ID code: '2VNU' 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' A B -9 beta 8 14 11 35 C1' A B -8 beta 30 36 33 57 C1' A B -7 beta 52 58 55 79 C1' A B -6 beta 74 80 77 101 C1' A B -5 beta 96 102 99 123 C1' A B -4 beta 118 124 121 145 C1' A B -3 beta 140 146 143 167 C1' A B -2 beta 162 168 165 189 C1' A B -1 beta 184 190 187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' A B -9 OK 13 9 12 33 C2' A B -8 OK 35 31 34 55 C2' A B -7 OK 57 53 56 77 C2' A B -6 OK 79 75 78 99 C2' A B -5 OK 101 97 100 121 C2' A B -4 OK 123 119 122 143 C2' A B -3 OK 145 141 144 165 C2' A B -2 OK 167 163 166 187 C2' A B -1 OK 189 185 188 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' A B -9 OK 7 10 11 31 C3' A B -8 OK 29 32 33 53 C3' A B -7 OK 51 54 55 75 C3' A B -6 OK 73 76 77 97 C3' A B -5 OK 95 98 99 119 C3' A B -4 OK 117 120 121 141 C3' A B -3 OK 139 142 143 163 C3' A B -2 OK 161 164 165 185 C3' A B -1 OK 183 186 187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' A B -9 OK 9 6 8 29 C4' A B -8 OK 31 28 30 51 C4' A B -7 OK 53 50 52 73 C4' A B -6 OK 75 72 74 95 C4' A B -5 OK 97 94 96 117 C4' A B -4 OK 119 116 118 139 C4' A B -3 OK 141 138 140 161 C4' A B -2 OK 163 160 162 183 C4' A B -1 OK 185 182 184 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' A B -9 5 7 28 C5' A B -8 27 29 50 C5' A B -7 49 51 72 C5' A B -6 71 73 94 C5' A B -5 93 95 116 C5' A B -4 115 117 138 C5' A B -3 137 139 160 C5' A B -2 159 161 182 C5' A B -1 181 183 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P A B -9 OK OK 1 3 4 5 24 P A B -8 OK OK 10 25 26 27 46 P A B -7 distorted distorted 32 47 48 49 68 P A B -6 distorted distorted 54 69 70 71 90 P A B -5 distorted distorted 76 91 92 93 112 P A B -4 distorted distorted 98 113 114 115 134 P A B -3 distorted distorted 120 135 136 137 156 P A B -2 distorted distorted 142 157 158 159 178 P A B -1 distorted distorted 164 179 180 181 ---------------------------------------------------------------------------------