ID code: '3Q0L' 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' --------------------------------------------------------------------------------- 5506 C1' U C 1 beta 5501 5507 5504 5526 C1' G C 2 beta 5521 5527 5524 5549 C1' U C 3 beta 5544 5550 5547 5569 C1' A C 4 beta 5564 5570 5567 5591 C1' A C 5 beta 5586 5592 5589 5613 C1' A C 6 beta 5608 5614 5611 5635 C1' U C 7 beta 5630 5636 5633 5655 C1' A C 8 beta 5650 5656 5653 5675 C1' U D 1 beta 5670 5676 5673 5695 C1' G D 2 beta 5690 5696 5693 5718 C1' U D 3 beta 5713 5719 5716 5738 C1' A D 4 beta 5733 5739 5736 5760 C1' A D 5 beta 5755 5761 5758 5782 C1' A D 6 beta 5777 5783 5780 5804 C1' U D 7 beta 5799 5805 5802 5824 C1' A D 8 beta 5819 5825 5822 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5504 C2' U C 1 OK 5506 5502 5505 5524 C2' G C 2 OK 5526 5522 5525 5547 C2' U C 3 OK 5549 5545 5548 5567 C2' A C 4 OK 5569 5565 5568 5589 C2' A C 5 OK 5591 5587 5590 5611 C2' A C 6 OK 5613 5609 5612 5633 C2' U C 7 OK 5635 5631 5634 5653 C2' A C 8 OK 5655 5651 5654 5673 C2' U D 1 OK 5675 5671 5674 5693 C2' G D 2 OK 5695 5691 5694 5716 C2' U D 3 OK 5718 5714 5717 5736 C2' A D 4 OK 5738 5734 5737 5758 C2' A D 5 OK 5760 5756 5759 5780 C2' A D 6 OK 5782 5778 5781 5802 C2' U D 7 OK 5804 5800 5803 5822 C2' A D 8 OK 5824 5820 5823 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5502 C3' U C 1 OK 5500 5503 5504 5522 C3' G C 2 OK 5520 5523 5524 5545 C3' U C 3 OK 5543 5546 5547 5565 C3' A C 4 OK 5563 5566 5567 5587 C3' A C 5 OK 5585 5588 5589 5609 C3' A C 6 OK 5607 5610 5611 5631 C3' U C 7 OK 5629 5632 5633 5651 C3' A C 8 OK 5649 5652 5653 5671 C3' U D 1 OK 5669 5672 5673 5691 C3' G D 2 OK 5689 5692 5693 5714 C3' U D 3 OK 5712 5715 5716 5734 C3' A D 4 OK 5732 5735 5736 5756 C3' A D 5 OK 5754 5757 5758 5778 C3' A D 6 OK 5776 5779 5780 5800 C3' U D 7 OK 5798 5801 5802 5820 C3' A D 8 OK 5818 5821 5822 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5500 C4' U C 1 OK 5502 5499 5501 5520 C4' G C 2 OK 5522 5519 5521 5543 C4' U C 3 OK 5545 5542 5544 5563 C4' A C 4 OK 5565 5562 5564 5585 C4' A C 5 OK 5587 5584 5586 5607 C4' A C 6 OK 5609 5606 5608 5629 C4' U C 7 OK 5631 5628 5630 5649 C4' A C 8 OK 5651 5648 5650 5669 C4' U D 1 OK 5671 5668 5670 5689 C4' G D 2 OK 5691 5688 5690 5712 C4' U D 3 OK 5714 5711 5713 5732 C4' A D 4 OK 5734 5731 5733 5754 C4' A D 5 OK 5756 5753 5755 5776 C4' A D 6 OK 5778 5775 5777 5798 C4' U D 7 OK 5800 5797 5799 5818 C4' A D 8 OK 5820 5817 5819 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5499 C5' U C 1 5498 5500 5519 C5' G C 2 5518 5520 5542 C5' U C 3 5541 5543 5562 C5' A C 4 5561 5563 5584 C5' A C 5 5583 5585 5606 C5' A C 6 5605 5607 5628 C5' U C 7 5627 5629 5648 C5' A C 8 5647 5649 5668 C5' U D 1 5667 5669 5688 C5' G D 2 5687 5689 5711 C5' U D 3 5710 5712 5731 C5' A D 4 5730 5732 5753 C5' A D 5 5752 5754 5775 C5' A D 6 5774 5776 5797 C5' U D 7 5796 5798 5817 C5' A D 8 5816 5818 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5515 P G C 2 distorted distorted 5503 5516 5517 5518 5538 P U C 3 distorted distorted 5523 5539 5540 5541 5558 P A C 4 distorted distorted 5546 5559 5560 5561 5580 P A C 5 distorted distorted 5566 5581 5582 5583 5602 P A C 6 distorted distorted 5588 5603 5604 5605 5624 P U C 7 distorted distorted 5610 5625 5626 5627 5644 P A C 8 distorted distorted 5632 5645 5646 5647 5684 P G D 2 distorted distorted 5672 5685 5686 5687 5707 P U D 3 distorted distorted 5692 5708 5709 5710 5727 P A D 4 distorted distorted 5715 5728 5729 5730 5749 P A D 5 distorted distorted 5735 5750 5751 5752 5771 P A D 6 distorted distorted 5757 5772 5773 5774 5793 P U D 7 distorted distorted 5779 5794 5795 5796 5813 P A D 8 distorted distorted 5801 5814 5815 5816 ---------------------------------------------------------------------------------