ID code: '1F5G' 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' A A 3 alpha beta 70 92 76 73 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' G A 7 alpha beta 202 225 208 205 241 C1' U A 8 alpha beta 236 256 242 239 271 C1' G A 9 alpha beta 266 289 272 269 305 C1' C A 10 alpha beta 300 321 306 303 335 C1' G B 1 alpha beta 330 353 336 333 370 C1' C B 2 alpha beta 365 385 371 368 401 C1' A B 3 alpha beta 396 418 402 399 434 C1' G B 4 alpha beta 429 452 435 432 468 C1' G B 5 alpha beta 463 486 469 466 502 C1' C B 6 alpha beta 497 517 503 500 533 C1' G B 7 alpha beta 528 551 534 531 567 C1' U B 8 alpha beta 562 582 568 565 597 C1' G B 9 alpha beta 592 615 598 595 631 C1' C B 10 alpha beta 626 647 632 629 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 75 71 90 74 106 C2' G A 4 OK OK 108 104 124 107 140 C2' G A 5 OK OK 142 138 158 141 174 C2' C A 6 OK OK 176 172 189 175 205 C2' G A 7 OK OK 207 203 223 206 239 C2' U A 8 OK OK 241 237 254 240 269 C2' G A 9 OK OK 271 267 287 270 303 C2' C A 10 OK OK 305 301 319 304 333 C2' G B 1 OK OK 335 331 351 334 368 C2' C B 2 OK OK 370 366 383 369 399 C2' A B 3 OK OK 401 397 416 400 432 C2' G B 4 OK OK 434 430 450 433 466 C2' G B 5 OK OK 468 464 484 467 500 C2' C B 6 OK OK 502 498 515 501 531 C2' G B 7 OK OK 533 529 549 532 565 C2' U B 8 OK OK 567 563 580 566 595 C2' G B 9 OK OK 597 593 613 596 629 C2' C B 10 OK OK 631 627 645 630 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 69 89 72 73 104 C3' G A 4 OK OK 102 123 105 106 138 C3' G A 5 OK OK 136 157 139 140 172 C3' C A 6 OK OK 170 188 173 174 203 C3' G A 7 OK OK 201 222 204 205 237 C3' U A 8 OK OK 235 253 238 239 267 C3' G A 9 OK OK 265 286 268 269 301 C3' C A 10 OK OK 299 317 302 303 331 C3' G B 1 OK OK 329 350 332 333 366 C3' C B 2 OK OK 364 382 367 368 397 C3' A B 3 OK OK 395 415 398 399 430 C3' G B 4 OK OK 428 449 431 432 464 C3' G B 5 OK OK 462 483 465 466 498 C3' C B 6 OK OK 496 514 499 500 529 C3' G B 7 OK OK 527 548 530 531 563 C3' U B 8 OK OK 561 579 564 565 593 C3' G B 9 OK OK 591 612 594 595 627 C3' C B 10 OK OK 625 643 628 629 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 71 88 68 70 102 C4' G A 4 OK OK 104 122 101 103 136 C4' G A 5 OK OK 138 156 135 137 170 C4' C A 6 OK OK 172 187 169 171 201 C4' G A 7 OK OK 203 221 200 202 235 C4' U A 8 OK OK 237 252 234 236 265 C4' G A 9 OK OK 267 285 264 266 299 C4' C A 10 OK OK 301 316 298 300 329 C4' G B 1 OK OK 331 349 328 330 364 C4' C B 2 OK OK 366 381 363 365 395 C4' A B 3 OK OK 397 414 394 396 428 C4' G B 4 OK OK 430 448 427 429 462 C4' G B 5 OK OK 464 482 461 463 496 C4' C B 6 OK OK 498 513 495 497 527 C4' G B 7 OK OK 529 547 526 528 561 C4' U B 8 OK OK 563 578 560 562 591 C4' G B 9 OK OK 593 611 590 592 625 C4' C B 10 OK OK 627 642 624 626 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 67 86 87 69 101 C5' G A 4 OK OK 100 120 121 102 135 C5' G A 5 OK OK 134 154 155 136 169 C5' C A 6 OK OK 168 185 186 170 200 C5' G A 7 OK OK 199 219 220 201 234 C5' U A 8 OK OK 233 250 251 235 264 C5' G A 9 OK OK 263 283 284 265 298 C5' C A 10 OK OK 297 314 315 299 328 C5' G B 1 OK OK 327 347 348 329 363 C5' C B 2 OK OK 362 379 380 364 394 C5' A B 3 OK OK 393 412 413 395 427 C5' G B 4 OK OK 426 446 447 428 461 C5' G B 5 OK OK 460 480 481 462 495 C5' C B 6 OK OK 494 511 512 496 526 C5' G B 7 OK OK 525 545 546 527 560 C5' U B 8 OK OK 559 576 577 561 590 C5' G B 9 OK OK 589 609 610 591 624 C5' C B 10 OK OK 623 640 641 625 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P A A 3 distorted distorted 41 65 66 67 97 P G A 4 distorted distorted 72 98 99 100 131 P G A 5 distorted distorted 105 132 133 134 165 P C A 6 distorted distorted 139 166 167 168 196 P G A 7 distorted distorted 173 197 198 199 230 P U A 8 distorted distorted 204 231 232 233 260 P G A 9 distorted distorted 238 261 262 263 294 P C A 10 distorted distorted 268 295 296 297 359 P C B 2 distorted distorted 332 360 361 362 390 P A B 3 distorted distorted 367 391 392 393 423 P G B 4 distorted distorted 398 424 425 426 457 P G B 5 distorted distorted 431 458 459 460 491 P C B 6 distorted distorted 465 492 493 494 522 P G B 7 distorted distorted 499 523 524 525 556 P U B 8 distorted distorted 530 557 558 559 586 P G B 9 distorted distorted 564 587 588 589 620 P C B 10 distorted distorted 594 621 622 623 ---------------------------------------------------------------------------------