ID code: '5T7B' 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' --------------------------------------------------------------------------------- 14 C1' UVP R 1 beta 8 15 11 34 C1' U R 2 beta 29 35 32 54 C1' A R 3 beta 49 55 52 76 C1' U R 4 beta 71 77 74 96 C1' A R 5 beta 91 97 94 118 C1' G R 6 beta 113 119 116 141 C1' A R 7 beta 136 142 139 163 C1' G R 8 beta 158 164 161 186 C1' C R 9 beta 181 187 184 206 C1' A R 10 beta 201 207 204 228 C1' U R 21 beta 223 229 226 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' UVP R 1 OK 14 9 12 32 C2' U R 2 OK 34 30 33 52 C2' A R 3 OK 54 50 53 74 C2' U R 4 OK 76 72 75 94 C2' A R 5 OK 96 92 95 116 C2' G R 6 OK 118 114 117 139 C2' A R 7 OK 141 137 140 161 C2' G R 8 OK 163 159 162 184 C2' C R 9 OK 186 182 185 204 C2' A R 10 OK 206 202 205 226 C2' U R 21 OK 228 224 227 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' UVP R 1 OK 7 10 11 30 C3' U R 2 OK 28 31 32 50 C3' A R 3 OK 48 51 52 72 C3' U R 4 OK 70 73 74 92 C3' A R 5 OK 90 93 94 114 C3' G R 6 OK 112 115 116 137 C3' A R 7 OK 135 138 139 159 C3' G R 8 OK 157 160 161 182 C3' C R 9 OK 180 183 184 202 C3' A R 10 OK 200 203 204 224 C3' U R 21 OK 222 225 226 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' UVP R 1 OK 9 6 8 28 C4' U R 2 OK 30 27 29 48 C4' A R 3 OK 50 47 49 70 C4' U R 4 OK 72 69 71 90 C4' A R 5 OK 92 89 91 112 C4' G R 6 OK 114 111 113 135 C4' A R 7 OK 137 134 136 157 C4' G R 8 OK 159 156 158 180 C4' C R 9 OK 182 179 181 200 C4' A R 10 OK 202 199 201 222 C4' U R 21 OK 224 221 223 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' UVP R 1 7 27 C5' U R 2 26 28 47 C5' A R 3 46 48 69 C5' U R 4 68 70 89 C5' A R 5 88 90 111 C5' G R 6 110 112 134 C5' A R 7 133 135 156 C5' G R 8 155 157 179 C5' C R 9 178 180 199 C5' A R 10 198 200 221 C5' U R 21 220 222 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P UVP R 1 3 4 23 P U R 2 distorted distorted 10 24 25 26 43 P A R 3 distorted distorted 31 44 45 46 65 P U R 4 distorted distorted 51 66 67 68 85 P A R 5 distorted distorted 73 86 87 88 107 P G R 6 distorted distorted 93 108 109 110 130 P A R 7 distorted distorted 115 131 132 133 152 P G R 8 distorted distorted 138 153 154 155 175 P C R 9 distorted distorted 160 176 177 178 195 P A R 10 distorted distorted 183 196 197 198 217 P U R 21 distorted distorted 218 219 220 ---------------------------------------------------------------------------------