ID code: '4JVH' 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' --------------------------------------------------------------------------------- 1425 C1' A D 4 beta 1420 1426 1423 1447 C1' C D 5 beta 1442 1448 1445 1467 C1' U D 6 beta 1462 1468 1465 1487 C1' A D 7 beta 1482 1488 1485 1509 C1' A D 8 beta 1504 1510 1507 1531 C1' C D 9 beta 1526 1532 1529 1551 C1' A D 10 beta 1546 1552 1549 1573 C1' A D 11 beta 1568 1574 1571 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1423 C2' A D 4 OK 1425 1421 1424 1445 C2' C D 5 OK 1447 1443 1446 1465 C2' U D 6 OK 1467 1463 1466 1485 C2' A D 7 OK 1487 1483 1486 1507 C2' A D 8 OK 1509 1505 1508 1529 C2' C D 9 OK 1531 1527 1530 1549 C2' A D 10 OK 1551 1547 1550 1571 C2' A D 11 OK 1573 1569 1572 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1421 C3' A D 4 OK 1419 1422 1423 1443 C3' C D 5 OK 1441 1444 1445 1463 C3' U D 6 OK 1461 1464 1465 1483 C3' A D 7 OK 1481 1484 1485 1505 C3' A D 8 OK 1503 1506 1507 1527 C3' C D 9 OK 1525 1528 1529 1547 C3' A D 10 OK 1545 1548 1549 1569 C3' A D 11 OK 1567 1570 1571 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1419 C4' A D 4 OK 1421 1418 1420 1441 C4' C D 5 OK 1443 1440 1442 1461 C4' U D 6 OK 1463 1460 1462 1481 C4' A D 7 OK 1483 1480 1482 1503 C4' A D 8 OK 1505 1502 1504 1525 C4' C D 9 OK 1527 1524 1526 1545 C4' A D 10 OK 1547 1544 1546 1567 C4' A D 11 OK 1569 1566 1568 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1418 C5' A D 4 1417 1419 1440 C5' C D 5 1439 1441 1460 C5' U D 6 1459 1461 1480 C5' A D 7 1479 1481 1502 C5' A D 8 1501 1503 1524 C5' C D 9 1523 1525 1544 C5' A D 10 1543 1545 1566 C5' A D 11 1565 1567 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1414 P A D 4 distorted distorted 1415 1416 1417 1436 P C D 5 distorted distorted 1422 1437 1438 1439 1456 P U D 6 distorted distorted 1444 1457 1458 1459 1476 P A D 7 distorted distorted 1464 1477 1478 1479 1498 P A D 8 distorted distorted 1484 1499 1500 1501 1520 P C D 9 distorted distorted 1506 1521 1522 1523 1540 P A D 10 distorted distorted 1528 1541 1542 1543 1562 P A D 11 distorted distorted 1548 1563 1564 1565 ---------------------------------------------------------------------------------