ID code: '1CF7' 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' --------------------------------------------------------------------------------- 1198 C1' T C 501 beta 1194 1199 1197 1218 C1' T C 502 beta 1214 1219 1217 1238 C1' T C 503 beta 1234 1239 1237 1258 C1' T C 504 beta 1254 1259 1257 1278 C1' C C 505 beta 1274 1279 1277 1297 C1' G C 506 beta 1293 1298 1296 1319 C1' C C 507 beta 1315 1320 1318 1338 C1' G C 508 beta 1334 1339 1337 1360 C1' C C 509 beta 1356 1361 1359 1379 C1' G C 510 beta 1375 1380 1378 1401 C1' G C 511 beta 1397 1402 1400 1423 C1' T C 512 beta 1419 1424 1422 1443 C1' T C 513 beta 1439 1444 1442 1463 C1' T C 514 beta 1459 1464 1462 1483 C1' T C 515 beta 1479 1484 1482 1504 C1' A D 601 beta 1500 1505 1503 1525 C1' A D 602 beta 1521 1526 1524 1546 C1' A D 603 beta 1542 1547 1545 1567 C1' A D 604 beta 1563 1568 1566 1588 C1' C D 605 beta 1584 1589 1587 1607 C1' C D 606 beta 1603 1608 1606 1626 C1' G D 607 beta 1622 1627 1625 1648 C1' C D 608 beta 1644 1649 1647 1667 C1' G D 609 beta 1663 1668 1666 1689 C1' C D 610 beta 1685 1690 1688 1708 C1' G D 611 beta 1704 1709 1707 1730 C1' A D 612 beta 1726 1731 1729 1751 C1' A D 613 beta 1747 1752 1750 1772 C1' A D 614 beta 1768 1773 1771 1793 C1' A D 615 beta 1789 1794 1792 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1197 C2' T C 501 1198 1195 1217 C2' T C 502 1218 1215 1237 C2' T C 503 1238 1235 1257 C2' T C 504 1258 1255 1277 C2' C C 505 1278 1275 1296 C2' G C 506 1297 1294 1318 C2' C C 507 1319 1316 1337 C2' G C 508 1338 1335 1359 C2' C C 509 1360 1357 1378 C2' G C 510 1379 1376 1400 C2' G C 511 1401 1398 1422 C2' T C 512 1423 1420 1442 C2' T C 513 1443 1440 1462 C2' T C 514 1463 1460 1482 C2' T C 515 1483 1480 1503 C2' A D 601 1504 1501 1524 C2' A D 602 1525 1522 1545 C2' A D 603 1546 1543 1566 C2' A D 604 1567 1564 1587 C2' C D 605 1588 1585 1606 C2' C D 606 1607 1604 1625 C2' G D 607 1626 1623 1647 C2' C D 608 1648 1645 1666 C2' G D 609 1667 1664 1688 C2' C D 610 1689 1686 1707 C2' G D 611 1708 1705 1729 C2' A D 612 1730 1727 1750 C2' A D 613 1751 1748 1771 C2' A D 614 1772 1769 1792 C2' A D 615 1793 1790 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1195 C3' T C 501 OK 1193 1196 1197 1215 C3' T C 502 OK 1213 1216 1217 1235 C3' T C 503 OK 1233 1236 1237 1255 C3' T C 504 OK 1253 1256 1257 1275 C3' C C 505 OK 1273 1276 1277 1294 C3' G C 506 OK 1292 1295 1296 1316 C3' C C 507 OK 1314 1317 1318 1335 C3' G C 508 OK 1333 1336 1337 1357 C3' C C 509 OK 1355 1358 1359 1376 C3' G C 510 OK 1374 1377 1378 1398 C3' G C 511 OK 1396 1399 1400 1420 C3' T C 512 OK 1418 1421 1422 1440 C3' T C 513 OK 1438 1441 1442 1460 C3' T C 514 OK 1458 1461 1462 1480 C3' T C 515 OK 1478 1481 1482 1501 C3' A D 601 OK 1499 1502 1503 1522 C3' A D 602 OK 1520 1523 1524 1543 C3' A D 603 OK 1541 1544 1545 1564 C3' A D 604 OK 1562 1565 1566 1585 C3' C D 605 OK 1583 1586 1587 1604 C3' C D 606 OK 1602 1605 1606 1623 C3' G D 607 OK 1621 1624 1625 1645 C3' C D 608 OK 1643 1646 1647 1664 C3' G D 609 OK 1662 1665 1666 1686 C3' C D 610 OK 1684 1687 1688 1705 C3' G D 611 OK 1703 1706 1707 1727 C3' A D 612 OK 1725 1728 1729 1748 C3' A D 613 OK 1746 1749 1750 1769 C3' A D 614 OK 1767 1770 1771 1790 C3' A D 615 OK 1788 1791 1792 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1193 C4' T C 501 OK 1195 1192 1194 1213 C4' T C 502 OK 1215 1212 1214 1233 C4' T C 503 OK 1235 1232 1234 1253 C4' T C 504 OK 1255 1252 1254 1273 C4' C C 