ID code: '5LTA' 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' --------------------------------------------------------------------------------- 5738 C1' U E 4 beta 5733 5739 5736 5758 C1' U E 5 beta 5753 5759 5756 5778 C1' U E 6 beta 5773 5779 5776 5798 C1' U E 7 beta 5793 5799 5796 5828 C1' ADP A 801 beta 5823 5829 5826 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5736 C2' U E 4 OK 5738 5734 5737 5756 C2' U E 5 OK 5758 5754 5757 5776 C2' U E 6 OK 5778 5774 5777 5796 C2' U E 7 OK 5798 5794 5797 5826 C2' ADP A 801 OK 5828 5824 5827 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5734 C3' U E 4 OK 5732 5735 5736 5754 C3' U E 5 OK 5752 5755 5756 5774 C3' U E 6 OK 5772 5775 5776 5794 C3' U E 7 OK 5792 5795 5796 5824 C3' ADP A 801 OK 5822 5825 5826 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5732 C4' U E 4 OK 5734 5731 5733 5752 C4' U E 5 OK 5754 5751 5753 5772 C4' U E 6 OK 5774 5771 5773 5792 C4' U E 7 OK 5794 5791 5793 5822 C4' ADP A 801 OK 5824 5821 5823 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5731 C5' U E 4 5730 5732 5751 C5' U E 5 5750 5752 5771 C5' U E 6 5770 5772 5791 C5' U E 7 5790 5792 5821 C5' ADP A 801 5820 5822 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5607 P U E 1 5608 P U E 1 5647 P U E 2 5648 P U E 2 5687 P U E 3 5688 P U E 3 5727 P U E 4 distorted distorted 5728 5729 5730 5747 P U E 5 distorted distorted 5735 5748 5749 5750 5767 P U E 6 distorted distorted 5755 5768 5769 5770 5787 P U E 7 distorted distorted 5775 5788 5789 5790 5807 P U E 8 distorted distorted 5795 5808 5809 5810 ---------------------------------------------------------------------------------