ID code: '1MIS' 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' C A 2 alpha beta 39 59 45 42 75 C1' G A 3 alpha beta 70 93 76 73 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' G A 7 alpha beta 202 225 208 205 241 C1' C A 8 alpha beta 236 257 242 239 271 C1' G B 9 alpha beta 266 289 272 269 306 C1' C B 10 alpha beta 301 321 307 304 337 C1' G B 11 alpha beta 332 355 338 335 371 C1' G B 12 alpha beta 366 389 372 369 405 C1' A B 13 alpha beta 400 422 406 403 438 C1' C B 14 alpha beta 433 453 439 436 469 C1' G B 15 alpha beta 464 487 470 467 503 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' C A 2 OK OK 44 40 57 43 73 C2' G A 3 OK OK 75 71 91 74 107 C2' G A 4 OK OK 109 105 125 108 141 C2' A A 5 OK OK 143 139 158 142 174 C2' C A 6 OK OK 176 172 189 175 205 C2' G A 7 OK OK 207 203 223 206 239 C2' C A 8 OK OK 241 237 255 240 269 C2' G B 9 OK OK 271 267 287 270 304 C2' C B 10 OK OK 306 302 319 305 335 C2' G B 11 OK OK 337 333 353 336 369 C2' G B 12 OK OK 371 367 387 370 403 C2' A B 13 OK OK 405 401 420 404 436 C2' C B 14 OK OK 438 434 451 437 467 C2' G B 15 OK OK 469 465 485 468 501 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' C A 2 OK OK 38 56 41 42 71 C3' G A 3 OK OK 69 90 72 73 105 C3' G A 4 OK OK 103 124 106 107 139 C3' A A 5 OK OK 137 157 140 141 172 C3' C A 6 OK OK 170 188 173 174 203 C3' G A 7 OK OK 201 222 204 205 237 C3' C A 8 OK OK 235 253 238 239 267 C3' G B 9 OK OK 265 286 268 269 302 C3' C B 10 OK OK 300 318 303 304 333 C3' G B 11 OK OK 331 352 334 335 367 C3' G B 12 OK OK 365 386 368 369 401 C3' A B 13 OK OK 399 419 402 403 434 C3' C B 14 OK OK 432 450 435 436 465 C3' G B 15 OK OK 463 484 466 467 499 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' C A 2 OK OK 40 55 37 39 69 C4' G A 3 OK OK 71 89 68 70 103 C4' G A 4 OK OK 105 123 102 104 137 C4' A A 5 OK OK 139 156 136 138 170 C4' C A 6 OK OK 172 187 169 171 201 C4' G A 7 OK OK 203 221 200 202 235 C4' C A 8 OK OK 237 252 234 236 265 C4' G B 9 OK OK 267 285 264 266 300 C4' C B 10 OK OK 302 317 299 301 331 C4' G B 11 OK OK 333 351 330 332 365 C4' G B 12 OK OK 367 385 364 366 399 C4' A B 13 OK OK 401 418 398 400 432 C4' C B 14 OK OK 434 449 431 433 463 C4' G B 15 OK OK 465 483 462 464 497 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' C A 2 OK OK 36 53 54 38 68 C5' G A 3 OK OK 67 87 88 69 102 C5' G A 4 OK OK 101 121 122 103 136 C5' A A 5 OK OK 135 154 155 137 169 C5' C A 6 OK OK 168 185 186 170 200 C5' G A 7 OK OK 199 219 220 201 234 C5' C A 8 OK OK 233 250 251 235 264 C5' G B 9 OK OK 263 283 284 265 299 C5' C B 10 OK OK 298 315 316 300 330 C5' G B 11 OK OK 329 349 350 331 364 C5' G B 12 OK OK 363 383 384 365 398 C5' A B 13 OK OK 397 416 417 399 431 C5' C B 14 OK OK 430 447 448 432 462 C5' G B 15 OK OK 461 481 482 463 496 C5' C B 16 OK OK 495 512 513 497 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P G A 3 distorted distorted 41 65 66 67 98 P G A 4 distorted distorted 72 99 100 101 132 P A A 5 distorted distorted 106 133 134 135 165 P C A 6 distorted distorted 140 166 167 168 196 P G A 7 distorted distorted 173 197 198 199 230 P C A 8 distorted distorted 204 231 232 233 295 P C B 10 distorted distorted 268 296 297 298 326 P G B 11 distorted distorted 303 327 328 329 360 P G B 12 distorted distorted 334 361 362 363 394 P A B 13 distorted distorted 368 395 396 397 427 P C B 14 distorted distorted 402 428 429 430 458 P G B 15 distorted distorted 435 459 460 461 492 P C B 16 distorted distorted 466 493 494 495 ---------------------------------------------------------------------------------