ID code: '5BUD' 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' --------------------------------------------------------------------------------- 6419 C1' U D 2 beta 6414 6420 6417 6439 C1' U D 3 beta 6434 6440 6437 6459 C1' U D 4 beta 6454 6460 6457 6479 C1' U D 5 beta 6474 6480 6477 6501 C1' U E 2 beta 6496 6502 6499 6521 C1' U E 3 beta 6516 6522 6519 6541 C1' U E 4 beta 6536 6542 6539 6561 C1' U E 5 beta 6556 6562 6559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6417 C2' U D 2 OK 6419 6415 6418 6437 C2' U D 3 OK 6439 6435 6438 6457 C2' U D 4 OK 6459 6455 6458 6477 C2' U D 5 OK 6479 6475 6478 6499 C2' U E 2 OK 6501 6497 6500 6519 C2' U E 3 OK 6521 6517 6520 6539 C2' U E 4 OK 6541 6537 6540 6559 C2' U E 5 OK 6561 6557 6560 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6415 C3' U D 2 OK 6413 6416 6417 6435 C3' U D 3 OK 6433 6436 6437 6455 C3' U D 4 OK 6453 6456 6457 6475 C3' U D 5 OK 6473 6476 6477 6497 C3' U E 2 OK 6495 6498 6499 6517 C3' U E 3 OK 6515 6518 6519 6537 C3' U E 4 OK 6535 6538 6539 6557 C3' U E 5 OK 6555 6558 6559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6413 C4' U D 2 OK 6415 6412 6414 6433 C4' U D 3 OK 6435 6432 6434 6453 C4' U D 4 OK 6455 6452 6454 6473 C4' U D 5 OK 6475 6472 6474 6495 C4' U E 2 OK 6497 6494 6496 6515 C4' U E 3 OK 6517 6514 6516 6535 C4' U E 4 OK 6537 6534 6536 6555 C4' U E 5 OK 6557 6554 6556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6412 C5' U D 2 6411 6413 6432 C5' U D 3 6431 6433 6452 C5' U D 4 6451 6453 6472 C5' U D 5 6471 6473 6494 C5' U E 2 6493 6495 6514 C5' U E 3 6513 6515 6534 C5' U E 4 6533 6535 6554 C5' U E 5 6553 6555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6408 P U D 2 OK OK 6409 6410 6411 6428 P U D 3 distorted distorted 6416 6429 6430 6431 6448 P U D 4 distorted distorted 6436 6449 6450 6451 6468 P U D 5 distorted distorted 6456 6469 6470 6471 6490 P U E 2 OK OK 6491 6492 6493 6510 P U E 3 distorted distorted 6498 6511 6512 6513 6530 P U E 4 distorted distorted 6518 6531 6532 6533 6550 P U E 5 distorted distorted 6538 6551 6552 6553 6570 P U E 6 distorted distorted 6558 6571 6572 6573 ---------------------------------------------------------------------------------