ID code: '1ROQ' 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 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' U A 3 alpha beta 72 92 78 75 107 C1' A A 4 alpha beta 102 124 108 105 140 C1' U A 5 alpha beta 135 155 141 138 170 C1' C A 6 alpha beta 165 185 171 168 201 C1' A A 7 alpha beta 196 218 202 199 234 C1' C A 8 alpha beta 229 249 235 232 265 C1' G A 9 alpha beta 260 283 266 263 299 C1' G A 10 alpha beta 294 317 300 297 333 C1' U A 11 alpha beta 328 348 334 331 363 C1' A A 12 alpha beta 358 380 364 361 396 C1' C A 13 alpha beta 391 411 397 394 427 C1' C A 14 alpha beta 422 443 428 425 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' G A 2 OK OK 43 39 59 42 75 C2' U A 3 OK OK 77 73 90 76 105 C2' A A 4 OK OK 107 103 122 106 138 C2' U A 5 OK OK 140 136 153 139 168 C2' C A 6 OK OK 170 166 183 169 199 C2' A A 7 OK OK 201 197 216 200 232 C2' C A 8 OK OK 234 230 247 233 263 C2' G A 9 OK OK 265 261 281 264 297 C2' G A 10 OK OK 299 295 315 298 331 C2' U A 11 OK OK 333 329 346 332 361 C2' A A 12 OK OK 363 359 378 362 394 C2' C A 13 OK OK 396 392 409 395 425 C2' C A 14 OK OK 427 423 441 426 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' U A 3 OK OK 71 89 74 75 103 C3' A A 4 OK OK 101 121 104 105 136 C3' U A 5 OK OK 134 152 137 138 166 C3' C A 6 OK OK 164 182 167 168 197 C3' A A 7 OK OK 195 215 198 199 230 C3' C A 8 OK OK 228 246 231 232 261 C3' G A 9 OK OK 259 280 262 263 295 C3' G A 10 OK OK 293 314 296 297 329 C3' U A 11 OK OK 327 345 330 331 359 C3' A A 12 OK OK 357 377 360 361 392 C3' C A 13 OK OK 390 408 393 394 423 C3' C A 14 OK OK 421 439 424 425 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' U A 3 OK OK 73 88 70 72 101 C4' A A 4 OK OK 103 120 100 102 134 C4' U A 5 OK OK 136 151 133 135 164 C4' C A 6 OK OK 166 181 163 165 195 C4' A A 7 OK OK 197 214 194 196 228 C4' C A 8 OK OK 230 245 227 229 259 C4' G A 9 OK OK 261 279 258 260 293 C4' G A 10 OK OK 295 313 292 294 327 C4' U A 11 OK OK 329 344 326 328 357 C4' A A 12 OK OK 359 376 356 358 390 C4' C A 13 OK OK 392 407 389 391 421 C4' C A 14 OK OK 423 438 420 422 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 36 C5' G A 2 OK OK 35 55 56 37 70 C5' U A 3 OK OK 69 86 87 71 100 C5' A A 4 OK OK 99 118 119 101 133 C5' U A 5 OK OK 132 149 150 134 163 C5' C A 6 OK OK 162 179 180 164 194 C5' A A 7 OK OK 193 212 213 195 227 C5' C A 8 OK OK 226 243 244 228 258 C5' G A 9 OK OK 257 277 278 259 292 C5' G A 10 OK OK 291 311 312 293 326 C5' U A 11 OK OK 325 342 343 327 356 C5' A A 12 OK OK 355 374 375 357 389 C5' C A 13 OK OK 388 405 406 390 420 C5' C A 14 OK OK 419 436 437 421 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P U A 3 distorted distorted 40 67 68 69 96 P A A 4 distorted distorted 74 97 98 99 129 P U A 5 distorted distorted 104 130 131 132 159 P C A 6 distorted distorted 137 160 161 162 190 P A A 7 distorted distorted 167 191 192 193 223 P C A 8 distorted distorted 198 224 225 226 254 P G A 9 distorted distorted 231 255 256 257 288 P G A 10 distorted distorted 262 289 290 291 322 P U A 11 distorted distorted 296 323 324 325 352 P A A 12 distorted distorted 330 353 354 355 385 P C A 13 distorted distorted 360 386 387 388 416 P C A 14 distorted distorted 393 417 418 419 ---------------------------------------------------------------------------------