680 1677 1699 C1' C D 26 1694 1697 1709 C1' G C 1 beta 1704 1710 1707 1732 C1' G C 2 beta 1727 1733 1730 1755 C1' C C 3 beta 1750 1756 1753 1775 C1' C C 4 beta 1770 1776 1773 1795 C1' A C 5 beta 1790 1796 1793 1817 C1' A C 6 beta 1812 1818 1815 1839 C1' A C 7 beta 1834 1840 1837 1861 C1' G C 8 beta 1856 1862 1859 1884 C1' G C 9 beta 1879 1885 1882 1907 C1' C C 10 beta 1902 1908 1905 1927 C1' C C 11 beta 1922 1928 1925 1947 C1' C C 12 beta 1942 1948 1945 1967 C1' U C 13 beta 1962 1968 1965 1987 C1' U C 14 beta 1982 1988 1985 2007 C1' U C 15 beta 2002 2008 2005 2027 C1' U C 16 beta 2022 2028 2025 2047 C1' C C 17 beta 2042 2048 2045 2067 C1' A C 18 beta 2062 2068 2065 2089 C1' G C 19 beta 2084 2090 2087 2112 C1' G C 20 beta 2107 2113 2110 2135 C1' G C 21 beta 2130 2136 2133 2158 C1' C C 22 beta 2153 2159 2156 2178 C1' C C 23 beta 2173 2179 2176 2198 C1' A C 24 beta 2193 2199 2196 2220 C1' C C 25 beta 2215 2221 2218 2240 C1' C C 26 beta 2235 2241 2238 2260 C1' C C 27 beta 2255 2261 2258 2280 C1' C C 28 2275 2278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1166 C2' G D 1 OK 1168 1164 1167 1189 C2' G D 2 OK 1191 1187 1190 1212 C2' C D 3 OK 1214 1210 1213 1232 C2' C D 4 OK 1234 1230 1233 1252 C2' A D 5 OK 1254 1250 1253 1274 C2' A D 6 OK 1276 1272 1275 1296 C2' A D 7 OK 1298 1294 1297 1318 C2' G D 8 OK 1320 1316 1319 1341 C2' G D 9 OK 1343 1339 1342 1364 C2' C D 10 OK 1366 1362 1365 1384 C2' C D 11 OK 1386 1382 1385 1404 C2' C D 12 OK 1406 1402 1405 1424 C2' U D 13 OK 1426 1422 1425 1444 C2' U D 14 OK 1446 1442 1445 1464 C2' U D 15 OK 1466 1462 1465 1484 C2' U D 16 OK 1486 1482 1485 1504 C2' C D 17 OK 1506 1502 1505 1524 C2' A D 18 OK 1526 1522 1525 1546 C2' G D 19 OK 1548 1544 1547 1569 C2' G D 20 OK 1571 1567 1570 1592 C2' G D 21 OK 1594 1590 1593 1615 C2' C D 22 OK 1617 1613 1616 1635 C2' C D 23 OK 1637 1633 1636 1655 C2' A D 24 OK 1657 1653 1656 1677 C2' C D 25 OK 1679 1675 1678 1697 C2' C D 26 OK 1699 1695 1698 1707 C2' G C 1 OK 1709 1705 1708 1730 C2' G C 2 OK 1732 1728 1731 1753 C2' C C 3 OK 1755 1751 1754 1773 C2' C C 4 OK 1775 1771 1774 1793 C2' A C 5 OK 1795 1791 1794 1815 C2' A C 6 OK 1817 1813 1816 1837 C2' A C 7 OK 1839 1835 1838 1859 C2' G C 8 OK 1861 1857 1860 1882 C2' G C 9 OK 1884 1880 1883 1905 C2' C C 10 OK 1907 1903 1906 1925 C2' C C 11 OK 1927 1923 1926 1945 C2' C C 12 OK 1947 1943 1946 1965 C2' U C 13 OK 1967 1963 1966 1985 C2' U C 14 OK 1987 1983 1986 2005 C2' U C 15 OK 2007 2003 2006 2025 C2' U C 16 OK 2027 2023 2026 2045 C2' C C 17 OK 2047 2043 2046 2065 C2' A C 18 OK 2067 2063 2066 2087 C2' G C 19 OK 2089 2085 2088 2110 C2' G C 20 OK 2112 2108 2111 2133 C2' G C 21 OK 2135 2131 2134 2156 C2' C C 22 OK 2158 2154 2157 2176 C2' C C 23 OK 2178 2174 2177 2196 C2' A C 24 OK 2198 