ID code: '2L2K' 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' --------------------------------------------------------------------------------- 1103 C1' G A 1 alpha beta 1098 1121 1104 1101 1138 C1' G A 2 alpha beta 1133 1156 1139 1136 1172 C1' U A 3 alpha beta 1167 1187 1173 1170 1202 C1' A A 4 alpha beta 1197 1219 1203 1200 1235 C1' A A 5 alpha beta 1230 1252 1236 1233 1268 C1' G A 6 alpha beta 1263 1286 1269 1266 1302 C1' G A 7 alpha beta 1297 1320 1303 1300 1336 C1' U A 8 alpha beta 1331 1351 1337 1334 1366 C1' G A 9 alpha beta 1361 1384 1367 1364 1400 C1' G A 10 alpha beta 1395 1418 1401 1398 1434 C1' G A 11 alpha beta 1429 1452 1435 1432 1468 C1' U A 12 alpha beta 1463 1483 1469 1466 1498 C1' G A 13 alpha beta 1493 1516 1499 1496 1532 C1' G A 14 alpha beta 1527 1550 1533 1530 1566 C1' A A 15 alpha beta 1561 1583 1567 1564 1599 C1' A A 16 alpha beta 1594 1616 1600 1597 1632 C1' U A 17 alpha beta 1627 1647 1633 1630 1662 C1' C A 18 alpha beta 1657 1677 1663 1660 1693 C1' C A 19 alpha beta 1688 1708 1694 1691 1724 C1' U A 20 alpha beta 1719 1739 1725 1722 1754 C1' U A 21 alpha beta 1749 1769 1755 1752 1784 C1' C A 22 alpha beta 1779 1799 1785 1782 1815 C1' G A 23 alpha beta 1810 1833 1816 1813 1849 C1' G A 24 alpha beta 1844 1867 1850 1847 1883 C1' G A 25 alpha beta 1878 1901 1884 1881 1917 C1' A A 26 alpha beta 1912 1934 1918 1915 1950 C1' U A 27 alpha beta 1945 1965 1951 1948 1980 C1' C A 28 alpha beta 1975 1995 1981 1978 2011 C1' C A 29 alpha beta 2006 2026 2012 2009 2042 C1' C A 30 alpha beta 2037 2057 2043 2040 2073 C1' A A 31 alpha beta 2068 2090 2074 2071 2106 C1' C A 32 alpha beta 2101 2121 2107 2104 2137 C1' C A 33 alpha beta 2132 2152 2138 2135 2168 C1' U A 34 alpha beta 2163 2183 2169 2166 2198 C1' A A 35 alpha beta 2193 2215 2199 2196 2231 C1' C A 36 alpha beta 2226 2246 2232 2229 2262 C1' C A 37 alpha beta 2257 2277 2263 2260 2293 C1' C A 38 alpha beta 2288 2308 2294 2291 2324 C1' U A 39 alpha beta 2319 2339 2325 2322 2354 C1' G A 40 alpha beta 2349 2372 2355 2352 2388 C1' C A 41 alpha beta 2383 2403 2389 2386 2419 C1' C A 42 alpha beta 2414 2435 2420 2417 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1101 C2' G A 1 OK OK 1103 1099 1119 1102 1136 C2' G A 2 OK OK 1138 1134 1154 1137 1170 C2' U A 3 OK OK 1172 1168 1185 1171 1200 C2' A A 4 OK OK 1202 1198 1217 1201 1233 C2' A A 5 OK OK 1235 1231 1250 1234 1266 C2' G A 6 OK OK 1268 1264 1284 1267 1300 C2' G A 7 OK OK 1302 1298 1318 1301 1334 C2' U A 8 OK OK 1336 1332 1349 1335 1364 C2' G A 9 OK OK 1366 1362 1382 1365 1398 C2' G A 10 OK OK 1400 1396 1416 1399 1432 C2' G A 11 OK OK 1434 1430 1450 1433 1466 C2' U A 12 OK OK 1468 1464 1481 1467 1496 C2' G A 13 OK OK 1498 1494 1514 1497 1530 C2' G A 14 OK OK 1532 1528 1548 1531 1564 C2' A A 15 OK OK 1566 1562 1581 1565 1597 C2' A A 16 OK OK 1599 1595 1614 1598 1630 C2' U A 17 OK OK 1632 1628 1645 1631 1660 C2' C A 18 OK OK 1662 1658 1675 1661 1691 