ID code: '3Q0M' 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' --------------------------------------------------------------------------------- 5497 C1' U C 1 beta 5492 5498 5495 5517 C1' G C 2 beta 5512 5518 5515 5540 C1' U C 3 beta 5535 5541 5538 5560 C1' A C 4 beta 5555 5561 5558 5582 C1' G C 5 beta 5577 5583 5580 5605 C1' A C 6 beta 5600 5606 5603 5627 C1' U C 7 beta 5622 5628 5625 5647 C1' A C 8 beta 5642 5648 5645 5667 C1' U D 1 beta 5662 5668 5665 5687 C1' G D 2 beta 5682 5688 5685 5710 C1' U D 3 beta 5705 5711 5708 5730 C1' A D 4 beta 5725 5731 5728 5752 C1' G D 5 beta 5747 5753 5750 5775 C1' A D 6 beta 5770 5776 5773 5797 C1' U D 7 beta 5792 5798 5795 5817 C1' A D 8 beta 5812 5818 5815 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5495 C2' U C 1 OK 5497 5493 5496 5515 C2' G C 2 OK 5517 5513 5516 5538 C2' U C 3 OK 5540 5536 5539 5558 C2' A C 4 OK 5560 5556 5559 5580 C2' G C 5 OK 5582 5578 5581 5603 C2' A C 6 OK 5605 5601 5604 5625 C2' U C 7 OK 5627 5623 5626 5645 C2' A C 8 OK 5647 5643 5646 5665 C2' U D 1 OK 5667 5663 5666 5685 C2' G D 2 OK 5687 5683 5686 5708 C2' U D 3 OK 5710 5706 5709 5728 C2' A D 4 OK 5730 5726 5729 5750 C2' G D 5 OK 5752 5748 5751 5773 C2' A D 6 OK 5775 5771 5774 5795 C2' U D 7 OK 5797 5793 5796 5815 C2' A D 8 OK 5817 5813 5816 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5493 C3' U C 1 OK 5491 5494 5495 5513 C3' G C 2 OK 5511 5514 5515 5536 C3' U C 3 OK 5534 5537 5538 5556 C3' A C 4 OK 5554 5557 5558 5578 C3' G C 5 OK 5576 5579 5580 5601 C3' A C 6 OK 5599 5602 5603 5623 C3' U C 7 OK 5621 5624 5625 5643 C3' A C 8 OK 5641 5644 5645 5663 C3' U D 1 OK 5661 5664 5665 5683 C3' G D 2 OK 5681 5684 5685 5706 C3' U D 3 OK 5704 5707 5708 5726 C3' A D 4 OK 5724 5727 5728 5748 C3' G D 5 OK 5746 5749 5750 5771 C3' A D 6 OK 5769 5772 5773 5793 C3' U D 7 OK 5791 5794 5795 5813 C3' A D 8 OK 5811 5814 5815 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5491 C4' U C 1 OK 5493 5490 5492 5511 C4' G C 2 OK 5513 5510 5512 5534 C4' U C 3 OK 5536 5533 5535 5554 C4' A C 4 OK 5556 5553 5555 5576 C4' G C 5 OK 5578 5575 5577 5599 C4' A C 6 OK 5601 5598 5600 5621 C4' U C 7 OK 5623 5620 5622 5641 C4' A C 8 OK 5643 5640 5642 5661 C4' U D 1 OK 5663 5660 5662 5681 C4' G D 2 OK 5683 5680 5682 5704 C4' U D 3 OK 5706 5703 5705 5724 C4' A D 4 OK 5726 5723 5725 5746 C4' G D 5 OK 5748 5745 5747 5769 C4' A D 6 OK 5771 5768 5770 5791 C4' U D 7 OK 5793 5790 5792 5811 C4' A D 8 OK 5813 5810 5812 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5490 C5' U C 1 5489 5491 5510 C5' G C 2 5509 5511 5533 C5' U C 3 5532 5534 5553 C5' A C 4 5552 5554 5575 C5' G C 5 5574 5576 5598 C5' A C 6 5597 5599 5620 C5' U C 7 5619 5621 5640 C5' A C 8 5639 5641 5660 C5' U D 1 5659 5661 5680 C5' G D 2 5679 5681 5703 C5' U D 3 5702 5704 5723 C5' A D 4 5722 5724 5745 C5' G D 5 5744 5746 5768 C5' A D 6 5767 5769 5790 C5' U D 7 5789 5791 5810 C5' A D 8 5809 5811 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5506 P G C 2 distorted distorted 5494 5507 5508 5509 5529 P U C 3 distorted distorted 5514 5530 5531 5532 5549 P A C 4 distorted distorted 5537 5550 5551 5552 5571 P G C 5 distorted distorted 5557 5572 5573 5574 5594 P A C 6 distorted distorted 5579 5595 5596 5597 5616 P U C 7 distorted distorted 5602 5617 5618 5619 5636 P A C 8 distorted distorted 5624 5637 5638 5639 5676 P G D 2 distorted distorted 5664 5677 5678 5679 5699 P U D 3 distorted distorted 5684 5700 5701 5702 5719 P A D 4 distorted distorted 5707 5720 5721 5722 5741 P G D 5 distorted distorted 5727 5742 5743 5744 5764 P A D 6 OK OK 5749 5765 5766 5767 5786 P U D 7 distorted distorted 5772 5787 5788 5789 5806 P A D 8 distorted distorted 5794 5807 5808 5809 ---------------------------------------------------------------------------------