ID code: '5T8Y' 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' --------------------------------------------------------------------------------- 5885 C1' A X 29 beta 5880 5886 5883 5907 C1' G X 30 beta 5902 5908 5905 5930 C1' A X 31 beta 5925 5931 5928 5952 C1' C X 32 beta 5947 5953 5950 5972 C1' U X 33 beta 5967 5973 5970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5883 C2' A X 29 OK 5885 5881 5884 5905 C2' G X 30 OK 5907 5903 5906 5928 C2' A X 31 OK 5930 5926 5929 5950 C2' C X 32 OK 5952 5948 5951 5970 C2' U X 33 OK 5972 5968 5971 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5881 C3' A X 29 OK 5879 5882 5883 5903 C3' G X 30 OK 5901 5904 5905 5926 C3' A X 31 OK 5924 5927 5928 5948 C3' C X 32 OK 5946 5949 5950 5968 C3' U X 33 OK 5966 5969 5970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5879 C4' A X 29 OK 5881 5878 5880 5901 C4' G X 30 OK 5903 5900 5902 5924 C4' A X 31 OK 5926 5923 5925 5946 C4' C X 32 OK 5948 5945 5947 5966 C4' U X 33 OK 5968 5965 5967 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5878 C5' A X 29 5877 5879 5900 C5' G X 30 5899 5901 5923 C5' A X 31 5922 5924 5945 C5' C X 32 5944 5946 5965 C5' U X 33 5964 5966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5874 P A X 29 distorted distorted 5875 5876 5877 5896 P G X 30 distorted distorted 5882 5897 5898 5899 5919 P A X 31 distorted distorted 5904 5920 5921 5922 5941 P C X 32 distorted distorted 5927 5942 5943 5944 5961 P U X 33 distorted distorted 5949 5962 5963 5964 6068 P B12 A 503 6089 P PO4 A 504 6094 P PO4 A 505 6185 P B12 B 503 6206 P PO4 B 504 6211 P PO4 B 505 6216 P PO4 B 506 6221 P PO4 B 507 6226 P PO4 B 508 ---------------------------------------------------------------------------------