ID code: '2G4B' 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' --------------------------------------------------------------------------------- 13 C1' U B 1 beta 8 14 11 33 C1' U B 2 beta 28 34 31 53 C1' U B 3 beta 48 54 51 73 C1' U B 4 beta 68 74 71 93 C1' U B 5 beta 88 94 91 113 C1' U B 6 beta 108 114 111 133 C1' U B 7 beta 128 134 131 1488 C1' DIO A 41 1491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' U B 1 OK 13 9 12 31 C2' U B 2 OK 33 29 32 51 C2' U B 3 OK 53 49 52 71 C2' U B 4 OK 73 69 72 91 C2' U B 5 OK 93 89 92 111 C2' U B 6 OK 113 109 112 131 C2' U B 7 OK 133 129 132 1489 C2' DIO A 41 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' U B 1 OK 7 10 11 29 C3' U B 2 OK 27 30 31 49 C3' U B 3 OK 47 50 51 69 C3' U B 4 OK 67 70 71 89 C3' U B 5 OK 87 90 91 109 C3' U B 6 OK 107 110 111 129 C3' U B 7 OK 127 130 131 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' U B 1 OK 9 6 8 27 C4' U B 2 OK 29 26 28 47 C4' U B 3 OK 49 46 48 67 C4' U B 4 OK 69 66 68 87 C4' U B 5 OK 89 86 88 107 C4' U B 6 OK 109 106 108 127 C4' U B 7 OK 129 126 128 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' U B 1 5 7 26 C5' U B 2 25 27 46 C5' U B 3 45 47 66 C5' U B 4 65 67 86 C5' U B 5 85 87 106 C5' U B 6 105 107 126 C5' U B 7 125 127 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P U B 1 OK OK 3 4 5 22 P U B 2 distorted distorted 10 23 24 25 42 P U B 3 distorted distorted 30 43 44 45 62 P U B 4 distorted distorted 50 63 64 65 82 P U B 5 distorted distorted 70 83 84 85 102 P U B 6 distorted distorted 90 103 104 105 122 P U B 7 distorted distorted 110 123 124 125 ---------------------------------------------------------------------------------