2194 2197 2218 C2' C C 25 OK 2220 2216 2219 2238 C2' C C 26 OK 2240 2236 2239 2258 C2' C C 27 OK 2260 2256 2259 2278 C2' C C 28 OK 2280 2276 2279 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1164 C3' G D 1 OK 1162 1165 1166 1187 C3' G D 2 OK 1185 1188 1189 1210 C3' C D 3 OK 1208 1211 1212 1230 C3' C D 4 OK 1228 1231 1232 1250 C3' A D 5 OK 1248 1251 1252 1272 C3' A D 6 OK 1270 1273 1274 1294 C3' A D 7 OK 1292 1295 1296 1316 C3' G D 8 OK 1314 1317 1318 1339 C3' G D 9 OK 1337 1340 1341 1362 C3' C D 10 OK 1360 1363 1364 1382 C3' C D 11 OK 1380 1383 1384 1402 C3' C D 12 OK 1400 1403 1404 1422 C3' U D 13 OK 1420 1423 1424 1442 C3' U D 14 OK 1440 1443 1444 1462 C3' U D 15 OK 1460 1463 1464 1482 C3' U D 16 OK 1480 1483 1484 1502 C3' C D 17 OK 1500 1503 1504 1522 C3' A D 18 OK 1520 1523 1524 1544 C3' G D 19 OK 1542 1545 1546 1567 C3' G D 20 OK 1565 1568 1569 1590 C3' G D 21 OK 1588 1591 1592 1613 C3' C D 22 OK 1611 1614 1615 1633 C3' C D 23 OK 1631 1634 1635 1653 C3' A D 24 OK 1651 1654 1655 1675 C3' C D 25 OK 1673 1676 1677 1695 C3' C D 26 OK 1693 1696 1697 1705 C3' G C 1 OK 1703 1706 1707 1728 C3' G C 2 OK 1726 1729 1730 1751 C3' C C 3 OK 1749 1752 1753 1771 C3' C C 4 OK 1769 1772 1773 1791 C3' A C 5 OK 1789 1792 1793 1813 C3' A C 6 OK 1811 1814 1815 1835 C3' A C 7 OK 1833 1836 1837 1857 C3' G C 8 OK 1855 1858 1859 1880 C3' G C 9 OK 1878 1881 1882 1903 C3' C C 10 OK 1901 1904 1905 1923 C3' C C 11 OK 1921 1924 1925 1943 C3' C C 12 OK 1941 1944 1945 1963 C3' U C 13 OK 1961 1964 1965 1983 C3' U C 14 OK 1981 1984 1985 2003 C3' U C 15 OK 2001 2004 2005 2023 C3' U C 16 OK 2021 2024 2025 2043 C3' C C 17 OK 2041 2044 2045 2063 C3' A C 18 OK 2061 2064 2065 2085 C3' G C 19 OK 2083 2086 2087 2108 C3' G C 20 OK 2106 2109 2110 2131 C3' G C 21 OK 2129 2132 2133 2154 C3' C C 22 OK 2152 2155 2156 2174 C3' C C 23 OK 2172 2175 2176 2194 C3' A C 24 OK 2192 2195 2196 2216 C3' C C 25 OK 2214 2217 2218 2236 C3' C C 26 OK 2234 2237 2238 2256 C3' C C 27 OK 2254 2257 2258 2276 C3' C C 28 OK 2274 2277 2278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1162 C4' G D 1 OK 1164 1161 1163 1185 C4' G D 2 OK 1187 1184 1186 1208 C4' C D 3 OK 1210 1207 1209 1228 C4' C D 4 OK 1230 1227 1229 1248 C4' A D 5 OK 1250 1247 1249 1270 C4' A D 6 OK 1272 1269 1271 1292 C4' A D 7 OK 1294 1291 1293 1314 C4' G D 8 OK 1316 1313 1315 1337 C4' G D 9 OK 1339 1336 1338 1360 C4' C D 10 OK 1362 1359 1361 1380 C4' C D 11 OK 1382 1379 1381 1400 C4' C D 12 OK 1402 1399 1401 1420 C4' U D 13 OK 1422 1419 1421 1440 C4' U D 14 OK 1442 1439 1441 1460 C4' U D 15 OK 1462 1459 1461 1480 C4' U D 16 OK 1482 1479 1481 1500 C4' C D 17 OK 1502 1499 1501 1520 C4' A D 18 OK 1522 1519 1521 1542 C4' G D 19 OK 1544 1541 1543 1565 C4' G D 20 OK 1567 1564 1566 1588 C4' G