ID code: '5ELR' 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' --------------------------------------------------------------------------------- 12 C1' A B 4 beta 7 13 10 34 C1' U B 5 beta 29 35 32 54 C1' A B 6 beta 49 55 52 76 C1' A B 7 beta 71 77 74 98 C1' U B 8 beta 93 99 96 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A B 4 OK 12 8 11 32 C2' U B 5 OK 34 30 33 52 C2' A B 6 OK 54 50 53 74 C2' A B 7 OK 76 72 75 96 C2' U B 8 OK 98 94 97 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A B 4 OK 6 9 10 30 C3' U B 5 OK 28 31 32 50 C3' A B 6 OK 48 51 52 72 C3' A B 7 OK 70 73 74 94 C3' U B 8 OK 92 95 96 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A B 4 OK 8 5 7 28 C4' U B 5 OK 30 27 29 48 C4' A B 6 OK 50 47 49 70 C4' A B 7 OK 72 69 71 92 C4' U B 8 OK 94 91 93 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A B 4 4 6 27 C5' U B 5 26 28 47 C5' A B 6 46 48 69 C5' A B 7 68 70 91 C5' U B 8 90 92 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A B 4 distorted distorted 2 3 4 23 P U B 5 distorted distorted 9 24 25 26 43 P A B 6 distorted distorted 31 44 45 46 65 P A B 7 distorted distorted 51 66 67 68 87 P U B 8 distorted distorted 73 88 89 90 ---------------------------------------------------------------------------------