ID code: '2M4W' 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' A A 3 alpha beta 73 95 79 76 111 C1' A A 4 alpha beta 106 128 112 109 144 C1' U A 5 alpha beta 139 159 145 142 174 C1' C A 6 alpha beta 169 189 175 172 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' A A 8 alpha beta 234 256 240 237 272 C1' A A 9 alpha beta 267 289 273 270 305 C1' A A 10 alpha beta 300 322 306 303 338 C1' G A 11 alpha beta 333 356 339 336 372 C1' A A 12 alpha beta 367 389 373 370 405 C1' U A 13 alpha beta 400 420 406 403 435 C1' G A 14 alpha beta 430 453 436 433 469 C1' U A 15 alpha beta 464 484 470 467 499 C1' C A 16 alpha beta 494 514 500 497 530 C1' C A 17 alpha beta 525 546 531 528 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' A A 4 OK OK 111 107 126 110 142 C2' U A 5 OK OK 144 140 157 143 172 C2' C A 6 OK OK 174 170 187 173 203 C2' G A 7 OK OK 205 201 221 204 237 C2' A A 8 OK OK 239 235 254 238 270 C2' A A 9 OK OK 272 268 287 271 303 C2' A A 10 OK OK 305 301 320 304 336 C2' G A 11 OK OK 338 334 354 337 370 C2' A A 12 OK OK 372 368 387 371 403 C2' U A 13 OK OK 405 401 418 404 433 C2' G A 14 OK OK 435 431 451 434 467 C2' U A 15 OK OK 469 465 482 468 497 C2' C A 16 OK OK 499 495 512 498 528 C2' C A 17 OK OK 530 526 544 529 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' A A 4 OK OK 105 125 108 109 140 C3' U A 5 OK OK 138 156 141 142 170 C3' C A 6 OK OK 168 186 171 172 201 C3' G A 7 OK OK 199 220 202 203 235 C3' A A 8 OK OK 233 253 236 237 268 C3' A A 9 OK OK 266 286 269 270 301 C3' A A 10 OK OK 299 319 302 303 334 C3' G A 11 OK OK 332 353 335 336 368 C3' A A 12 OK OK 366 386 369 370 401 C3' U A 13 OK OK 399 417 402 403 431 C3' G A 14 OK OK 429 450 432 433 465 C3' U A 15 OK OK 463 481 466 467 495 C3' C A 16 OK OK 493 511 496 497 526 C3' C A 17 OK OK 524 542 527 528 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' A A 4 OK OK 107 124 104 106 138 C4' U A 5 OK OK 140 155 137 139 168 C4' C A 6 OK OK 170 185 167 169 199 C4' G A 7 OK OK 201 219 198 200 233 C4' A A 8 OK OK 235 252 232 234 266 C4' A A 9 OK OK 268 285 265 267 299 C4' A A 10 OK OK 301 318 298 300 332 C4' G A 11 OK OK 334 352 331 333 366 C4' A A 12 OK OK 368 385 365 367 399 C4' U A 13 OK OK 401 416 398 400 429 C4' G A 14 OK OK 431 449 428 430 463 C4' U A 15 OK OK 465 480 462 464 493 C4' C A 16 OK OK 495 510 492 494 524 C4' C A 17 OK OK 526 541 523 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' A A 4 OK OK 103 122 123 105 137 C5' U A 5 OK OK 136 153 154 138 167 C5' C A 6 OK OK 166 183 184 168 198 C5' G A 7 OK OK 197 217 218 199 232 C5' A A 8 OK OK 231 250 251 233 265 C5' A A 9 OK OK 264 283 284 266 298 C5' A A 10 OK OK 297 316 317 299 331 C5' G A 11 OK OK 330 350 351 332 365 C5' A A 12 OK OK 364 383 384 366 398 C5' U A 13 OK OK 397 414 415 399 428 C5' G A 14 OK OK 427 447 448 429 462 C5' U A 15 OK OK 461 478 479 463 492 C5' C A 16 OK OK 491 508 509 493 523 C5' C A 17 OK OK 522 539 540 524 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P A A 4 distorted distorted 75 101 102 103 133 P U A 5 distorted distorted 108 134 135 136 163 P C A 6 distorted distorted 141 164 165 166 194 P G A 7 distorted distorted 171 195 196 197 228 P A A 8 distorted distorted 202 229 230 231 261 P A A 9 distorted distorted 236 262 263 264 294 P A A 10 distorted distorted 269 295 296 297 327 P G A 11 distorted distorted 302 328 329 330 361 P A A 12 distorted distorted 335 362 363 364 394 P U A 13 distorted distorted 369 395 396 397 424 P G A 14 distorted distorted 402 425 426 427 458 P U A 15 distorted distorted 432 459 460 461 488 P C A 16 distorted distorted 466 489 490 491 519 P C A 17 distorted distorted 496 520 521 522 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