ID code: '5E02' 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' --------------------------------------------------------------------------------- 7698 C1' A C 1 beta 7693 7699 7696 7720 C1' A C 2 beta 7715 7721 7718 7742 C1' A C 3 beta 7737 7743 7740 7764 C1' A C 4 beta 7759 7765 7762 7792 C1' ADP A1201 beta 7787 7793 7790 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7696 C2' A C 1 OK 7698 7694 7697 7718 C2' A C 2 OK 7720 7716 7719 7740 C2' A C 3 OK 7742 7738 7741 7762 C2' A C 4 OK 7764 7760 7763 7790 C2' ADP A1201 OK 7792 7788 7791 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7694 C3' A C 1 OK 7692 7695 7696 7716 C3' A C 2 OK 7714 7717 7718 7738 C3' A C 3 OK 7736 7739 7740 7760 C3' A C 4 OK 7758 7761 7762 7788 C3' ADP A1201 OK 7786 7789 7790 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7692 C4' A C 1 OK 7694 7691 7693 7714 C4' A C 2 OK 7716 7713 7715 7736 C4' A C 3 OK 7738 7735 7737 7758 C4' A C 4 OK 7760 7757 7759 7786 C4' ADP A1201 OK 7788 7785 7787 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7691 C5' A C 1 7690 7692 7713 C5' A C 2 7712 7714 7735 C5' A C 3 7734 7736 7757 C5' A C 4 7756 7758 7785 C5' ADP A1201 7784 7786 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7709 P A C 2 distorted distorted 7695 7710 7711 7712 7731 P A C 3 distorted distorted 7717 7732 7733 7734 7753 P A C 4 distorted distorted 7739 7754 7755 7756 ---------------------------------------------------------------------------------