ID code: '1IK1' 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' A A 4 alpha beta 103 125 109 106 141 C1' C A 5 alpha beta 136 156 142 139 172 C1' U A 6 alpha beta 167 187 173 170 202 C1' A A 7 alpha beta 197 219 203 200 235 C1' U A 8 alpha beta 230 250 236 233 265 C1' G A 9 alpha beta 260 283 266 263 299 C1' U A 10 alpha beta 294 314 300 297 329 C1' A A 11 alpha beta 324 346 330 327 362 C1' C A 12 alpha beta 357 377 363 360 393 C1' C A 13 alpha beta 388 408 394 391 424 C1' A A 14 alpha beta 419 442 425 422 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 4 OK OK 108 104 123 107 139 C2' C A 5 OK OK 141 137 154 140 170 C2' U A 6 OK OK 172 168 185 171 200 C2' A A 7 OK OK 202 198 217 201 233 C2' U A 8 OK OK 235 231 248 234 263 C2' G A 9 OK OK 265 261 281 264 297 C2' U A 10 OK OK 299 295 312 298 327 C2' A A 11 OK OK 329 325 344 328 360 C2' C A 12 OK OK 362 358 375 361 391 C2' C A 13 OK OK 393 389 406 392 422 C2' A A 14 OK OK 424 420 440 423 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 102 122 105 106 137 C3' C A 5 OK OK 135 153 138 139 168 C3' U A 6 OK OK 166 184 169 170 198 C3' A A 7 OK OK 196 216 199 200 231 C3' U A 8 OK OK 229 247 232 233 261 C3' G A 9 OK OK 259 280 262 263 295 C3' U A 10 OK OK 293 311 296 297 325 C3' A A 11 OK OK 323 343 326 327 358 C3' C A 12 OK OK 356 374 359 360 389 C3' C A 13 OK OK 387 405 390 391 420 C3' A A 14 OK OK 418 438 421 422 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 104 121 101 103 135 C4' C A 5 OK OK 137 152 134 136 166 C4' U A 6 OK OK 168 183 165 167 196 C4' A A 7 OK OK 198 215 195 197 229 C4' U A 8 OK OK 231 246 228 230 259 C4' G A 9 OK OK 261 279 258 260 293 C4' U A 10 OK OK 295 310 292 294 323 C4' A A 11 OK OK 325 342 322 324 356 C4' C A 12 OK OK 358 373 355 357 387 C4' C A 13 OK OK 389 404 386 388 418 C4' A A 14 OK OK 420 437 417 419 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 100 119 120 102 134 C5' C A 5 OK OK 133 150 151 135 165 C5' U A 6 OK OK 164 181 182 166 195 C5' A A 7 OK OK 194 213 214 196 228 C5' U A 8 OK OK 227 244 245 229 258 C5' G A 9 OK OK 257 277 278 259 292 C5' U A 10 OK OK 291 308 309 293 322 C5' A A 11 OK OK 321 340 341 323 355 C5' C A 12 OK OK 354 371 372 356 386 C5' C A 13 OK OK 385 402 403 387 417 C5' A A 14 OK OK 416 435 436 418 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 4 distorted distorted 75 98 99 100 130 P C A 5 distorted distorted 105 131 132 133 161 P U A 6 distorted distorted 138 162 163 164 191 P A A 7 distorted distorted 169 192 193 194 224 P U A 8 distorted distorted 199 225 226 227 254 P G A 9 distorted distorted 232 255 256 257 288 P U A 10 distorted distorted 262 289 290 291 318 P A A 11 distorted distorted 296 319 320 321 351 P C A 12 distorted distorted 326 352 353 354 382 P C A 13 distorted distorted 359 383 384 385 413 P A A 14 distorted distorted 390 414 415 416 ---------------------------------------------------------------------------------