ID code: '3VAL' 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' --------------------------------------------------------------------------------- 5369 C1' DU E 2 beta 5365 5370 5368 5388 C1' DU E 3 beta 5384 5389 5387 5407 C1' DU E 4 beta 5403 5408 5406 5425 C1' BRU E 5 beta 5430 5416 5426 5446 C1' DU E 6 beta 5442 5447 5445 5465 C1' DU E 7 beta 5461 5466 5464 5486 C1' DU H 2 beta 5482 5487 5485 5505 C1' DU H 3 beta 5501 5506 5504 5524 C1' DU H 4 beta 5520 5525 5523 5542 C1' BRU H 5 beta 5547 5533 5543 5563 C1' DU H 6 beta 5559 5564 5562 5582 C1' DU H 7 beta 5578 5583 5581 5603 C1' DU K 2 beta 5599 5604 5602 5622 C1' DU K 3 beta 5618 5623 5621 5641 C1' DU K 4 beta 5637 5642 5640 5659 C1' BRU K 5 beta 5664 5650 5660 5680 C1' DU K 6 beta 5676 5681 5679 5699 C1' DU K 7 beta 5695 5700 5698 5720 C1' DU P 3 beta 5716 5721 5719 5739 C1' DU P 4 beta 5735 5740 5738 5757 C1' BRU P 5 beta 5762 5748 5758 5778 C1' DU P 6 beta 5774 5779 5777 5797 C1' DU P 7 beta 5793 5798 5796 5809 C1' DIO A 401 5812 5825 C1' DIO B 401 5828 5841 C1' DIO D 401 5844 5862 C1' DIO I 401 5865 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5368 C2' DU E 2 5369 5366 5387 C2' DU E 3 5388 5385 5406 C2' DU E 4 5407 5404 5426 C2' BRU E 5 5425 5427 5445 C2' DU E 6 5446 5443 5464 C2' DU E 7 5465 5462 5485 C2' DU H 2 5486 5483 5504 C2' DU H 3 5505 5502 5523 C2' DU H 4 5524 5521 5543 C2' BRU H 5 5542 5544 5562 C2' DU H 6 5563 5560 5581 C2' DU H 7 5582 5579 5602 C2' DU K 2 5603 5600 5621 C2' DU K 3 5622 5619 5640 C2' DU K 4 5641 5638 5660 C2' BRU K 5 5659 5661 5679 C2' DU K 6 5680 5677 5698 C2' DU K 7 5699 5696 5719 C2' DU P 3 5720 5717 5738 C2' DU P 4 5739 5736 5758 C2' BRU P 5 5757 5759 5777 C2' DU P 6 5778 5775 5796 C2' DU P 7 5797 5794 5810 C2' DIO A 401 5826 C2' DIO B 401 5842 C2' DIO D 401 5863 C2' DIO I 401 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5366 C3' DU E 2 OK 5364 5367 5368 5385 C3' DU E 3 OK 5383 5386 5387 5404 C3' DU E 4 OK 5402 5405 5406 5427 C3' BRU E 5 OK 5428 5429 5426 5443 C3' DU E 6 OK 5441 5444 5445 5462 C3' DU E 7 OK 5460 5463 5464 5483 C3' DU H 2 OK 5481 5484 5485 5502 C3' DU H 3 OK 5500 5503 5504 5521 C3' DU H 4 OK 5519 5522 5523 5544 C3' BRU H 5 OK 5545 5546 5543 5560 C3' DU H 6 OK 5558 5561 5562 5579 C3' DU H 7 OK 5577 5580 5581 5600 C3' DU K 2 OK 5598 5601 5602 5619 C3' DU K 3 OK 5617 5620 5621 5638 C3' DU K 4 OK 5636 5639 5640 5661 C3' BRU K 5 OK 5662 5663 5660 5677 C3' DU K 6 OK 5675 5678 5679 5696 C3' DU K 7 OK 5694 5697 5698 5717 C3' DU P 3 OK 5715 5718 5719 5736 C3' DU P 4 OK 5734 5737 5738 5759 C3' BRU P 5 OK 5760 5761 5758 5775 C3' DU P 6 OK 5773 5776 5777 5794 C3' DU P 7 OK 5792 5795 5796 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5364 C4' DU E 2 OK 5366 5363 