ID code: '1ESH' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' A A 6 alpha beta 168 190 174 171 206 C1' U A 7 alpha beta 201 221 207 204 236 C1' A A 8 alpha beta 231 253 237 234 269 C1' G A 9 alpha beta 264 287 270 267 303 C1' C A 10 alpha beta 298 318 304 301 334 C1' A A 11 alpha beta 329 351 335 332 367 C1' C A 12 alpha beta 362 382 368 365 398 C1' C A 13 alpha beta 393 414 399 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' C A 5 OK OK 142 138 155 141 171 C2' A A 6 OK OK 173 169 188 172 204 C2' U A 7 OK OK 206 202 219 205 234 C2' A A 8 OK OK 236 232 251 235 267 C2' G A 9 OK OK 269 265 285 268 301 C2' C A 10 OK OK 303 299 316 302 332 C2' A A 11 OK OK 334 330 349 333 365 C2' C A 12 OK OK 367 363 380 366 396 C2' C A 13 OK OK 398 394 412 397 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' C A 5 OK OK 136 154 139 140 169 C3' A A 6 OK OK 167 187 170 171 202 C3' U A 7 OK OK 200 218 203 204 232 C3' A A 8 OK OK 230 250 233 234 265 C3' G A 9 OK OK 263 284 266 267 299 C3' C A 10 OK OK 297 315 300 301 330 C3' A A 11 OK OK 328 348 331 332 363 C3' C A 12 OK OK 361 379 364 365 394 C3' C A 13 OK OK 392 410 395 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' C A 5 OK OK 138 153 135 137 167 C4' A A 6 OK OK 169 186 166 168 200 C4' U A 7 OK OK 202 217 199 201 230 C4' A A 8 OK OK 232 249 229 231 263 C4' G A 9 OK OK 265 283 262 264 297 C4' C A 10 OK OK 299 314 296 298 328 C4' A A 11 OK OK 330 347 327 329 361 C4' C A 12 OK OK 363 378 360 362 392 C4' C A 13 OK OK 394 409 391 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' C A 5 OK OK 134 151 152 136 166 C5' A A 6 OK OK 165 184 185 167 199 C5' U A 7 OK OK 198 215 216 200 229 C5' A A 8 OK OK 228 247 248 230 262 C5' G A 9 OK OK 261 281 282 263 296 C5' C A 10 OK OK 295 312 313 297 327 C5' A A 11 OK OK 326 345 346 328 360 C5' C A 12 OK OK 359 376 377 361 391 C5' C A 13 OK OK 390 407 408 392 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P C A 5 distorted distorted 105 132 133 134 162 P A A 6 distorted distorted 139 163 164 165 195 P U A 7 distorted distorted 170 196 197 198 225 P A A 8 distorted distorted 203 226 227 228 258 P G A 9 distorted distorted 233 259 260 261 292 P C A 10 distorted distorted 266 293 294 295 323 P A A 11 distorted distorted 300 324 325 326 356 P C A 12 distorted distorted 331 357 358 359 387 P C A 13 distorted distorted 364 388 389 390 ---------------------------------------------------------------------------------