ID code: '3Q0P' 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' --------------------------------------------------------------------------------- 5501 C1' U C 1 beta 5496 5502 5499 5521 C1' G C 2 beta 5516 5522 5519 5544 C1' U C 3 beta 5539 5545 5542 5564 C1' A C 4 beta 5559 5565 5562 5586 C1' U C 5 beta 5581 5587 5584 5606 C1' A C 6 beta 5601 5607 5604 5628 C1' U C 7 beta 5623 5629 5626 5648 C1' A C 8 beta 5643 5649 5646 5668 C1' U D 1 beta 5663 5669 5666 5688 C1' G D 2 beta 5683 5689 5686 5711 C1' U D 3 beta 5706 5712 5709 5731 C1' A D 4 beta 5726 5732 5729 5753 C1' U D 5 beta 5748 5754 5751 5773 C1' A D 6 beta 5768 5774 5771 5795 C1' U D 7 beta 5790 5796 5793 5815 C1' A D 8 beta 5810 5816 5813 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5499 C2' U C 1 OK 5501 5497 5500 5519 C2' G C 2 OK 5521 5517 5520 5542 C2' U C 3 OK 5544 5540 5543 5562 C2' A C 4 OK 5564 5560 5563 5584 C2' U C 5 OK 5586 5582 5585 5604 C2' A C 6 OK 5606 5602 5605 5626 C2' U C 7 OK 5628 5624 5627 5646 C2' A C 8 OK 5648 5644 5647 5666 C2' U D 1 OK 5668 5664 5667 5686 C2' G D 2 OK 5688 5684 5687 5709 C2' U D 3 OK 5711 5707 5710 5729 C2' A D 4 OK 5731 5727 5730 5751 C2' U D 5 OK 5753 5749 5752 5771 C2' A D 6 OK 5773 5769 5772 5793 C2' U D 7 OK 5795 5791 5794 5813 C2' A D 8 OK 5815 5811 5814 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5497 C3' U C 1 OK 5495 5498 5499 5517 C3' G C 2 OK 5515 5518 5519 5540 C3' U C 3 OK 5538 5541 5542 5560 C3' A C 4 OK 5558 5561 5562 5582 C3' U C 5 OK 5580 5583 5584 5602 C3' A C 6 OK 5600 5603 5604 5624 C3' U C 7 OK 5622 5625 5626 5644 C3' A C 8 OK 5642 5645 5646 5664 C3' U D 1 OK 5662 5665 5666 5684 C3' G D 2 OK 5682 5685 5686 5707 C3' U D 3 OK 5705 5708 5709 5727 C3' A D 4 OK 5725 5728 5729 5749 C3' U D 5 OK 5747 5750 5751 5769 C3' A D 6 OK 5767 5770 5771 5791 C3' U D 7 OK 5789 5792 5793 5811 C3' A D 8 OK 5809 5812 5813 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5495 C4' U C 1 OK 5497 5494 5496 5515 C4' G C 2 OK 5517 5514 5516 5538 C4' U C 3 OK 5540 5537 5539 5558 C4' A C 4 OK 5560 5557 5559 5580 C4' U C 5 OK 5582 5579 5581 5600 C4' A C 6 OK 5602 5599 5601 5622 C4' U C 7 OK 5624 5621 5623 5642 C4' A C 8 OK 5644 5641 5643 5662 C4' U D 1 OK 5664 5661 5663 5682 C4' G D 2 OK 5684 5681 5683 5705 C4' U D 3 OK 5707 5704 5706 5725 C4' A D 4 OK 5727 5724 5726 5747 C4' U D 5 OK 5749 5746 5748 5767 C4' A D 6 OK 5769 5766 5768 5789 C4' U D 7 OK 5791 5788 5790 5809 C4' A D 8 OK 5811 5808 5810 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5494 C5' U C 1 5493 5495 5514 C5' G C 2 5513 5515 5537 C5' U C 3 5536 5538 5557 C5' A C 4 5556 5558 5579 C5' U C 5 5578 5580 5599 C5' A C 6 5598 5600 5621 C5' U C 7 5620 5622 5641 C5' A C 8 5640 5642 5661 C5' U D 1 5660 5662 5681 C5' G D 2 5680 5682 5704 C5' U D 3 5703 5705 5724 C5' A D 4 5723 5725 5746 C5' U D 5 5745 5747 5766 C5' A D 6 5765 5767 5788 C5' U D 7 5787 5789 5808 C5' A D 8 5807 5809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5510 P G C 2 distorted distorted 5498 5511 5512 5513 5533 P U C 3 distorted distorted 5518 5534 5535 5536 5553 P A C 4 distorted distorted 5541 5554 5555 5556 5575 P U C 5 distorted distorted 5561 5576 5577 5578 5595 P A C 6 distorted distorted 5583 5596 5597 5598 5617 P U C 7 distorted distorted 5603 5618 5619 5620 5637 P A C 8 distorted distorted 5625 5638 5639 5640 5677 P G D 2 distorted distorted 5665 5678 5679 5680 5700 P U D 3 distorted distorted 5685 5701 5702 5703 5720 P A D 4 distorted distorted 5708 5721 5722 5723 5742 P U D 5 distorted distorted 5728 5743 5744 5745 5762 P A D 6 distorted distorted 5750 5763 5764 5765 5784 P U D 7 distorted distorted 5770 5785 5786 5787 5804 P A D 8 distorted distorted 5792 5805 5806 5807 ---------------------------------------------------------------------------------