ID code: '1Q2M' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 alpha beta 7 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' C A 3 alpha beta 75 95 81 78 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' G A 5 alpha beta 140 163 146 143 179 C1' U A 6 alpha beta 174 194 180 177 209 C1' U A 7 alpha beta 204 224 210 207 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' C A 9 alpha beta 268 288 274 271 304 C1' A A 10 alpha beta 299 321 305 302 337 C1' G A 11 alpha beta 332 355 338 335 371 C1' G A 12 alpha beta 366 389 372 369 405 C1' U A 13 alpha beta 400 420 406 403 435 C1' C A 14 alpha beta 430 450 436 433 466 C1' U A 15 alpha beta 461 481 467 464 496 C1' G A 16 alpha beta 491 514 497 494 530 C1' C A 17 alpha beta 525 545 531 528 561 C1' A A 18 alpha beta 556 578 562 559 594 C1' C A 19 alpha beta 589 609 595 592 625 C1' C A 20 alpha beta 620 640 626 623 656 C1' G A 21 alpha beta 651 674 657 654 690 C1' C A 22 alpha beta 685 705 691 688 721 C1' C A 23 alpha beta 716 736 722 719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' G A 2 OK OK 46 42 62 45 78 C2' C A 3 OK OK 80 76 93 79 109 C2' G A 4 OK OK 111 107 127 110 143 C2' G A 5 OK OK 145 141 161 144 177 C2' U A 6 OK OK 179 175 192 178 207 C2' U A 7 OK OK 209 205 222 208 237 C2' G A 8 OK OK 239 235 255 238 271 C2' C A 9 OK OK 273 269 286 272 302 C2' A A 10 OK OK 304 300 319 303 335 C2' G A 11 OK OK 337 333 353 336 369 C2' G A 12 OK OK 371 367 387 370 403 C2' U A 13 OK OK 405 401 418 404 433 C2' C A 14 OK OK 435 431 448 434 464 C2' U A 15 OK OK 466 462 479 465 494 C2' G A 16 OK OK 496 492 512 495 528 C2' C A 17 OK OK 530 526 543 529 559 C2' A A 18 OK OK 561 557 576 560 592 C2' C A 19 OK OK 594 590 607 593 623 C2' C A 20 OK OK 625 621 638 624 654 C2' G A 21 OK OK 656 652 672 655 688 C2' C A 22 OK OK 690 686 703 689 719 C2' C A 23 OK OK 721 717 734 720 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' C A 3 OK OK 74 92 77 78 107 C3' G A 4 OK OK 105 126 108 109 141 C3' G A 5 OK OK 139 160 142 143 175 C3' U A 6 OK OK 173 191 176 177 205 C3' U A 7 OK OK 203 221 206 207 235 C3' G A 8 OK OK 233 254 236 237 269 C3' C A 9 OK OK 267 285 270 271 300 C3' A A 10 OK OK 298 318 301 302 333 C3' G A 11 OK OK 331 352 334 335 367 C3' G A 12 OK OK 365 386 368 369 401 C3' U A 13 OK OK 399 417 402 403 431 C3' C A 14 OK OK 429 447 432 433 462 C3' U A 15 OK OK 460 478 463 464 492 C3' G A 16 OK OK 490 511 493 494 526 C3' C A 17 OK OK 524 542 527 528 557 C3' A A 18 OK OK 555 575 558 559 590 C3' C A 19 OK OK 588 606 591 592 621 C3' C A 20 OK OK 619 637 622 623 652 C3' G A 21 OK OK 650 671 653 654 686 C3' C A 22 OK OK 684 702 687 688 717 C3' C A 23 OK OK 715 733 718 719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' C A 3 OK OK 76 91 73 75 105 C4' G A 4 OK OK 107 125 104 106 139 C4' G A 5 OK OK 141 159 138 140 173 C4' U A 6 OK OK 175 190 172 174 203 C4' U A 7 OK OK 205 220 202 204 233 C4' G A 8 OK OK 235 253 232 234 267 C4' C A 9 OK OK 269 284 266 268 298 C4' A A 10 OK OK 300 317 297 299 331 C4' G A 11 OK OK 333 351 330 332 365 C4' G A 12 OK OK 367 385 364 366 399 C4' U A 13 OK OK 401 416 398 400 429 C4' C A 14 OK OK 431 446 428 430 460 C4' U A 15 OK OK 462 477 459 461 490 C4' G A 16 OK OK 492 510 489 491 524 C4' C A 17 OK OK 526 541 523 525 555 C4' A A 18 OK OK 557 574 554 556 588 C4' C A 19 OK OK 590 605 587 589 619 C4' C A 20 OK OK 621 636 618 620 650 C4' G A 21 OK OK 652 670 649 651 684 C4' C A 22 OK OK 686 701 683 685 715 C4' C A 23 OK OK 717 732 714 716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' G A 2 OK OK 38 58 59 40 73 C5' C A 3 OK OK 72 89 90 74 104 C5' G A 4 OK OK 103 123 124 105 138 C5' G A 5 OK OK 137 157 158 139 172 C5' U A 6 OK OK 171 188 189 173 202 C5' U A 7 OK OK 201 218 219 203 232 C5' G A 8 OK OK 231 251 252 233 266 C5' C A 9 OK OK 265 282 283 267 297 C5' A A 10 OK OK 296 315 316 298 330 C5' G A 11 OK OK 329 349 350 331 364 C5' G A 12 OK OK 363 383 384 365 398 C5' U A 13 OK OK 397 414 415 399 428 C5' C A 14 OK OK 427 444 445 429 459 C5' U A 15 OK OK 458 475 476 460 489 C5' G A 16 OK OK 488 508 509 490 523 C5' C A 17 OK OK 522 539 540 524 554 C5' A A 18 OK OK 553 572 573 555 587 C5' C A 19 OK OK 586 603 604 588 618 C5' C A 20 OK OK 617 634 635 619 649 C5' G A 21 OK OK 648 668 669 650 683 C5' C A 22 OK OK 682 699 700 684 714 C5' C A 23 OK OK 713 730 731 715 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P C A 3 distorted distorted 43 70 71 72 100 P G A 4 distorted distorted 77 101 102 103 134 P G A 5 distorted distorted 108 135 136 137 168 P U A 6 distorted distorted 142 169 170 171 198 P U A 7 distorted distorted 176 199 200 201 228 P G A 8 distorted distorted 206 229 230 231 262 P C A 9 distorted distorted 236 263 264 265 293 P A A 10 distorted distorted 270 294 295 296 326 P G A 11 distorted distorted 301 327 328 329 360 P G A 12 distorted distorted 334 361 362 363 394 P U A 13 distorted distorted 368 395 396 397 424 P C A 14 distorted distorted 402 425 426 427 455 P U A 15 distorted distorted 432 456 457 458 485 P G A 16 distorted distorted 463 486 487 488 519 P C A 17 distorted distorted 493 520 521 522 550 P A A 18 distorted distorted 527 551 552 553 583 P C A 19 distorted distorted 558 584 585 586 614 P C A 20 distorted distorted 591 615 616 617 645 P G A 21 distorted distorted 622 646 647 648 679 P C A 22 distorted distorted 653 680 681 682 710 P C A 23 distorted distorted 687 711 712 713 ---------------------------------------------------------------------------------