ID code: '1GPV' 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' --------------------------------------------------------------------------------- 11 C1' A C 1 beta 7 12 10 32 C1' A C 2 beta 28 33 31 53 C1' A C 3 beta 49 54 52 74 C1' A C 4 beta 70 75 73 96 C1' A D 1 beta 92 97 95 117 C1' A D 2 beta 113 118 116 138 C1' A D 3 beta 134 139 137 159 C1' A D 4 beta 155 160 158 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A C 1 11 8 31 C2' A C 2 32 29 52 C2' A C 3 53 50 73 C2' A C 4 74 71 95 C2' A D 1 96 93 116 C2' A D 2 117 114 137 C2' A D 3 138 135 158 C2' A D 4 159 156 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A C 1 OK 6 9 10 29 C3' A C 2 OK 27 30 31 50 C3' A C 3 OK 48 51 52 71 C3' A C 4 OK 69 72 73 93 C3' A D 1 OK 91 94 95 114 C3' A D 2 OK 112 115 116 135 C3' A D 3 OK 133 136 137 156 C3' A D 4 OK 154 157 158 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A C 1 OK 8 5 7 27 C4' A C 2 OK 29 26 28 48 C4' A C 3 OK 50 47 49 69 C4' A C 4 OK 71 68 70 91 C4' A D 1 OK 93 90 92 112 C4' A D 2 OK 114 111 113 133 C4' A D 3 OK 135 132 134 154 C4' A D 4 OK 156 153 155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A C 1 4 6 26 C5' A C 2 25 27 47 C5' A C 3 46 48 68 C5' A C 4 67 69 90 C5' A D 1 89 91 111 C5' A D 2 110 112 132 C5' A D 3 131 133 153 C5' A D 4 152 154 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A C 1 OK OK 2 3 4 22 P A C 2 distorted distorted 9 23 24 25 43 P A C 3 distorted distorted 30 44 45 46 64 P A C 4 distorted distorted 51 65 66 67 86 P A D 1 OK OK 87 88 89 107 P A D 2 distorted distorted 94 108 109 110 128 P A D 3 distorted distorted 115 129 130 131 149 P A D 4 distorted distorted 136 150 151 152 ---------------------------------------------------------------------------------