C2' C A 19 OK OK 1693 1689 1706 1692 1722 C2' U A 20 OK OK 1724 1720 1737 1723 1752 C2' U A 21 OK OK 1754 1750 1767 1753 1782 C2' C A 22 OK OK 1784 1780 1797 1783 1813 C2' G A 23 OK OK 1815 1811 1831 1814 1847 C2' G A 24 OK OK 1849 1845 1865 1848 1881 C2' G A 25 OK OK 1883 1879 1899 1882 1915 C2' A A 26 OK OK 1917 1913 1932 1916 1948 C2' U A 27 OK OK 1950 1946 1963 1949 1978 C2' C A 28 OK OK 1980 1976 1993 1979 2009 C2' C A 29 OK OK 2011 2007 2024 2010 2040 C2' C A 30 OK OK 2042 2038 2055 2041 2071 C2' A A 31 OK OK 2073 2069 2088 2072 2104 C2' C A 32 OK OK 2106 2102 2119 2105 2135 C2' C A 33 OK OK 2137 2133 2150 2136 2166 C2' U A 34 OK OK 2168 2164 2181 2167 2196 C2' A A 35 OK OK 2198 2194 2213 2197 2229 C2' C A 36 OK OK 2231 2227 2244 2230 2260 C2' C A 37 OK OK 2262 2258 2275 2261 2291 C2' C A 38 OK OK 2293 2289 2306 2292 2322 C2' U A 39 OK OK 2324 2320 2337 2323 2352 C2' G A 40 OK OK 2354 2350 2370 2353 2386 C2' C A 41 OK OK 2388 2384 2401 2387 2417 C2' C A 42 OK OK 2419 2415 2433 2418 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1099 C3' G A 1 OK OK 1097 1118 1100 1101 1134 C3' G A 2 OK OK 1132 1153 1135 1136 1168 C3' U A 3 OK OK 1166 1184 1169 1170 1198 C3' A A 4 OK OK 1196 1216 1199 1200 1231 C3' A A 5 OK OK 1229 1249 1232 1233 1264 C3' G A 6 OK OK 1262 1283 1265 1266 1298 C3' G A 7 OK OK 1296 1317 1299 1300 1332 C3' U A 8 OK OK 1330 1348 1333 1334 1362 C3' G A 9 OK OK 1360 1381 1363 1364 1396 C3' G A 10 OK OK 1394 1415 1397 1398 1430 C3' G A 11 OK OK 1428 1449 1431 1432 1464 C3' U A 12 OK OK 1462 1480 1465 1466 1494 C3' G A 13 OK OK 1492 1513 1495 1496 1528 C3' G A 14 OK OK 1526 1547 1529 1530 1562 C3' A A 15 OK OK 1560 1580 1563 1564 1595 C3' A A 16 OK OK 1593 1613 1596 1597 1628 C3' U A 17 OK OK 1626 1644 1629 1630 1658 C3' C A 18 OK OK 1656 1674 1659 1660 1689 C3' C A 19 OK OK 1687 1705 1690 1691 1720 C3' U A 20 OK OK 1718 1736 1721 1722 1750 C3' U A 21 OK OK 1748 1766 1751 1752 1780 C3' C A 22 OK OK 1778 1796 1781 1782 1811 C3' G A 23 OK OK 1809 1830 1812 1813 1845 C3' G A 24 OK OK 1843 1864 1846 1847 1879 C3' G A 25 OK OK 1877 1898 1880 1881 1913 C3' A A 26 OK OK 1911 1931 1914 1915 1946 C3' U A 27 OK OK 1944 1962 1947 1948 1976 C3' C A 28 OK OK 1974 1992 1977 1978 2007 C3' C A 29 OK OK 2005 2023 2008 2009 2038 C3' C A 30 OK OK 2036 2054 2039 2040 2069 C3' A A 31 OK OK 2067 2087 2070 2071 2102 C3' C A 32 OK OK 2100 2118 2103 2104 2133 C3' C A 33 OK OK 2131 2149 2134 2135 2164 C3' U A 34 OK OK 2162 2180 2165 2166 2194 C3' A A 35 OK OK 2192 2212 2195 2196 2227 C3' C A 36 OK OK 2225 2243 2228 2229 2258 C3' C A 37 OK OK 2256 2274 2259 2260 2289 C3' C A 38 OK OK 2287 2305 2290 2291 2320 C3' U A 39 OK OK 2318 2336 2321 2322 2350 C3' G A 40 OK OK 2348 2369 2351 2352 2384 C3' C A 41 OK OK 2382 2400 2385 2386 2415 C3' C A 42 OK OK 2413 2431 2416 2417 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1097 C4' G A 1 OK OK 1099 1117 1096 1098 1132 C4' G A 2 OK