ID code: '1MWG' 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' C A 3 alpha beta 73 93 79 76 109 C1' A A 4 alpha beta 104 126 110 107 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' C A 7 alpha beta 205 225 211 208 241 C1' C A 8 alpha beta 236 257 242 239 271 C1' G B 9 alpha beta 266 289 272 269 306 C1' G B 10 alpha beta 301 324 307 304 340 C1' C B 11 alpha beta 335 355 341 338 371 C1' A B 12 alpha beta 366 388 372 369 404 C1' G B 13 alpha beta 399 422 405 402 438 C1' G B 14 alpha beta 433 456 439 436 472 C1' C B 15 alpha beta 467 487 473 470 503 C1' C B 16 alpha beta 498 519 504 501 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' A A 4 OK OK 109 105 124 108 140 C2' G A 5 OK OK 142 138 158 141 174 C2' G A 6 OK OK 176 172 192 175 208 C2' C A 7 OK OK 210 206 223 209 239 C2' C A 8 OK OK 241 237 255 240 269 C2' G B 9 OK OK 271 267 287 270 304 C2' G B 10 OK OK 306 302 322 305 338 C2' C B 11 OK OK 340 336 353 339 369 C2' A B 12 OK OK 371 367 386 370 402 C2' G B 13 OK OK 404 400 420 403 436 C2' G B 14 OK OK 438 434 454 437 470 C2' C B 15 OK OK 472 468 485 471 501 C2' C B 16 OK OK 503 499 517 502 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' A A 4 OK OK 103 123 106 107 138 C3' G A 5 OK OK 136 157 139 140 172 C3' G A 6 OK OK 170 191 173 174 206 C3' C A 7 OK OK 204 222 207 208 237 C3' C A 8 OK OK 235 253 238 239 267 C3' G B 9 OK OK 265 286 268 269 302 C3' G B 10 OK OK 300 321 303 304 336 C3' C B 11 OK OK 334 352 337 338 367 C3' A B 12 OK OK 365 385 368 369 400 C3' G B 13 OK OK 398 419 401 402 434 C3' G B 14 OK OK 432 453 435 436 468 C3' C B 15 OK OK 466 484 469 470 499 C3' C B 16 OK OK 497 515 500 501 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' A A 4 OK OK 105 122 102 104 136 C4' G A 5 OK OK 138 156 135 137 170 C4' G A 6 OK OK 172 190 169 171 204 C4' C A 7 OK OK 206 221 203 205 235 C4' C A 8 OK OK 237 252 234 236 265 C4' G B 9 OK OK 267 285 264 266 300 C4' G B 10 OK OK 302 320 299 301 334 C4' C B 11 OK OK 336 351 333 335 365 C4' A B 12 OK OK 367 384 364 366 398 C4' G B 13 OK OK 400 418 397 399 432 C4' G B 14 OK OK 434 452 431 433 466 C4' C B 15 OK OK 468 483 465 467 497 C4' C B 16 OK OK 499 514 496 498 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' A A 4 OK OK 101 120 121 103 135 C5' G A 5 OK OK 134 154 155 136 169 C5' G A 6 OK OK 168 188 189 170 203 C5' C A 7 OK OK 202 219 220 204 234 C5' C A 8 OK OK 233 250 251 235 264 C5' G B 9 OK OK 263 283 284 265 299 C5' G B 10 OK OK 298 318 319 300 333 C5' C B 11 OK OK 332 349 350 334 364 C5' A B 12 OK OK 363 382 383 365 397 C5' G B 13 OK OK 396 416 417 398 431 C5' G B 14 OK OK 430 450 451 432 465 C5' C B 15 OK OK 464 481 482 466 496 C5' C B 16 OK OK 495 512 513 497 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P A A 4 distorted distorted 75 99 100 101 131 P G A 5 distorted distorted 106 132 133 134 165 P G A 6 distorted distorted 139 166 167 168 199 P C A 7 distorted distorted 173 200 201 202 230 P C A 8 distorted distorted 207 231 232 233 295 P G B 10 distorted distorted 268 296 297 298 329 P C B 11 distorted distorted 303 330 331 332 360 P A B 12 distorted distorted 337 361 362 363 393 P G B 13 distorted distorted 368 394 395 396 427 P G B 14 distorted distorted 401 428 429 430 461 P C B 15 distorted distorted 435 462 463 464 492 P C B 16 distorted distorted 469 493 494 495 ---------------------------------------------------------------------------------