D 21 OK 1590 1587 1589 1611 C4' C D 22 OK 1613 1610 1612 1631 C4' C D 23 OK 1633 1630 1632 1651 C4' A D 24 OK 1653 1650 1652 1673 C4' C D 25 OK 1675 1672 1674 1693 C4' C D 26 OK 1695 1692 1694 1703 C4' G C 1 OK 1705 1702 1704 1726 C4' G C 2 OK 1728 1725 1727 1749 C4' C C 3 OK 1751 1748 1750 1769 C4' C C 4 OK 1771 1768 1770 1789 C4' A C 5 OK 1791 1788 1790 1811 C4' A C 6 OK 1813 1810 1812 1833 C4' A C 7 OK 1835 1832 1834 1855 C4' G C 8 OK 1857 1854 1856 1878 C4' G C 9 OK 1880 1877 1879 1901 C4' C C 10 OK 1903 1900 1902 1921 C4' C C 11 OK 1923 1920 1922 1941 C4' C C 12 OK 1943 1940 1942 1961 C4' U C 13 OK 1963 1960 1962 1981 C4' U C 14 OK 1983 1980 1982 2001 C4' U C 15 OK 2003 2000 2002 2021 C4' U C 16 OK 2023 2020 2022 2041 C4' C C 17 OK 2043 2040 2042 2061 C4' A C 18 OK 2063 2060 2062 2083 C4' G C 19 OK 2085 2082 2084 2106 C4' G C 20 OK 2108 2105 2107 2129 C4' G C 21 OK 2131 2128 2130 2152 C4' C C 22 OK 2154 2151 2153 2172 C4' C C 23 OK 2174 2171 2173 2192 C4' A C 24 OK 2194 2191 2193 2214 C4' C C 25 OK 2216 2213 2215 2234 C4' C C 26 OK 2236 2233 2235 2254 C4' C C 27 OK 2256 2253 2255 2274 C4' C C 28 OK 2276 2273 2275 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1161 C5' G D 1 1160 1162 1184 C5' G D 2 1183 1185 1207 C5' C D 3 1206 1208 1227 C5' C D 4 1226 1228 1247 C5' A D 5 1246 1248 1269 C5' A D 6 1268 1270 1291 C5' A D 7 1290 1292 1313 C5' G D 8 1312 1314 1336 C5' G D 9 1335 1337 1359 C5' C D 10 1358 1360 1379 C5' C D 11 1378 1380 1399 C5' C D 12 1398 1400 1419 C5' U D 13 1418 1420 1439 C5' U D 14 1438 1440 1459 C5' U D 15 1458 1460 1479 C5' U D 16 1478 1480 1499 C5' C D 17 1498 1500 1519 C5' A D 18 1518 1520 1541 C5' G D 19 1540 1542 1564 C5' G D 20 1563 1565 1587 C5' G D 21 1586 1588 1610 C5' C D 22 1609 1611 1630 C5' C D 23 1629 1631 1650 C5' A D 24 1649 1651 1672 C5' C D 25 1671 1673 1692 C5' C D 26 1691 1693 1702 C5' G C 1 1701 1703 1725 C5' G C 2 1724 1726 1748 C5' C C 3 1747 1749 1768 C5' C C 4 1767 1769 1788 C5' A C 5 1787 1789 1810 C5' A C 6 1809 1811 1832 C5' A C 7 1831 1833 1854 C5' G C 8 1853 1855 1877 C5' G C 9 1876 1878 1900 C5' C C 10 1899 1901 1920 C5' C C 11 1919 1921 1940 C5' C C 12 1939 1941 1960 C5' U C 13 1959 1961 1980 C5' U C 14 1979 1981 2000 C5' U C 15 1999 2001 2020 C5' U C 16 2019 2021 2040 C5' C C 17 2039 2041 2060 C5' A C 18 2059 2061 2082 C5' G C 19 2081 2083 2105 C5' G C 20 2104 2106 2128 C5' G C 21 2127 2129 2151 C5' C C 22 2150 2152 2171 C5' C C 23 2170 2172 2191 C5' A C 24 2190 2192 2213 C5' C C 25 2212 2214 2233 C5' C C 26 2232 2234 2253 C5' C C 27 2252 2254 2273 C5' C C 28 2272 2274 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1180 P G D 2 distorted distorted 1165 1181 1182 1183 1203 P C D 3 distorted distorted 1188 1204 1205 1206 1223 P C D 4 