ID code: '1QAA' 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' --------------------------------------------------------------------------------- 11 C1' T C 1 beta 7 12 10 31 C1' A C 2 beta 27 32 30 52 C1' C C 3 beta 48 53 51 71 C1' T C 4 beta 67 72 70 91 C1' G C 5 beta 87 92 90 113 C1' T C 6 beta 109 114 112 133 C1' A C 7 beta 129 134 132 154 C1' T C 8 beta 150 155 153 174 C1' G C 9 beta 170 175 173 196 C1' A C 10 beta 192 197 195 217 C1' G C 11 beta 213 218 216 239 C1' C C 12 beta 235 240 238 258 C1' A C 13 beta 254 259 257 279 C1' T C 14 beta 275 280 278 299 C1' A C 15 beta 295 300 298 320 C1' C C 16 beta 316 321 319 339 C1' A C 17 beta 335 340 338 360 C1' G C 18 beta 356 361 359 382 C1' T C 19 beta 378 383 381 402 C1' A C 20 beta 398 403 401 424 C1' T D 1 beta 420 425 423 444 C1' A D 2 beta 440 445 443 465 C1' C D 3 beta 461 466 464 484 C1' T D 4 beta 480 485 483 504 C1' G D 5 beta 500 505 503 526 C1' T D 6 beta 522 527 525 546 C1' A D 7 beta 542 547 545 567 C1' T D 8 beta 563 568 566 587 C1' G D 9 beta 583 588 586 609 C1' C D 10 beta 605 610 608 628 C1' T D 11 beta 624 629 627 648 C1' C D 12 beta 644 649 647 667 C1' A D 13 beta 663 668 666 688 C1' T D 14 beta 684 689 687 708 C1' A D 15 beta 704 709 707 729 C1' C D 16 beta 725 730 728 748 C1' A D 17 beta 744 749 747 769 C1' G D 18 beta 765 770 768 791 C1' T D 19 beta 787 792 790 811 C1' A D 20 beta 807 812 810 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T C 1 11 8 30 C2' A C 2 31 28 51 C2' C C 3 52 49 70 C2' T C 4 71 68 90 C2' G C 5 91 88 112 C2' T C 6 113 110 132 C2' A C 7 133 130 153 C2' T C 8 154 151 173 C2' G C 9 174 171 195 C2' A C 10 196 193 216 C2' G C 11 217 214 238 C2' C C 12 239 236 257 C2' A C 13 258 255 278 C2' T C 14 279 276 298 C2' A C 15 299 296 319 C2' C C 16 320 317 338 C2' A C 17 339 336 359 C2' G C 18 360 357 381 C2' T C 19 382 379 401 C2' A C 20 402 399 423 C2' T D 1 424 421 443 C2' A D 2 444 441 464 C2' C D 3 465 462 483 C2' T D 4 484 481 503 C2' G D 5 504 501 525 C2' T D 6 526 523 545 C2' A D 7 546 543 566 C2' T D 8 567 564 586 C2' G D 9 587 584 608 C2' C D 10 609 606 627 C2' T D 11 628 625 647 C2' C D 12 648 645 666 C2' A D 13 667 664 687 C2' T D 14 688 685 707 C2' A D 15 708 705 728 C2' C D 16 729 726 747 C2' A D 17 748 745 768 C2' G D 18 769 766 790 C2' T D 19 791 788 810 C2' A D 20 811 808 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T C 1 OK 6 9 10 28 C3' A C 2 OK 26 29 30 49 C3' C C 3 OK 47 50 51 68 C3' T C 4 OK 66 69 70 88 C3' G C 5 OK 86 89 90 110 C3' T C 6 OK 108 111 112 130 C3' A C 7 OK 128 131 132 151 C3' T C 8 OK 149 152 153 171 C3' G C 9 OK 169 172 173 193 C3' A C 10 OK 191 194 195 214 C3' G C 11 OK 212 215 216 236 C3' C C 12 OK 234 237 238 255 C3' A C 13 OK 253 256 257 276 C3' T C 14 OK 274 277 278 296 C3' A C 15 OK 294 297 298 317 C3' C C 16 OK 315 318 319 336 C3' A C 17 OK 334 337 338 357 C3' G C 18 OK 355 358 359 379 C3' T C 19 OK 377 380 381 399 C3' A C 20 OK 397 400 401 421 C3' T D 1 OK 419 422 423 441 C3' A D 2 OK 439 442 443 462 C3' C D 3 OK 460 463 464 481 C3' T D 4 OK 479 482 483 501 C3' G D 5 OK 499 502 503 523 C3' T D 6 OK 521 524 525 543 C3' A D 7 OK 541 544 545 564 C3' T D 8 OK 562 565 566 584 C3' G D 9 OK 582 585 586 606 C3' C D 10 OK 604 607 608 625 C3' T D 11 OK 623 626 627 645 C3' C D 12 OK 643 646 647 664 C3' A D 13 OK 662 665 666 685 C3' T D 14 OK 683 686 687 705 C3' A D 15 OK 703 706 707 726 C3' C D 16 OK 724 727 728 745 C3' A D 17 OK 743 746 747 766 C3' G D 18 OK 764 767 768 788 C3' T D 19 OK 786 789 790 808 C3' A D 20 OK 806 809 810 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T C 1 OK 8 5 7 26 C4' A C 2 OK 28 25 27 47 C4' C C 3 OK 49 46 48 66 C4' T C 4 OK 68 65 67 86 C4' G C 5 OK 88 85 87 108 C4' T C 6 OK 110 107 109 128 C4' A C 7 OK 130 127 129 149 C4' T C 8 OK 151 148 150 169 C4' G C 9 OK 171 168 170 191 C4' A C 10 OK 193 190 192 212 