ID code: '1HLO' 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' --------------------------------------------------------------------------------- 1293 C1' C C 102 beta 1289 1294 1292 1312 C1' A C 103 beta 1308 1313 1311 1333 C1' C C 104 beta 1329 1334 1332 1352 C1' C C 105 beta 1348 1353 1351 1371 C1' A C 106 beta 1367 1372 1370 1392 C1' C C 107 beta 1388 1393 1391 1411 C1' G C 108 beta 1407 1412 1410 1433 C1' T C 109 beta 1429 1434 1432 1453 C1' G C 110 beta 1449 1454 1452 1475 C1' G C 111 beta 1471 1476 1474 1497 C1' T C 112 beta 1493 1498 1496 1515 C1' A D 116 beta 1511 1516 1514 1536 C1' C D 117 beta 1532 1537 1535 1555 C1' C D 118 beta 1551 1556 1554 1574 C1' A D 119 beta 1570 1575 1573 1595 C1' C D 120 beta 1591 1596 1594 1614 C1' G D 121 beta 1610 1615 1613 1636 C1' T D 122 beta 1632 1637 1635 1656 C1' G D 123 beta 1652 1657 1655 1678 C1' G D 124 beta 1674 1679 1677 1700 C1' T D 125 beta 1696 1701 1699 1720 C1' G D 126 beta 1716 1721 1719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1292 C2' C C 102 1293 1290 1311 C2' A C 103 1312 1309 1332 C2' C C 104 1333 1330 1351 C2' C C 105 1352 1349 1370 C2' A C 106 1371 1368 1391 C2' C C 107 1392 1389 1410 C2' G C 108 1411 1408 1432 C2' T C 109 1433 1430 1452 C2' G C 110 1453 1450 1474 C2' G C 111 1475 1472 1496 C2' T C 112 1497 1494 1514 C2' A D 116 1515 1512 1535 C2' C D 117 1536 1533 1554 C2' C D 118 1555 1552 1573 C2' A D 119 1574 1571 1594 C2' C D 120 1595 1592 1613 C2' G D 121 1614 1611 1635 C2' T D 122 1636 1633 1655 C2' G D 123 1656 1653 1677 C2' G D 124 1678 1675 1699 C2' T D 125 1700 1697 1719 C2' G D 126 1720 1717 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1290 C3' C C 102 OK 1288 1291 1292 1309 C3' A C 103 OK 1307 1310 1311 1330 C3' C C 104 OK 1328 1331 1332 1349 C3' C C 105 OK 1347 1350 1351 1368 C3' A C 106 OK 1366 1369 1370 1389 C3' C C 107 OK 1387 1390 1391 1408 C3' G C 108 OK 1406 1409 1410 1430 C3' T C 109 OK 1428 1431 1432 1450 C3' G C 110 OK 1448 1451 1452 1472 C3' G C 111 OK 1470 1473 1474 1494 C3' T C 112 OK 1492 1495 1496 1512 C3' A D 116 OK 1510 1513 1514 1533 C3' C D 117 OK 1531 1534 1535 1552 C3' C D 118 OK 1550 1553 1554 1571 C3' A D 119 OK 1569 1572 1573 1592 C3' C D 120 OK 1590 1593 1594 1611 C3' G D 121 OK 1609 1612 1613 1633 C3' T D 122 OK 1631 1634 1635 1653 C3' G D 123 OK 1651 1654 1655 1675 C3' G D 124 OK 1673 1676 1677 1697 C3' T D 125 OK 1695 1698 1699 1717 C3' G D 126 OK 1715 1718 1719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1288 C4' C C 102 OK 1290 1287 1289 1307 C4' A C 103 OK 1309 1306 1308 1328 C4' C C 104 OK 1330 1327 1329 1347 C4' C C 105 OK 1349 1346 1348 1366 C4' A C 106 OK 1368 1365 1367 1387 C4' C C 107 OK 1389 1386 1388 1406 C4' G C 108 OK 1408 1405 1407 1428 C4' T C 109 OK 1430 1427 1429 1448 C4' G C 110 OK 1450 1447 1449 1470 C4' G C 111 OK 1472 1469 1471 1492 C4' T C 112 OK 1494 1491 1493 1510 C4' A D 116 OK 1512 1509 1511 1531 C4' C D 117 OK 1533 1530 1532 1550 C4' C D 118 OK 1552 1549 1551 1569 C4' A D 119 OK 1571 1568 1570 1590 C4' C D 120 OK 1592 1589 1591 1609 C4' G D 121 OK 1611 1608 1610 1631 C4' T D 122 OK 1633 1630 1632 1651 C4' G D 123 OK 1653 1650 1652 1673 C4' G D 124 OK 1675 1672 1674 1695 C4' T D 125 OK 1697 1694 1696 1715 C4' G D 126 OK 1717 1714 1716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1287 C5' C C 102 1286 1288 1306 C5' A C 103 1305 1307 1327 C5' C C 104 1326 1328 1346 C5' C C 105 1345 1347 1365 C5' A C 106 1364 1366 1386 C5' C C 107 1385 1387 1405 C5' G C 108 1404 1406 1427 C5' T C 109 1426 1428 1447 C5' G C 110 1446 1448 1469 C5' G C 111 1468 1470 1491 C5' T C 112 1490 1492 1509 C5' A D 116 1508 1510 1530 C5' C D 117 1529 1531 1549 C5' C D 118 1548 1550 1568 C5' A D 119 1567 1569 1589 C5' C D 120 1588 1590 1608 C5' G D 121 1607 1609 1630 C5' T D 122 1629 1631 1650 C5' G D 123 1649 1651 1672 C5' G D 124 1671 1673 1694 C5' T D 125 1693 1695 1714 C5' G D 126 1713 1715 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1302 P A C 103 distorted distorted 1291 1303 1304 1305 1323 P C C 104 distorted distorted 1310 1324 1325 1326 1342 P C C 105 distorted distorted 1331 1343 1344 1345 1361 P A C 106 distorted distorted 1350 1362 1363 1364 1382 P C C 107 distorted distorted 1369 1383 1384 1385 1401 P G C 108 distorted distorted 1390 1402 1403 1404 1423 P T C 109 distorted distorted 1409 1424 1425 1426 1443 P G C 110 distorted distorted 1431 1444 1445 1446 1465 P G C 111 distorted distorted 1451 1466 1467 1468 1487 P T C 112 distorted distorted 1473 1488 1489 1490 1526 P C D 117 distorted distorted 1513 1527 1528 1529 1545 P C D 118 distorted distorted 1534 1546 1547 1548 1564 P A D 119 distorted distorted 1553 1565 1566 1567 1585 P C D 120 distorted distorted 1572 1586 1587 1588 1604 P G D 121 distorted distorted 1593 1605 1606 1607 1626 P T D 122 distorted distorted 1612 1627 1628 1629 1646 P G D 123 distorted distorted 1634 1647 1648 1649 1668 P G D 124 distorted distorted 1654 1669 1670 1671 1690 P T D 125 distorted distorted 1676 1691 1692 1693 1710 P G D 126 distorted distorted 1698 1711 1712 1713 ---------------------------------------------------------------------------------