OK 1134 1152 1131 1133 1166 C4' U A 3 OK OK 1168 1183 1165 1167 1196 C4' A A 4 OK OK 1198 1215 1195 1197 1229 C4' A A 5 OK OK 1231 1248 1228 1230 1262 C4' G A 6 OK OK 1264 1282 1261 1263 1296 C4' G A 7 OK OK 1298 1316 1295 1297 1330 C4' U A 8 OK OK 1332 1347 1329 1331 1360 C4' G A 9 OK OK 1362 1380 1359 1361 1394 C4' G A 10 OK OK 1396 1414 1393 1395 1428 C4' G A 11 OK OK 1430 1448 1427 1429 1462 C4' U A 12 OK OK 1464 1479 1461 1463 1492 C4' G A 13 OK OK 1494 1512 1491 1493 1526 C4' G A 14 OK OK 1528 1546 1525 1527 1560 C4' A A 15 OK OK 1562 1579 1559 1561 1593 C4' A A 16 OK OK 1595 1612 1592 1594 1626 C4' U A 17 OK OK 1628 1643 1625 1627 1656 C4' C A 18 OK OK 1658 1673 1655 1657 1687 C4' C A 19 OK OK 1689 1704 1686 1688 1718 C4' U A 20 OK OK 1720 1735 1717 1719 1748 C4' U A 21 OK OK 1750 1765 1747 1749 1778 C4' C A 22 OK OK 1780 1795 1777 1779 1809 C4' G A 23 OK OK 1811 1829 1808 1810 1843 C4' G A 24 OK OK 1845 1863 1842 1844 1877 C4' G A 25 OK OK 1879 1897 1876 1878 1911 C4' A A 26 OK OK 1913 1930 1910 1912 1944 C4' U A 27 OK OK 1946 1961 1943 1945 1974 C4' C A 28 OK OK 1976 1991 1973 1975 2005 C4' C A 29 OK OK 2007 2022 2004 2006 2036 C4' C A 30 OK OK 2038 2053 2035 2037 2067 C4' A A 31 OK OK 2069 2086 2066 2068 2100 C4' C A 32 OK OK 2102 2117 2099 2101 2131 C4' C A 33 OK OK 2133 2148 2130 2132 2162 C4' U A 34 OK OK 2164 2179 2161 2163 2192 C4' A A 35 OK OK 2194 2211 2191 2193 2225 C4' C A 36 OK OK 2227 2242 2224 2226 2256 C4' C A 37 OK OK 2258 2273 2255 2257 2287 C4' C A 38 OK OK 2289 2304 2286 2288 2318 C4' U A 39 OK OK 2320 2335 2317 2319 2348 C4' G A 40 OK OK 2350 2368 2347 2349 2382 C4' C A 41 OK OK 2384 2399 2381 2383 2413 C4' C A 42 OK OK 2415 2430 2412 2414 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1096 C5' G A 1 OK OK 1095 1115 1116 1097 1131 C5' G A 2 OK OK 1130 1150 1151 1132 1165 C5' U A 3 OK OK 1164 1181 1182 1166 1195 C5' A A 4 OK OK 1194 1213 1214 1196 1228 C5' A A 5 OK OK 1227 1246 1247 1229 1261 C5' G A 6 OK OK 1260 1280 1281 1262 1295 C5' G A 7 OK OK 1294 1314 1315 1296 1329 C5' U A 8 OK OK 1328 1345 1346 1330 1359 C5' G A 9 OK OK 1358 1378 1379 1360 1393 C5' G A 10 OK OK 1392 1412 1413 1394 1427 C5' G A 11 OK OK 1426 1446 1447 1428 1461 C5' U A 12 OK OK 1460 1477 1478 1462 1491 C5' G A 13 OK OK 1490 1510 1511 1492 1525 C5' G A 14 OK OK 1524 1544 1545 1526 1559 C5' A A 15 OK OK 1558 1577 1578 1560 1592 C5' A A 16 OK OK 1591 1610 1611 1593 1625 C5' U A 17 OK OK 1624 1641 1642 1626 1655 C5' C A 18 OK OK 1654 1671 1672 1656 1686 C5' C A 19 OK OK 1685 1702 1703 1687 1717 C5' U A 20 OK OK 1716 1733 1734 1718 1747 C5' U A 21 OK OK 1746 1763 1764 1748 1777 C5' C A 22 OK OK 1776 1793 1794 1778 1808 C5' G A 23 OK OK 1807 1827 1828 1809 1842 C5' G A 24 OK OK 1841 1861 1862 1843 1876 C5' G A 25 OK OK 1875 1895 1896 1877 1910 C5' A A 26 OK OK 1909 1928 1929 1911 1943 C5' U A 27 OK OK 1942 1959 1960 1944 1973 C5' C A 28 OK OK 1972 1989 1990 1974 2004 