C4' G C 11 OK 214 211 213 234 C4' C C 12 OK 236 233 235 253 C4' A C 13 OK 255 252 254 274 C4' T C 14 OK 276 273 275 294 C4' A C 15 OK 296 293 295 315 C4' C C 16 OK 317 314 316 334 C4' A C 17 OK 336 333 335 355 C4' G C 18 OK 357 354 356 377 C4' T C 19 OK 379 376 378 397 C4' A C 20 OK 399 396 398 419 C4' T D 1 OK 421 418 420 439 C4' A D 2 OK 441 438 440 460 C4' C D 3 OK 462 459 461 479 C4' T D 4 OK 481 478 480 499 C4' G D 5 OK 501 498 500 521 C4' T D 6 OK 523 520 522 541 C4' A D 7 OK 543 540 542 562 C4' T D 8 OK 564 561 563 582 C4' G D 9 OK 584 581 583 604 C4' C D 10 OK 606 603 605 623 C4' T D 11 OK 625 622 624 643 C4' C D 12 OK 645 642 644 662 C4' A D 13 OK 664 661 663 683 C4' T D 14 OK 685 682 684 703 C4' A D 15 OK 705 702 704 724 C4' C D 16 OK 726 723 725 743 C4' A D 17 OK 745 742 744 764 C4' G D 18 OK 766 763 765 786 C4' T D 19 OK 788 785 787 806 C4' A D 20 OK 808 805 807 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T C 1 4 6 25 C5' A C 2 24 26 46 C5' C C 3 45 47 65 C5' T C 4 64 66 85 C5' G C 5 84 86 107 C5' T C 6 106 108 127 C5' A C 7 126 128 148 C5' T C 8 147 149 168 C5' G C 9 167 169 190 C5' A C 10 189 191 211 C5' G C 11 210 212 233 C5' C C 12 232 234 252 C5' A C 13 251 253 273 C5' T C 14 272 274 293 C5' A C 15 292 294 314 C5' C C 16 313 315 333 C5' A C 17 332 334 354 C5' G C 18 353 355 376 C5' T C 19 375 377 396 C5' A C 20 395 397 418 C5' T D 1 417 419 438 C5' A D 2 437 439 459 C5' C D 3 458 460 478 C5' T D 4 477 479 498 C5' G D 5 497 499 520 C5' T D 6 519 521 540 C5' A D 7 539 541 561 C5' T D 8 560 562 581 C5' G D 9 580 582 603 C5' C D 10 602 604 622 C5' T D 11 621 623 642 C5' C D 12 641 643 661 C5' A D 13 660 662 682 C5' T D 14 681 683 702 C5' A D 15 701 703 723 C5' C D 16 722 724 742 C5' A D 17 741 743 763 C5' G D 18 762 764 785 C5' T D 19 784 786 805 C5' A D 20 804 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T C 1 distorted distorted 2 3 4 21 P A C 2 distorted distorted 9 22 23 24 42 P C C 3 distorted distorted 29 43 44 45 61 P T C 4 distorted distorted 50 62 63 64 81 P G C 5 distorted distorted 69 82 83 84 103 P T C 6 distorted distorted 89 104 105 106 123 P A C 7 distorted distorted 111 124 125 126 144 P T C 8 distorted distorted 131 145 146 147 164 P G C 9 distorted distorted 152 165 166 167 186 P A C 10 distorted distorted 172 187 188 189 207 P G C 11 distorted distorted 194 208 209 210 229 P C C 12 distorted distorted 215 230 231 232 248 P A C 13 distorted distorted 237 249 250 251 269 P T C 14 distorted distorted 256 270 271 272 289 P A C 15 distorted distorted 277 290 291 292 310 P C C 16 distorted distorted 297 311 312 313 329 P A C 17 distorted distorted 318 330 331 332 350 P G C 18 distorted distorted 337 351 352 353 372 P T C 19 distorted distorted 358 373 374 375 392 P A C 20 distorted distorted 380 393 394 395 414 P T D 1 distorted distorted 415 416 417 434 P A D 2 distorted distorted 422 435 436 437 455 P C D 3 distorted distorted 442 456 457 458 474 P T D 4 distorted distorted 463 475 476 477 494 P G D 5 distorted distorted 482 495 496 497 516 P T D 6 distorted distorted 502 517 518 519 536 P A D 7 distorted distorted 524 537 538 539 557 P T D 8 distorted distorted 544 558 559 560 577 P G D 9 distorted distorted 565 578 579 580 599 P C D 10 distorted distorted 585 600 601 602 618 P T D 11 distorted distorted 607 619 620 621 638 P C D 12 distorted distorted 626 639 640 641 657 P A D 13 distorted distorted 646 658 659 660 678 P T D 14 distorted distorted 665 679 680 681 698 P A D 15 distorted distorted 686 699 700 701 719 P C D 16 distorted distorted 706 720 721 722 738 P A D 17 distorted distorted 727 739 740 741 759 P G D 18 distorted distorted 746 760 761 762 781 P T D 19 distorted distorted 767 782 783 784 801 P A D 20 distorted distorted 789 802 803 804 ---------------------------------------------------------------------------------