ID code: '1BL0' 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' --------------------------------------------------------------------------------- 1172 C1' G C 403 beta 1168 1173 1171 1194 C1' G C 404 beta 1190 1195 1193 1216 C1' A C 405 beta 1212 1217 1215 1237 C1' T C 406 beta 1233 1238 1236 1257 C1' T C 407 beta 1253 1258 1256 1277 C1' T C 408 beta 1273 1278 1276 1297 C1' A C 409 beta 1293 1298 1296 1318 C1' G C 410 beta 1314 1319 1317 1340 C1' C C 411 beta 1336 1341 1339 1359 C1' A C 412 beta 1355 1360 1358 1380 C1' A C 413 beta 1376 1381 1379 1401 C1' A C 414 beta 1397 1402 1400 1422 C1' A C 415 beta 1418 1423 1421 1443 C1' C C 416 beta 1439 1444 1442 1462 C1' G C 417 beta 1458 1463 1461 1484 C1' T C 418 beta 1480 1485 1483 1504 C1' G C 419 beta 1500 1505 1503 1526 C1' G C 420 beta 1522 1527 1525 1548 C1' C C 421 beta 1544 1549 1547 1567 C1' A C 422 beta 1563 1568 1566 1588 C1' T C 423 beta 1584 1589 1587 1608 C1' C C 424 beta 1604 1609 1607 1663 C1' G D 427 beta 1659 1664 1662 1685 C1' A D 428 beta 1681 1686 1684 1706 C1' T D 429 beta 1702 1707 1705 1726 C1' G D 430 beta 1722 1727 1725 1748 C1' C D 431 beta 1744 1749 1747 1767 C1' C D 432 beta 1763 1768 1766 1786 C1' A D 433 beta 1782 1787 1785 1807 C1' C D 434 beta 1803 1808 1806 1826 C1' G D 435 beta 1822 1827 1825 1848 C1' T D 436 beta 1844 1849 1847 1868 C1' T D 437 beta 1864 1869 1867 1888 C1' T D 438 beta 1884 1889 1887 1908 C1' T D 439 beta 1904 1909 1907 1928 C1' G D 440 beta 1924 1929 1927 1950 C1' C D 441 beta 1946 1951 1949 1969 C1' T D 442 beta 1965 1970 1968 1989 C1' A D 443 beta 1985 1990 1988 2010 C1' A D 444 beta 2006 2011 2009 2031 C1' A D 445 beta 2027 2032 2030 2052 C1' T D 446 beta 2048 2053 2051 2072 C1' C D 447 beta 2068 2073 2071 2091 C1' C D 448 beta 2087 2092 2090 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1171 C2' G C 403 1172 1169 1193 C2' G C 404 1194 1191 1215 C2' A C 405 1216 1213 1236 C2' T C 406 1237 1234 1256 C2' T C 407 1257 1254 1276 C2' T C 408 1277 1274 1296 C2' A C 409 1297 1294 1317 C2' G C 410 1318 1315 1339 C2' C C 411 1340 1337 1358 C2' A C 412 1359 1356 1379 C2' A C 413 1380 1377 1400 C2' A C 414 1401 1398 1421 C2' A C 415 1422 1419 1442 C2' C C 416 1443 1440 1461 C2' G C 417 1462 1459 1483 C2' T C 418 1484 1481 1503 C2' G C 419 1504 1501 1525 C2' G C 420 1526 1523 1547 C2' C C 421 1548 1545 1566 C2' A C 422 1567 1564 1587 C2' T C 423 1588 1585 1607 C2' C C 424 1608 1605 1662 C2' G D 427 1663 1660 1684 C2' A D 428 1685 1682 1705 C2' T D 429 1706 1703 1725 C2' G D 430 1726 1723 1747 C2' C D 431 1748 1745 1766 C2' C D 432 1767 1764 1785 C2' A D 433 1786 1783 1806 C2' C D 434 1807 1804 1825 C2' G D 435 1826 1823 1847 C2' T D 436 1848 1845 1867 C2' T D 437 1868 1865 1887 C2' T D 438 1888 1885 1907 C2' T D 439 1908 1905 1927 C2' G D 440 1928 1925 1949 C2' C D 441 1950 1947 1968 C2' T D 442 1969 1966 1988 C2' A D 443 1989 1986 2009 C2' A D 444 2010 2007 2030 C2' A D 445 2031 2028 2051 C2' T D 446 2052 2049 2071 C2' C D 447 2072 2069 2090 C2' C D 448 2091 2088 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1169 C3' G C 403 OK 1167 