ID code: '5IP2' 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' --------------------------------------------------------------------------------- 5454 C1' U E 1 beta 5449 5455 5452 5474 C1' U E 2 beta 5469 5475 5472 5494 C1' U E 3 beta 5489 5495 5492 5514 C1' U E 4 beta 5509 5515 5512 5534 C1' U E 5 beta 5529 5535 5532 5555 C1' U F 1 beta 5550 5556 5553 5575 C1' U F 2 beta 5570 5576 5573 5595 C1' U F 3 beta 5590 5596 5593 5616 C1' U D 1 beta 5611 5617 5614 5636 C1' U D 2 beta 5631 5637 5634 5656 C1' U D 3 beta 5651 5657 5654 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5452 C2' U E 1 OK 5454 5450 5453 5472 C2' U E 2 OK 5474 5470 5473 5492 C2' U E 3 OK 5494 5490 5493 5512 C2' U E 4 OK 5514 5510 5513 5532 C2' U E 5 OK 5534 5530 5533 5553 C2' U F 1 OK 5555 5551 5554 5573 C2' U F 2 OK 5575 5571 5574 5593 C2' U F 3 OK 5595 5591 5594 5614 C2' U D 1 OK 5616 5612 5615 5634 C2' U D 2 OK 5636 5632 5635 5654 C2' U D 3 OK 5656 5652 5655 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5450 C3' U E 1 OK 5448 5451 5452 5470 C3' U E 2 OK 5468 5471 5472 5490 C3' U E 3 OK 5488 5491 5492 5510 C3' U E 4 OK 5508 5511 5512 5530 C3' U E 5 OK 5528 5531 5532 5551 C3' U F 1 OK 5549 5552 5553 5571 C3' U F 2 OK 5569 5572 5573 5591 C3' U F 3 OK 5589 5592 5593 5612 C3' U D 1 OK 5610 5613 5614 5632 C3' U D 2 OK 5630 5633 5634 5652 C3' U D 3 OK 5650 5653 5654 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5448 C4' U E 1 OK 5450 5447 5449 5468 C4' U E 2 OK 5470 5467 5469 5488 C4' U E 3 OK 5490 5487 5489 5508 C4' U E 4 OK 5510 5507 5509 5528 C4' U E 5 OK 5530 5527 5529 5549 C4' U F 1 OK 5551 5548 5550 5569 C4' U F 2 OK 5571 5568 5570 5589 C4' U F 3 OK 5591 5588 5590 5610 C4' U D 1 OK 5612 5609 5611 5630 C4' U D 2 OK 5632 5629 5631 5650 C4' U D 3 OK 5652 5649 5651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5447 C5' U E 1 5446 5448 5467 C5' U E 2 5466 5468 5487 C5' U E 3 5486 5488 5507 C5' U E 4 5506 5508 5527 C5' U E 5 5526 5528 5548 C5' U F 1 5547 5549 5568 C5' U F 2 5567 5569 5588 C5' U F 3 5587 5589 5609 C5' U D 1 5608 5610 5629 C5' U D 2 5628 5630 5649 C5' U D 3 5648 5650 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5443 P U E 1 distorted distorted 5444 5445 5446 5463 P U E 2 distorted distorted 5451 5464 5465 5466 5483 P U E 3 distorted distorted 5471 5484 5485 5486 5503 P U E 4 distorted distorted 5491 5504 5505 5506 5523 P U E 5 distorted distorted 5511 5524 5525 5526 5544 P U F 1 distorted distorted 5545 5546 5547 5564 P U F 2 distorted distorted 5552 5565 5566 5567 5584 P U F 3 distorted distorted 5572 5585 5586 5587 5605 P U D 1 distorted distorted 5606 5607 5608 5625 P U D 2 distorted distorted 5613 5626 5627 5628 5645 P U D 3 distorted distorted 5633 5646 5647 5648 ---------------------------------------------------------------------------------