5365 5383 C4' DU E 3 OK 5385 5382 5384 5402 C4' DU E 4 OK 5404 5401 5403 5428 C4' BRU E 5 OK 5427 5431 5430 5441 C4' DU E 6 OK 5443 5440 5442 5460 C4' DU E 7 OK 5462 5459 5461 5481 C4' DU H 2 OK 5483 5480 5482 5500 C4' DU H 3 OK 5502 5499 5501 5519 C4' DU H 4 OK 5521 5518 5520 5545 C4' BRU H 5 OK 5544 5548 5547 5558 C4' DU H 6 OK 5560 5557 5559 5577 C4' DU H 7 OK 5579 5576 5578 5598 C4' DU K 2 OK 5600 5597 5599 5617 C4' DU K 3 OK 5619 5616 5618 5636 C4' DU K 4 OK 5638 5635 5637 5662 C4' BRU K 5 OK 5661 5665 5664 5675 C4' DU K 6 OK 5677 5674 5676 5694 C4' DU K 7 OK 5696 5693 5695 5715 C4' DU P 3 OK 5717 5714 5716 5734 C4' DU P 4 OK 5736 5733 5735 5760 C4' BRU P 5 OK 5759 5763 5762 5773 C4' DU P 6 OK 5775 5772 5774 5792 C4' DU P 7 OK 5794 5791 5793 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5363 C5' DU E 2 5362 5364 5382 C5' DU E 3 5381 5383 5401 C5' DU E 4 5400 5402 5431 C5' BRU E 5 5432 5428 5440 C5' DU E 6 5439 5441 5459 C5' DU E 7 5458 5460 5480 C5' DU H 2 5479 5481 5499 C5' DU H 3 5498 5500 5518 C5' DU H 4 5517 5519 5548 C5' BRU H 5 5549 5545 5557 C5' DU H 6 5556 5558 5576 C5' DU H 7 5575 5577 5597 C5' DU K 2 5596 5598 5616 C5' DU K 3 5615 5617 5635 C5' DU K 4 5634 5636 5665 C5' BRU K 5 5666 5662 5674 C5' DU K 6 5673 5675 5693 C5' DU K 7 5692 5694 5714 C5' DU P 3 5713 5715 5733 C5' DU P 4 5732 5734 5763 C5' BRU P 5 5764 5760 5772 C5' DU P 6 5771 5773 5791 C5' DU P 7 5790 5792 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5378 P DU E 3 distorted distorted 5367 5379 5380 5381 5397 P DU E 4 distorted distorted 5386 5398 5399 5400 5433 P BRU E 5 distorted distorted 5405 5434 5435 5432 5436 P DU E 6 distorted distorted 5429 5437 5438 5439 5455 P DU E 7 distorted distorted 5444 5456 5457 5458 5476 P DU H 2 distorted distorted 5475 5477 5478 5479 5495 P DU H 3 distorted distorted 5484 5496 5497 5498 5514 P DU H 4 distorted distorted 5503 5515 5516 5517 5550 P BRU H 5 distorted distorted 5522 5551 5552 5549 5553 P DU H 6 distorted distorted 5546 5554 5555 5556 5572 P DU H 7 distorted distorted 5561 5573 5574 5575 5593 P DU K 2 distorted distorted 5592 5594 5595 5596 5612 P DU K 3 distorted distorted 5601 5613 5614 5615 5631 P DU K 4 distorted distorted 5620 5632 5633 5634 5667 P BRU K 5 distorted distorted 5639 5668 5669 5666 5670 P DU K 6 distorted distorted 5663 5671 5672 5673 5689 P DU K 7 distorted distorted 5678 5690 5691 5692 5710 P DU P 3 distorted distorted 5709 5711 5712 5713 5729 P DU P 4 distorted distorted 5718 5730 5731 5732 5765 P BRU P 5 distorted distorted 5737 5766 5767 5764 5768 P DU P 6 distorted distorted 5761 5769 5770 5771 5787 P DU P 7 distorted distorted 5776 5788 5789 5790 ---------------------------------------------------------------------------------