505 OK 1275 1272 1274 1292 C4' G C 506 OK 1294 1291 1293 1314 C4' C C 507 OK 1316 1313 1315 1333 C4' G C 508 OK 1335 1332 1334 1355 C4' C C 509 OK 1357 1354 1356 1374 C4' G C 510 OK 1376 1373 1375 1396 C4' G C 511 OK 1398 1395 1397 1418 C4' T C 512 OK 1420 1417 1419 1438 C4' T C 513 OK 1440 1437 1439 1458 C4' T C 514 OK 1460 1457 1459 1478 C4' T C 515 OK 1480 1477 1479 1499 C4' A D 601 OK 1501 1498 1500 1520 C4' A D 602 OK 1522 1519 1521 1541 C4' A D 603 OK 1543 1540 1542 1562 C4' A D 604 OK 1564 1561 1563 1583 C4' C D 605 OK 1585 1582 1584 1602 C4' C D 606 OK 1604 1601 1603 1621 C4' G D 607 OK 1623 1620 1622 1643 C4' C D 608 OK 1645 1642 1644 1662 C4' G D 609 OK 1664 1661 1663 1684 C4' C D 610 OK 1686 1683 1685 1703 C4' G D 611 OK 1705 1702 1704 1725 C4' A D 612 OK 1727 1724 1726 1746 C4' A D 613 OK 1748 1745 1747 1767 C4' A D 614 OK 1769 1766 1768 1788 C4' A D 615 OK 1790 1787 1789 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1192 C5' T C 501 1191 1193 1212 C5' T C 502 1211 1213 1232 C5' T C 503 1231 1233 1252 C5' T C 504 1251 1253 1272 C5' C C 505 1271 1273 1291 C5' G C 506 1290 1292 1313 C5' C C 507 1312 1314 1332 C5' G C 508 1331 1333 1354 C5' C C 509 1353 1355 1373 C5' G C 510 1372 1374 1395 C5' G C 511 1394 1396 1417 C5' T C 512 1416 1418 1437 C5' T C 513 1436 1438 1457 C5' T C 514 1456 1458 1477 C5' T C 515 1476 1478 1498 C5' A D 601 1497 1499 1519 C5' A D 602 1518 1520 1540 C5' A D 603 1539 1541 1561 C5' A D 604 1560 1562 1582 C5' C D 605 1581 1583 1601 C5' C D 606 1600 1602 1620 C5' G D 607 1619 1621 1642 C5' C D 608 1641 1643 1661 C5' G D 609 1660 1662 1683 C5' C D 610 1682 1684 1702 C5' G D 611 1701 1703 1724 C5' A D 612 1723 1725 1745 C5' A D 613 1744 1746 1766 C5' A D 614 1765 1767 1787 C5' A D 615 1786 1788 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1208 P T C 502 distorted distorted 1196 1209 1210 1211 1228 P T C 503 distorted distorted 1216 1229 1230 1231 1248 P T C 504 distorted distorted 1236 1249 1250 1251 1268 P C C 505 distorted distorted 1256 1269 1270 1271 1287 P G C 506 distorted distorted 1276 1288 1289 1290 1309 P C C 507 distorted distorted 1295 1310 1311 1312 1328 P G C 508 distorted distorted 1317 1329 1330 1331 1350 P C C 509 distorted distorted 1336 1351 1352 1353 1369 P G C 510 distorted distorted 1358 1370 1371 1372 1391 P G C 511 distorted distorted 1377 1392 1393 1394 1413 P T C 512 distorted distorted 1399 1414 1415 1416 1433 P T C 513 distorted distorted 1421 1434 1435 1436 1453 P T C 514 distorted distorted 1441 1454 1455 1456 1473 P T C 515 distorted distorted 1461 1474 1475 1476 1515 P A D 602 distorted distorted 1502 1516 1517 1518 1536 P A D 603 distorted distorted 1523 1537 1538 1539 1557 P A D 604 distorted distorted 1544 1558 1559 1560 1578 P C D 605 distorted distorted 1565 1579 1580 1581 1597 P C D 606 distorted distorted 1586 1598 1599 1600 1616 P G D 607 distorted distorted 1605 1617 1618 1619 1638 P C D 608 distorted distorted 1624 1639 1640 1641 1657 P G D 609 distorted distorted 1646 1658 1659 1660 1679 P C D 610 distorted distorted 1665 1680 1681 1682 1698 P G D 611 distorted distorted 1687 1699 1700 1701 1720 P A D 612 distorted distorted 1706 1721 1722 1723 1741 P A D 613 distorted distorted 1728 1742 1743 1744 1762 P A D 614 distorted distorted 1749 1763 1764 1765 1783 P A D 615 distorted distorted 1770 1784 1785 1786 ---------------------------------------------------------------------------------