ID code: '2XZO' 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' --------------------------------------------------------------------------------- 4638 C1' U D 1 beta 4633 4639 4636 4658 C1' U D 2 beta 4653 4659 4656 4678 C1' U D 3 beta 4673 4679 4676 4698 C1' U D 4 beta 4693 4699 4696 4718 C1' U D 5 beta 4713 4719 4716 4738 C1' U D 6 beta 4733 4739 4736 4792 C1' ADP A1004 beta 4787 4793 4790 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4636 C2' U D 1 OK 4638 4634 4637 4656 C2' U D 2 OK 4658 4654 4657 4676 C2' U D 3 OK 4678 4674 4677 4696 C2' U D 4 OK 4698 4694 4697 4716 C2' U D 5 OK 4718 4714 4717 4736 C2' U D 6 OK 4738 4734 4737 4790 C2' ADP A1004 OK 4792 4788 4791 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4634 C3' U D 1 OK 4632 4635 4636 4654 C3' U D 2 OK 4652 4655 4656 4674 C3' U D 3 OK 4672 4675 4676 4694 C3' U D 4 OK 4692 4695 4696 4714 C3' U D 5 OK 4712 4715 4716 4734 C3' U D 6 OK 4732 4735 4736 4788 C3' ADP A1004 OK 4786 4789 4790 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4632 C4' U D 1 OK 4634 4631 4633 4652 C4' U D 2 OK 4654 4651 4653 4672 C4' U D 3 OK 4674 4671 4673 4692 C4' U D 4 OK 4694 4691 4693 4712 C4' U D 5 OK 4714 4711 4713 4732 C4' U D 6 OK 4734 4731 4733 4786 C4' ADP A1004 OK 4788 4785 4787 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4631 C5' U D 1 4630 4632 4651 C5' U D 2 4650 4652 4671 C5' U D 3 4670 4672 4691 C5' U D 4 4690 4692 4711 C5' U D 5 4710 4712 4731 C5' U D 6 4730 4732 4785 C5' ADP A1004 4784 4786 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4627 P U D 1 OK OK 4628 4629 4630 4647 P U D 2 distorted distorted 4635 4648 4649 4650 4667 P U D 3 distorted distorted 4655 4668 4669 4670 4687 P U D 4 distorted distorted 4675 4688 4689 4690 4707 P U D 5 distorted distorted 4695 4708 4709 4710 4727 P U D 6 distorted distorted 4715 4728 4729 4730 4747 P U D 7 distorted distorted 4735 4748 4749 4750 ---------------------------------------------------------------------------------