ID code: '2XLI' 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' --------------------------------------------------------------------------------- 1329 C1' C B 6 beta 1324 1330 1327 1349 C1' U B 7 beta 1344 1350 1347 1369 C1' G B 8 beta 1364 1370 1367 1392 C1' C B 9 beta 1387 1393 1390 1412 C1' C B 10 beta 1407 1413 1410 1432 C1' G B 11 beta 1427 1433 1430 1455 C1' U B 12 beta 1450 1456 1453 1475 C1' A B 13 beta 1470 1476 1473 1497 C1' U B 14 1492 1495 1509 C1' A B 15 beta 1504 1510 1507 1531 C1' G B 16 beta 1526 1532 1529 1554 C1' G B 17 beta 1549 1555 1552 1577 C1' C B 18 beta 1572 1578 1575 1597 C1' A B 19 beta 1592 1598 1595 1618 C1' DG B 20 beta 1614 1619 1617 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1327 C2' C B 6 OK 1329 1325 1328 1347 C2' U B 7 OK 1349 1345 1348 1367 C2' G B 8 OK 1369 1365 1368 1390 C2' C B 9 OK 1392 1388 1391 1410 C2' C B 10 OK 1412 1408 1411 1430 C2' G B 11 OK 1432 1428 1431 1453 C2' U B 12 OK 1455 1451 1454 1473 C2' A B 13 OK 1475 1471 1474 1495 C2' U B 14 OK 1497 1493 1496 1507 C2' A B 15 OK 1509 1505 1508 1529 C2' G B 16 OK 1531 1527 1530 1552 C2' G B 17 OK 1554 1550 1553 1575 C2' C B 18 OK 1577 1573 1576 1595 C2' A B 19 OK 1597 1593 1596 1617 C2' DG B 20 1618 1615 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1325 C3' C B 6 OK 1323 1326 1327 1345 C3' U B 7 OK 1343 1346 1347 1365 C3' G B 8 OK 1363 1366 1367 1388 C3' C B 9 OK 1386 1389 1390 1408 C3' C B 10 OK 1406 1409 1410 1428 C3' G B 11 OK 1426 1429 1430 1451 C3' U B 12 OK 1449 1452 1453 1471 C3' A B 13 OK 1469 1472 1473 1493 C3' U B 14 OK 1491 1494 1495 1505 C3' A B 15 OK 1503 1506 1507 1527 C3' G B 16 OK 1525 1528 1529 1550 C3' G B 17 OK 1548 1551 1552 1573 C3' C B 18 OK 1571 1574 1575 1593 C3' A B 19 OK 1591 1594 1595 1615 C3' DG B 20 OK 1613 1616 1617 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1323 C4' C B 6 OK 1325 1322 1324 1343 C4' U B 7 OK 1345 1342 1344 1363 C4' G B 8 OK 1365 1362 1364 1386 C4' C B 9 OK 1388 1385 1387 1406 C4' C B 10 OK 1408 1405 1407 1426 C4' G B 11 OK 1428 1425 1427 1449 C4' U B 12 OK 1451 1448 1450 1469 C4' A B 13 OK 1471 1468 1470 1491 C4' U B 14 OK 1493 1490 1492 1503 C4' A B 15 OK 1505 1502 1504 1525 C4' G B 16 OK 1527 1524 1526 1548 C4' G B 17 OK 1550 1547 1549 1571 C4' C B 18 OK 1573 1570 1572 1591 C4' A B 19 OK 1593 1590 1592 1613 C4' DG B 20 OK 1615 1612 1614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1322 C5' C B 6 1321 1323 1342 C5' U B 7 1341 1343 1362 C5' G B 8 1361 1363 1385 C5' C B 9 1384 1386 1405 C5' C B 10 1404 1406 1425 C5' G B 11 1424 1426 1448 C5' U B 12 1447 1449 1468 C5' A B 13 1467 1469 1490 C5' U B 14 1489 1491 1502 C5' A B 15 1501 1503 1524 C5' G B 16 1523 1525 1547 C5' G B 17 1546 1548 1570 C5' C B 18 1569 1571 1590 C5' A B 19 1589 1591 1612 C5' DG B 20 1611 1613 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1338 P U B 7 distorted distorted 1326 1339 1340 1341 1358 P G B 8 distorted distorted 1346 1359 1360 1361 1381 P C B 9 distorted distorted 1366 1382 1383 1384 1401 P C B 10 distorted distorted 1389 1402 1403 1404 1421 P G B 11 distorted distorted 1409 1422 1423 1424 1444 P U B 12 OK OK 1429 1445 1446 1447 1464 P A B 13 distorted distorted 1452 1465 1466 1467 1486 P U B 14 distorted distorted 1472 1487 1488 1489 1498 P A B 15 OK OK 1494 1499 1500 1501 1520 P G B 16 distorted distorted 1506 1521 1522 1523 1543 P G B 17 OK OK 1528 1544 1545 1546 1566 P C B 18 distorted distorted 1551 1567 1568 1569 1586 P A B 19 distorted distorted 1574 1587 1588 1589 1608 P DG B 20 distorted distorted 1594 1609 1610 1611 1630 P C B 21 distorted distorted 1616 1631 1632 1633 ---------------------------------------------------------------------------------