ID code: '1TJZ' 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 5 alpha beta 4 27 10 7 44 C1' G A 6 alpha beta 39 62 45 42 78 C1' U A 7 alpha beta 73 93 79 76 108 C1' G A 8 alpha beta 103 126 109 106 142 C1' A A 9 alpha beta 137 159 143 140 175 C1' C A 10 alpha beta 170 190 176 173 206 C1' G A 11 alpha beta 201 224 207 204 240 C1' C A 12 alpha beta 235 255 241 238 271 C1' C A 13 alpha beta 266 286 272 269 302 C1' G A 14 alpha beta 297 320 303 300 336 C1' U A 15 alpha beta 331 351 337 334 366 C1' A A 16 alpha beta 361 383 367 364 399 C1' A A 17 alpha beta 394 416 400 397 432 C1' G A 18 alpha beta 427 450 433 430 466 C1' G A 19 alpha beta 461 484 467 464 500 C1' C A 20 alpha beta 495 515 501 498 531 C1' G A 21 alpha beta 526 549 532 529 565 C1' C A 22 alpha beta 560 580 566 563 596 C1' A A 23 alpha beta 591 613 597 594 629 C1' G A 24 alpha beta 624 647 630 627 663 C1' C A 25 alpha beta 658 678 664 661 694 C1' C A 26 alpha beta 689 710 695 692 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 5 OK OK 9 5 25 8 42 C2' G A 6 OK OK 44 40 60 43 76 C2' U A 7 OK OK 78 74 91 77 106 C2' G A 8 OK OK 108 104 124 107 140 C2' A A 9 OK OK 142 138 157 141 173 C2' C A 10 OK OK 175 171 188 174 204 C2' G A 11 OK OK 206 202 222 205 238 C2' C A 12 OK OK 240 236 253 239 269 C2' C A 13 OK OK 271 267 284 270 300 C2' G A 14 OK OK 302 298 318 301 334 C2' U A 15 OK OK 336 332 349 335 364 C2' A A 16 OK OK 366 362 381 365 397 C2' A A 17 OK OK 399 395 414 398 430 C2' G A 18 OK OK 432 428 448 431 464 C2' G A 19 OK OK 466 462 482 465 498 C2' C A 20 OK OK 500 496 513 499 529 C2' G A 21 OK OK 531 527 547 530 563 C2' C A 22 OK OK 565 561 578 564 594 C2' A A 23 OK OK 596 592 611 595 627 C2' G A 24 OK OK 629 625 645 628 661 C2' C A 25 OK OK 663 659 676 662 692 C2' C A 26 OK OK 694 690 708 693 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 5 OK OK 3 24 6 7 40 C3' G A 6 OK OK 38 59 41 42 74 C3' U A 7 OK OK 72 90 75 76 104 C3' G A 8 OK OK 102 123 105 106 138 C3' A A 9 OK OK 136 156 139 140 171 C3' C A 10 OK OK 169 187 172 173 202 C3' G A 11 OK OK 200 221 203 204 236 C3' C A 12 OK OK 234 252 237 238 267 C3' C A 13 OK OK 265 283 268 269 298 C3' G A 14 OK OK 296 317 299 300 332 C3' U A 15 OK OK 330 348 333 334 362 C3' A A 16 OK OK 360 380 363 364 395 C3' A A 17 OK OK 393 413 396 397 428 C3' G A 18 OK OK 426 447 429 430 462 C3' G A 19 OK OK 460 481 463 464 496 C3' C A 20 OK OK 494 512 497 498 527 C3' G A 21 OK OK 525 546 528 529 561 C3' C A 22 OK OK 559 577 562 563 592 C3' A A 23 OK OK 590 610 593 594 625 C3' G A 24 OK OK 623 644 626 627 659 C3' C A 25 OK OK 657 675 660 661 690 C3' C A 26 OK OK 688 706 691 692 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 5 OK OK 5 23 2 4 38 C4' G A 6 OK OK 40 58 37 39 72 C4' U A 7 OK OK 74 89 71 73 102 C4' G A 8 OK OK 104 122 101 103 136 C4' A A 9 OK OK 138 155 135 137 169 C4' C A 10 OK OK 171 186 168 170 200 C4' G A 11 OK OK 202 220 199 201 234 C4' C A 12 OK OK 236 251 233 235 265 C4' C A 13 OK OK 267 282 264 266 296 C4' G A 14 OK OK 298 316 295 297 330 C4' U A 15 OK OK 332 347 329 331 360 C4' A A 16 OK OK 362 379 359 361 393 C4' A A 17 OK OK 395 412 392 394 426 C4' G A 18 OK OK 428 446 425 427 460 C4' G A 19 OK OK 462 480 459 461 494 C4' C A 20 OK OK 496 511 493 495 525 C4' G A 21 OK OK 527 545 524 526 559 C4' C A 22 OK OK 561 576 558 560 590 C4' A A 23 OK OK 592 609 589 591 623 C4' G A 24 OK OK 625 643 622 624 657 C4' C A 25 OK OK 659 674 656 658 688 C4' C A 26 OK OK 690 705 687 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 5 OK OK 1 21 22 3 37 C5' G A 6 OK OK 36 56 57 38 71 C5' U A 7 OK OK 70 87 88 72 101 C5' G A 8 OK OK 100 120 121 102 135 C5' A A 9 OK OK 134 153 154 136 168 C5' C A 10 OK OK 167 184 185 169 199 C5' G A 11 OK OK 198 218 219 200 233 C5' C A 12 OK OK 232 249 250 234 264 C5' C A 13 OK OK 263 280 281 265 295 C5' G A 14 OK OK 294 314 315 296 329 C5' U A 15 OK OK 328 345 346 330 359 C5' A A 16 OK OK 358 377 378 360 392 C5' A A 17 OK OK 391 410 411 393 425 C5' G A 18 OK OK 424 444 445 426 459 C5' G A 19 OK OK 458 478 479 460 493 C5' C A 20 OK OK 492 509 510 494 524 C5' G A 21 OK OK 523 543 544 525 558 C5' C A 22 OK OK 557 574 575 559 589 C5' A A 23 OK OK 588 607 608 590 622 C5' G A 24 OK OK 621 641 642 623 656 C5' C A 25 OK OK 655 672 673 657 687 C5' C A 26 OK OK 686 703 704 688 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 6 distorted distorted 6 34 35 36 67 P U A 7 distorted distorted 41 68 69 70 97 P G A 8 distorted distorted 75 98 99 100 131 P A A 9 distorted distorted 105 132 133 134 164 P C A 10 distorted distorted 139 165 166 167 195 P G A 11 distorted distorted 172 196 197 198 229 P C A 12 distorted distorted 203 230 231 232 260 P C A 13 distorted distorted 237 261 262 263 291 P G A 14 distorted distorted 268 292 293 294 325 P U A 15 distorted distorted 299 326 327 328 355 P A A 16 distorted distorted 333 356 357 358 388 P A A 17 distorted distorted 363 389 390 391 421 P G A 18 distorted distorted 396 422 423 424 455 P G A 19 distorted distorted 429 456 457 458 489 P C A 20 distorted distorted 463 490 491 492 520 P G A 21 distorted distorted 497 521 522 523 554 P C A 22 distorted distorted 528 555 556 557 585 P A A 23 distorted distorted 562 586 587 588 618 P G A 24 distorted distorted 593 619 620 621 652 P C A 25 distorted distorted 626 653 654 655 683 P C A 26 distorted distorted 660 684 685 686 ---------------------------------------------------------------------------------