ID code: '5HBY' 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' --------------------------------------------------------------------------------- 5 C1' LCC A 1 beta 4 6 16 24 C1' LCC A 2 beta 23 25 35 46 C1' LCC A 3 beta 45 47 57 79 C1' LCG A 4 beta 82 70 76 99 C1' A A 5 beta 94 100 97 121 C1' C A 6 beta 116 122 119 141 C1' U A 7 beta 136 142 139 161 C1' U A 8 beta 156 162 159 181 C1' A A 9 beta 176 182 179 203 C1' A A 10 beta 198 204 201 225 C1' G A 11 beta 220 226 223 248 C1' U A 12 beta 243 249 246 268 C1' C A 13 beta 263 269 266 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 16 C2' LCC A 1 OK 5 15 17 35 C2' LCC A 2 OK 24 34 36 57 C2' LCC A 3 OK 46 56 58 76 C2' LCG A 4 OK 79 68 86 97 C2' A A 5 OK 99 95 98 119 C2' C A 6 OK 121 117 120 139 C2' U A 7 OK 141 137 140 159 C2' U A 8 OK 161 157 160 179 C2' A A 9 OK 181 177 180 201 C2' A A 10 OK 203 199 202 223 C2' G A 11 OK 225 221 224 246 C2' U A 12 OK 248 244 247 266 C2' C A 13 OK 268 264 267 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 15 C3' LCC A 1 OK 3 18 16 34 C3' LCC A 2 OK 22 37 35 56 C3' LCC A 3 OK 44 59 57 68 C3' LCG A 4 OK 78 87 76 95 C3' A A 5 OK 93 96 97 117 C3' C A 6 OK 115 118 119 137 C3' U A 7 OK 135 138 139 157 C3' U A 8 OK 155 158 159 177 C3' A A 9 OK 175 178 179 199 C3' A A 10 OK 197 200 201 221 C3' G A 11 OK 219 222 223 244 C3' U A 12 OK 242 245 246 264 C3' C A 13 OK 262 265 266 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' LCC A 1 OK 15 2 4 22 C4' LCC A 2 OK 34 21 23 44 C4' LCC A 3 OK 56 43 45 78 C4' LCG A 4 OK 68 67 82 93 C4' A A 5 OK 95 92 94 115 C4' C A 6 OK 117 114 116 135 C4' U A 7 OK 137 134 136 155 C4' U A 8 OK 157 154 156 175 C4' A A 9 OK 177 174 176 197 C4' A A 10 OK 199 196 198 219 C4' G A 11 OK 221 218 220 242 C4' U A 12 OK 244 241 243 262 C4' C A 13 OK 264 261 263 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' LCC A 1 1 3 21 C5' LCC A 2 20 22 43 C5' LCC A 3 42 44 67 C5' LCG A 4 66 78 92 C5' A A 5 91 93 114 C5' C A 6 113 115 134 C5' U A 7 133 135 154 C5' U A 8 153 155 174 C5' A A 9 173 175 196 C5' A A 10 195 197 218 C5' G A 11 217 219 241 C5' U A 12 240 242 261 C5' C A 13 260 262 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 39 P LCC A 2 distorted distorted 18 40 41 20 61 P LCC A 3 distorted distorted 37 62 63 42 64 P LCG A 4 distorted distorted 59 65 83 66 88 P A A 5 distorted distorted 87 89 90 91 110 P C A 6 distorted distorted 96 111 112 113 130 P U A 7 distorted distorted 118 131 132 133 150 P U A 8 distorted distorted 138 151 152 153 170 P A A 9 distorted distorted 158 171 172 173 192 P A A 10 distorted distorted 178 193 194 195 214 P G A 11 distorted distorted 200 215 216 217 237 P U A 12 distorted distorted 222 238 239 240 257 P C A 13 distorted distorted 245 258 259 260 ---------------------------------------------------------------------------------