1170 1171 1191 C3' G C 404 OK 1189 1192 1193 1213 C3' A C 405 OK 1211 1214 1215 1234 C3' T C 406 OK 1232 1235 1236 1254 C3' T C 407 OK 1252 1255 1256 1274 C3' T C 408 OK 1272 1275 1276 1294 C3' A C 409 OK 1292 1295 1296 1315 C3' G C 410 OK 1313 1316 1317 1337 C3' C C 411 OK 1335 1338 1339 1356 C3' A C 412 OK 1354 1357 1358 1377 C3' A C 413 OK 1375 1378 1379 1398 C3' A C 414 OK 1396 1399 1400 1419 C3' A C 415 OK 1417 1420 1421 1440 C3' C C 416 OK 1438 1441 1442 1459 C3' G C 417 OK 1457 1460 1461 1481 C3' T C 418 OK 1479 1482 1483 1501 C3' G C 419 OK 1499 1502 1503 1523 C3' G C 420 OK 1521 1524 1525 1545 C3' C C 421 OK 1543 1546 1547 1564 C3' A C 422 OK 1562 1565 1566 1585 C3' T C 423 OK 1583 1586 1587 1605 C3' C C 424 OK 1603 1606 1607 1660 C3' G D 427 OK 1658 1661 1662 1682 C3' A D 428 OK 1680 1683 1684 1703 C3' T D 429 OK 1701 1704 1705 1723 C3' G D 430 OK 1721 1724 1725 1745 C3' C D 431 OK 1743 1746 1747 1764 C3' C D 432 OK 1762 1765 1766 1783 C3' A D 433 OK 1781 1784 1785 1804 C3' C D 434 OK 1802 1805 1806 1823 C3' G D 435 OK 1821 1824 1825 1845 C3' T D 436 OK 1843 1846 1847 1865 C3' T D 437 OK 1863 1866 1867 1885 C3' T D 438 OK 1883 1886 1887 1905 C3' T D 439 OK 1903 1906 1907 1925 C3' G D 440 OK 1923 1926 1927 1947 C3' C D 441 OK 1945 1948 1949 1966 C3' T D 442 OK 1964 1967 1968 1986 C3' A D 443 OK 1984 1987 1988 2007 C3' A D 444 OK 2005 2008 2009 2028 C3' A D 445 OK 2026 2029 2030 2049 C3' T D 446 OK 2047 2050 2051 2069 C3' C D 447 OK 2067 2070 2071 2088 C3' C D 448 OK 2086 2089 2090 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1167 C4' G C 403 OK 1169 1166 1168 1189 C4' G C 404 OK 1191 1188 1190 1211 C4' A C 405 OK 1213 1210 1212 1232 C4' T C 406 OK 1234 1231 1233 1252 C4' T C 407 OK 1254 1251 1253 1272 C4' T C 408 OK 1274 1271 1273 1292 C4' A C 409 OK 1294 1291 1293 1313 C4' G C 410 OK 1315 1312 1314 1335 C4' C C 411 OK 1337 1334 1336 1354 C4' A C 412 OK 1356 1353 1355 1375 C4' A C 413 OK 1377 1374 1376 1396 C4' A C 414 OK 1398 1395 1397 1417 C4' A C 415 OK 1419 1416 1418 1438 C4' C C 416 OK 1440 1437 1439 1457 C4' G C 417 OK 1459 1456 1458 1479 C4' T C 418 OK 1481 1478 1480 1499 C4' G C 419 OK 1501 1498 1500 1521 C4' G C 420 OK 1523 1520 1522 1543 C4' C C 421 OK 1545 1542 1544 1562 C4' A C 422 OK 1564 1561 1563 1583 C4' T C 423 OK 1585 1582 1584 1603 C4' C C 424 OK 1605 1602 1604 1658 C4' G D 427 OK 1660 1657 1659 1680 C4' A D 428 OK 1682 1679 1681 1701 C4' T D 429 OK 1703 1700 1702 1721 C4' G D 430 OK 1723 1720 1722 1743 C4' C D 431 OK 1745 1742 1744 1762 C4' C D 432 OK 1764 1761 1763 1781 C4' A D 433 OK 1783 1780 1782 1802 C4' C D 434 OK 1804 1801 1803 1821 C4' G D 435 OK 1823 1820 1822 1843 C4' T D 436 OK 1845 1842 1844 1863 C4' T D 437 OK 1865 1862 1864 1883 C4' T D 438 OK 1885 1882 1884 1903 C4' T D 439 OK 1905 1902 1904 1923 C4' G D 440 OK 1925 1922 1924 1945 C4' C D 441 OK 1947 1944 1946 1964 C4' T D 442 OK 1966 1963 1965 1984 C4' A D 443 OK 1986 1983 1985 2005 C4' A D 444 OK 2007 2004 2006 2026 C4' A D 445 OK 2028 2025 2027 2047 C4' T D 446 OK 2049 2046 2048 2067 C4' C D 447 OK 2069 2066 2068 2086 C4' C D 448 OK 2088 2085 