ID code: '2GPX' 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' --------------------------------------------------------------------------------- 8 C1' DG A 1 beta 4 9 7 31 C1' UMS A 2 beta 26 33 29 51 C1' DG A 3 beta 47 52 50 72 C1' BRU A 4 beta 77 63 73 93 C1' DA A 5 beta 89 94 92 114 C1' DC A 6 beta 110 115 113 133 C1' DA A 7 beta 129 134 132 154 C1' DC A 8 beta 150 155 153 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG A 1 8 5 29 C2' UMS A 2 31 27 50 C2' DG A 3 51 48 73 C2' BRU A 4 72 74 92 C2' DA A 5 93 90 113 C2' DC A 6 114 111 132 C2' DA A 7 133 130 153 C2' DC A 8 154 151 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG A 1 OK 3 6 7 27 C3' UMS A 2 OK 25 28 29 48 C3' DG A 3 OK 46 49 50 74 C3' BRU A 4 OK 75 76 73 90 C3' DA A 5 OK 88 91 92 111 C3' DC A 6 OK 109 112 113 130 C3' DA A 7 OK 128 131 132 151 C3' DC A 8 OK 149 152 153 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG A 1 OK 5 2 4 25 C4' UMS A 2 OK 27 24 26 46 C4' DG A 3 OK 48 45 47 75 C4' BRU A 4 OK 74 78 77 88 C4' DA A 5 OK 90 87 89 109 C4' DC A 6 OK 111 108 110 128 C4' DA A 7 OK 130 127 129 149 C4' DC A 8 OK 151 148 150 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG A 1 1 3 24 C5' UMS A 2 23 25 45 C5' DG A 3 44 46 78 C5' BRU A 4 79 75 87 C5' DA A 5 86 88 108 C5' DC A 6 107 109 127 C5' DA A 7 126 128 148 C5' DC A 8 147 149 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P UMS A 2 distorted distorted 6 21 22 23 41 P DG A 3 distorted distorted 28 42 43 44 80 P BRU A 4 distorted distorted 49 81 82 79 83 P DA A 5 distorted distorted 76 84 85 86 104 P DC A 6 distorted distorted 91 105 106 107 123 P DA A 7 distorted distorted 112 124 125 126 144 P DC A 8 distorted distorted 131 145 146 147 ---------------------------------------------------------------------------------