ID code: '4E6B' 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' --------------------------------------------------------------------------------- 12 C1' C A 8 beta 7 13 10 32 C1' G A 9 beta 27 33 30 55 C1' C A 10 beta 50 56 53 75 C1' G A 11 beta 70 76 73 99 C1' C B 7 beta 94 100 97 119 C1' G B 8 beta 114 120 117 142 C1' C B 9 beta 137 143 140 162 C1' G B 10 beta 157 163 160 186 C1' G F 8 beta 181 187 184 209 C1' C F 9 beta 204 210 207 229 C1' G F 10 beta 224 230 227 252 C1' C F 11 beta 247 253 250 273 C1' G E 7 beta 268 274 271 296 C1' C E 8 beta 291 297 294 316 C1' G E 9 beta 311 317 314 339 C1' C E 10 beta 334 340 337 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C A 8 OK 12 8 11 30 C2' G A 9 OK 32 28 31 53 C2' C A 10 OK 55 51 54 73 C2' G A 11 OK 75 71 74 97 C2' C B 7 OK 99 95 98 117 C2' G B 8 OK 119 115 118 140 C2' C B 9 OK 142 138 141 160 C2' G B 10 OK 162 158 161 184 C2' G F 8 OK 186 182 185 207 C2' C F 9 OK 209 205 208 227 C2' G F 10 OK 229 225 228 250 C2' C F 11 OK 252 248 251 271 C2' G E 7 OK 273 269 272 294 C2' C E 8 OK 296 292 295 314 C2' G E 9 OK 316 312 315 337 C2' C E 10 OK 339 335 338 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A 8 OK 6 9 10 28 C3' G A 9 OK 26 29 30 51 C3' C A 10 OK 49 52 53 71 C3' G A 11 OK 69 72 73 95 C3' C B 7 OK 93 96 97 115 C3' G B 8 OK 113 116 117 138 C3' C B 9 OK 136 139 140 158 C3' G B 10 OK 156 159 160 182 C3' G F 8 OK 180 183 184 205 C3' C F 9 OK 203 206 207 225 C3' G F 10 OK 223 226 227 248 C3' C F 11 OK 246 249 250 269 C3' G E 7 OK 267 270 271 292 C3' C E 8 OK 290 293 294 312 C3' G E 9 OK 310 313 314 335 C3' C E 10 OK 333 336 337 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A 8 OK 8 5 7 26 C4' G A 9 OK 28 25 27 49 C4' C A 10 OK 51 48 50 69 C4' G A 11 OK 71 68 70 93 C4' C B 7 OK 95 92 94 113 C4' G B 8 OK 115 112 114 136 C4' C B 9 OK 138 135 137 156 C4' G B 10 OK 158 155 157 180 C4' G F 8 OK 182 179 181 203 C4' C F 9 OK 205 202 204 223 C4' G F 10 OK 225 222 224 246 C4' C F 11 OK 248 245 247 267 C4' G E 7 OK 269 266 268 290 C4' C E 8 OK 292 289 291 310 C4' G E 9 OK 312 309 311 333 C4' C E 10 OK 335 332 334 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A 8 4 6 25 C5' G A 9 24 26 48 C5' C A 10 47 49 68 C5' G A 11 67 69 92 C5' C B 7 91 93 112 C5' G B 8 111 113 135 C5' C B 9 134 136 155 C5' G B 10 154 156 179 C5' G F 8 178 180 202 C5' C F 9 201 203 222 C5' G F 10 221 223 245 C5' C F 11 244 246 266 C5' G E 7 265 267 289 C5' C E 8 288 290 309 C5' G E 9 308 310 332 C5' C E 10 331 333 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A 8 distorted distorted 2 3 4 21 P G A 9 distorted distorted 9 22 23 24 44 P C A 10 distorted distorted 29 45 46 47 64 P G A 11 distorted distorted 52 65 66 67 88 P C B 7 distorted distorted 336 89 90 91 108 P G B 8 distorted distorted 96 109 110 111 131 P C B 9 distorted distorted 116 132 133 134 151 P G B 10 distorted distorted 139 152 153 154 175 P G F 8 distorted distorted 72 176 177 178 198 P C F 9 distorted distorted 183 199 200 201 218 P G F 10 distorted distorted 206 219 220 221 241 P C F 11 distorted distorted 226 242 243 244 262 P G E 7 distorted distorted 263 264 265 285 P C E 8 distorted distorted 270 286 287 288 305 P G E 9 distorted distorted 293 306 307 308 328 P C E 10 distorted distorted 313 329 330 331 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