C5' C A 29 OK OK 2003 2020 2021 2005 2035 C5' C A 30 OK OK 2034 2051 2052 2036 2066 C5' A A 31 OK OK 2065 2084 2085 2067 2099 C5' C A 32 OK OK 2098 2115 2116 2100 2130 C5' C A 33 OK OK 2129 2146 2147 2131 2161 C5' U A 34 OK OK 2160 2177 2178 2162 2191 C5' A A 35 OK OK 2190 2209 2210 2192 2224 C5' C A 36 OK OK 2223 2240 2241 2225 2255 C5' C A 37 OK OK 2254 2271 2272 2256 2286 C5' C A 38 OK OK 2285 2302 2303 2287 2317 C5' U A 39 OK OK 2316 2333 2334 2318 2347 C5' G A 40 OK OK 2346 2366 2367 2348 2381 C5' C A 41 OK OK 2380 2397 2398 2382 2412 C5' C A 42 OK OK 2411 2428 2429 2413 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1127 P G A 2 distorted distorted 1100 1128 1129 1130 1161 P U A 3 distorted distorted 1135 1162 1163 1164 1191 P A A 4 distorted distorted 1169 1192 1193 1194 1224 P A A 5 distorted distorted 1199 1225 1226 1227 1257 P G A 6 distorted distorted 1232 1258 1259 1260 1291 P G A 7 distorted distorted 1265 1292 1293 1294 1325 P U A 8 distorted distorted 1299 1326 1327 1328 1355 P G A 9 distorted distorted 1333 1356 1357 1358 1389 P G A 10 distorted distorted 1363 1390 1391 1392 1423 P G A 11 distorted distorted 1397 1424 1425 1426 1457 P U A 12 distorted distorted 1431 1458 1459 1460 1487 P G A 13 distorted distorted 1465 1488 1489 1490 1521 P G A 14 distorted distorted 1495 1522 1523 1524 1555 P A A 15 distorted distorted 1529 1556 1557 1558 1588 P A A 16 distorted distorted 1563 1589 1590 1591 1621 P U A 17 distorted distorted 1596 1622 1623 1624 1651 P C A 18 distorted distorted 1629 1652 1653 1654 1682 P C A 19 distorted distorted 1659 1683 1684 1685 1713 P U A 20 distorted distorted 1690 1714 1715 1716 1743 P U A 21 distorted distorted 1721 1744 1745 1746 1773 P C A 22 distorted distorted 1751 1774 1775 1776 1804 P G A 23 distorted distorted 1781 1805 1806 1807 1838 P G A 24 distorted distorted 1812 1839 1840 1841 1872 P G A 25 distorted distorted 1846 1873 1874 1875 1906 P A A 26 distorted distorted 1880 1907 1908 1909 1939 P U A 27 distorted distorted 1914 1940 1941 1942 1969 P C A 28 distorted distorted 1947 1970 1971 1972 2000 P C A 29 distorted distorted 1977 2001 2002 2003 2031 P C A 30 distorted distorted 2008 2032 2033 2034 2062 P A A 31 distorted distorted 2039 2063 2064 2065 2095 P C A 32 distorted distorted 2070 2096 2097 2098 2126 P C A 33 distorted distorted 2103 2127 2128 2129 2157 P U A 34 distorted distorted 2134 2158 2159 2160 2187 P A A 35 distorted distorted 2165 2188 2189 2190 2220 P C A 36 distorted distorted 2195 2221 2222 2223 2251 P C A 37 distorted distorted 2228 2252 2253 2254 2282 P C A 38 distorted distorted 2259 2283 2284 2285 2313 P U A 39 distorted distorted 2290 2314 2315 2316 2343 P G A 40 distorted distorted 2321 2344 2345 2346 2377 P C A 41 distorted distorted 2351 2378 2379 2380 2408 P C A 42 distorted distorted 2385 2409 2410 2411 ---------------------------------------------------------------------------------