distorted distorted 1211 1224 1225 1226 1243 P A D 5 distorted distorted 1231 1244 1245 1246 1265 P A D 6 distorted distorted 1251 1266 1267 1268 1287 P A D 7 distorted distorted 1273 1288 1289 1290 1309 P G D 8 distorted distorted 1295 1310 1311 1312 1332 P G D 9 distorted distorted 1317 1333 1334 1335 1355 P C D 10 distorted distorted 1340 1356 1357 1358 1375 P C D 11 distorted distorted 1363 1376 1377 1378 1395 P C D 12 distorted distorted 1383 1396 1397 1398 1415 P U D 13 distorted distorted 1403 1416 1417 1418 1435 P U D 14 distorted distorted 1423 1436 1437 1438 1455 P U D 15 distorted distorted 1443 1456 1457 1458 1475 P U D 16 distorted distorted 1463 1476 1477 1478 1495 P C D 17 distorted distorted 1483 1496 1497 1498 1515 P A D 18 distorted distorted 1503 1516 1517 1518 1537 P G D 19 distorted distorted 1523 1538 1539 1540 1560 P G D 20 distorted distorted 1545 1561 1562 1563 1583 P G D 21 distorted distorted 1568 1584 1585 1586 1606 P C D 22 distorted distorted 1591 1607 1608 1609 1626 P C D 23 distorted distorted 1614 1627 1628 1629 1646 P A D 24 distorted distorted 1634 1647 1648 1649 1668 P C D 25 distorted distorted 1654 1669 1670 1671 1688 P C D 26 distorted distorted 1676 1689 1690 1691 1721 P G C 2 distorted distorted 1706 1722 1723 1724 1744 P C C 3 distorted distorted 1729 1745 1746 1747 1764 P C C 4 distorted distorted 1752 1765 1766 1767 1784 P A C 5 distorted distorted 1772 1785 1786 1787 1806 P A C 6 distorted distorted 1792 1807 1808 1809 1828 P A C 7 distorted distorted 1814 1829 1830 1831 1850 P G C 8 distorted distorted 1836 1851 1852 1853 1873 P G C 9 distorted distorted 1858 1874 1875 1876 1896 P C C 10 distorted distorted 1881 1897 1898 1899 1916 P C C 11 distorted distorted 1904 1917 1918 1919 1936 P C C 12 distorted distorted 1924 1937 1938 1939 1956 P U C 13 distorted distorted 1944 1957 1958 1959 1976 P U C 14 distorted distorted 1964 1977 1978 1979 1996 P U C 15 distorted distorted 1984 1997 1998 1999 2016 P U C 16 distorted distorted 2004 2017 2018 2019 2036 P C C 17 distorted distorted 2024 2037 2038 2039 2056 P A C 18 distorted distorted 2044 2057 2058 2059 2078 P G C 19 distorted distorted 2064 2079 2080 2081 2101 P G C 20 distorted distorted 2086 2102 2103 2104 2124 P G C 21 distorted distorted 2109 2125 2126 2127 2147 P C C 22 distorted distorted 2132 2148 2149 2150 2167 P C C 23 distorted distorted 2155 2168 2169 2170 2187 P A C 24 distorted distorted 2175 2188 2189 2190 2209 P C C 25 distorted distorted 2195 2210 2211 2212 2229 P C C 26 distorted distorted 2217 2230 2231 2232 2249 P C C 27 distorted distorted 2237 2250 2251 2252 2269 P C C 28 distorted distorted 2257 2270 2271 2272 ---------------------------------------------------------------------------------