2087 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1166 C5' G C 403 1165 1167 1188 C5' G C 404 1187 1189 1210 C5' A C 405 1209 1211 1231 C5' T C 406 1230 1232 1251 C5' T C 407 1250 1252 1271 C5' T C 408 1270 1272 1291 C5' A C 409 1290 1292 1312 C5' G C 410 1311 1313 1334 C5' C C 411 1333 1335 1353 C5' A C 412 1352 1354 1374 C5' A C 413 1373 1375 1395 C5' A C 414 1394 1396 1416 C5' A C 415 1415 1417 1437 C5' C C 416 1436 1438 1456 C5' G C 417 1455 1457 1478 C5' T C 418 1477 1479 1498 C5' G C 419 1497 1499 1520 C5' G C 420 1519 1521 1542 C5' C C 421 1541 1543 1561 C5' A C 422 1560 1562 1582 C5' T C 423 1581 1583 1602 C5' C C 424 1601 1603 1657 C5' G D 427 1656 1658 1679 C5' A D 428 1678 1680 1700 C5' T D 429 1699 1701 1720 C5' G D 430 1719 1721 1742 C5' C D 431 1741 1743 1761 C5' C D 432 1760 1762 1780 C5' A D 433 1779 1781 1801 C5' C D 434 1800 1802 1820 C5' G D 435 1819 1821 1842 C5' T D 436 1841 1843 1862 C5' T D 437 1861 1863 1882 C5' T D 438 1881 1883 1902 C5' T D 439 1901 1903 1922 C5' G D 440 1921 1923 1944 C5' C D 441 1943 1945 1963 C5' T D 442 1962 1964 1983 C5' A D 443 1982 1984 2004 C5' A D 444 2003 2005 2025 C5' A D 445 2024 2026 2046 C5' T D 446 2045 2047 2066 C5' C D 447 2065 2067 2085 C5' C D 448 2084 2086 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1184 P G C 404 OK OK 1170 1185 1186 1187 1206 P A C 405 OK OK 1192 1207 1208 1209 1227 P T C 406 OK OK 1214 1228 1229 1230 1247 P T C 407 OK OK 1235 1248 1249 1250 1267 P T C 408 OK OK 1255 1268 1269 1270 1287 P A C 409 OK OK 1275 1288 1289 1290 1308 P G C 410 OK OK 1295 1309 1310 1311 1330 P C C 411 OK OK 1316 1331 1332 1333 1349 P A C 412 OK OK 1338 1350 1351 1352 1370 P A C 413 OK OK 1357 1371 1372 1373 1391 P A C 414 OK OK 1378 1392 1393 1394 1412 P A C 415 OK OK 1399 1413 1414 1415 1433 P C C 416 OK OK 1420 1434 1435 1436 1452 P G C 417 OK OK 1441 1453 1454 1455 1474 P T C 418 OK OK 1460 1475 1476 1477 1494 P G C 419 OK OK 1482 1495 1496 1497 1516 P G C 420 OK OK 1502 1517 1518 1519 1538 P C C 421 OK OK 1524 1539 1540 1541 1557 P A C 422 OK OK 1546 1558 1559 1560 1578 P T C 423 OK OK 1565 1579 1580 1581 1598 P C C 424 OK OK 1586 1599 1600 1601 1675 P A D 428 OK OK 1661 1676 1677 1678 1696 P T D 429 OK OK 1683 1697 1698 1699 1716 P G D 430 OK OK 1704 1717 1718 1719 1738 P C D 431 OK OK 1724 1739 1740 1741 1757 P C D 432 OK OK 1746 1758 1759 1760 1776 P A D 433 OK OK 1765 1777 1778 1779 1797 P C D 434 OK OK 1784 1798 1799 1800 1816 P G D 435 OK OK 1805 1817 1818 1819 1838 P T D 436 OK OK 1824 1839 1840 1841 1858 P T D 437 OK OK 1846 1859 1860 1861 1878 P T D 438 OK OK 1866 1879 1880 1881 1898 P T D 439 OK OK 1886 1899 1900 1901 1918 P G D 440 OK OK 1906 1919 1920 1921 1940 P C D 441 OK OK 1926 1941 1942 1943 1959 P T D 442 OK OK 1948 1960 1961 1962 1979 P A D 443 OK OK 1967 1980 1981 1982 2000 P A D 444 OK OK 1987 2001 2002 2003 2021 P A D 445 OK OK 2008 2022 2023 2024 2042 P T D 446 OK OK 2029 2043 2044 2045 2062 P C D 447 OK OK 2050 2063 2064 2065 2081 P C D 448 OK OK 2070 2082 2083 2084 ---------------------------------------------------------------------------------