ID code: '3GPQ' 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' --------------------------------------------------------------------------------- 4771 C1' A E 1 beta 4766 4772 4769 4793 C1' A E 2 4788 4791 4807 C1' A F 1 beta 4802 4808 4805 4829 C1' A F 2 beta 4824 4830 4827 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4769 C2' A E 1 OK 4771 4767 4770 4791 C2' A E 2 OK 4793 4789 4792 4805 C2' A F 1 OK 4807 4803 4806 4827 C2' A F 2 OK 4829 4825 4828 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4767 C3' A E 1 OK 4765 4768 4769 4789 C3' A E 2 OK 4787 4790 4791 4803 C3' A F 1 OK 4801 4804 4805 4825 C3' A F 2 OK 4823 4826 4827 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4765 C4' A E 1 OK 4767 4764 4766 4787 C4' A E 2 OK 4789 4786 4788 4801 C4' A F 1 OK 4803 4800 4802 4823 C4' A F 2 OK 4825 4822 4824 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4764 C5' A E 1 4763 4765 4786 C5' A E 2 4785 4787 4800 C5' A F 1 4799 4801 4822 C5' A F 2 4821 4823 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4760 P A E 1 OK OK 4761 4762 4763 4782 P A E 2 distorted distorted 4768 4783 4784 4785 4796 P A F 1 distorted distorted 4797 4798 4799 4818 P A F 2 distorted distorted 4804 4819 4820 4821 ---------------------------------------------------------------------------------