ID code: '5ELH' 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' --------------------------------------------------------------------------------- 4606 C1' U R 1 alpha beta 4601 4621 4607 4604 4637 C1' U R 2 alpha beta 4632 4652 4638 4635 4667 C1' A R 3 alpha beta 4662 4684 4668 4665 4700 C1' U R 4 alpha beta 4695 4715 4701 4698 4730 C1' U R 5 alpha beta 4725 4746 4731 4728 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4604 C2' U R 1 OK OK 4606 4602 4619 4605 4635 C2' U R 2 OK OK 4637 4633 4650 4636 4665 C2' A R 3 OK OK 4667 4663 4682 4666 4698 C2' U R 4 OK OK 4700 4696 4713 4699 4728 C2' U R 5 OK OK 4730 4726 4744 4729 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4602 C3' U R 1 OK OK 4600 4618 4603 4604 4633 C3' U R 2 OK OK 4631 4649 4634 4635 4663 C3' A R 3 OK OK 4661 4681 4664 4665 4696 C3' U R 4 OK OK 4694 4712 4697 4698 4726 C3' U R 5 OK OK 4724 4742 4727 4728 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4600 C4' U R 1 OK OK 4602 4617 4599 4601 4631 C4' U R 2 OK OK 4633 4648 4630 4632 4661 C4' A R 3 OK OK 4663 4680 4660 4662 4694 C4' U R 4 OK OK 4696 4711 4693 4695 4724 C4' U R 5 OK OK 4726 4741 4723 4725 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4599 C5' U R 1 OK OK 4598 4615 4616 4600 4630 C5' U R 2 OK OK 4629 4646 4647 4631 4660 C5' A R 3 OK OK 4659 4678 4679 4661 4693 C5' U R 4 OK OK 4692 4709 4710 4694 4723 C5' U R 5 OK OK 4722 4739 4740 4724 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4626 P U R 2 distorted distorted 4603 4627 4628 4629 4656 P A R 3 distorted distorted 4634 4657 4658 4659 4689 P U R 4 distorted distorted 4664 4690 4691 4692 4719 P U R 5 distorted distorted 4697 4720 4721 4722 ---------------------------------------------------------------------------------