ID code: '1TK8' 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' DA P 806 beta 7 12 10 32 C1' DC P 807 beta 28 33 31 51 C1' DG P 808 beta 47 52 50 73 C1' DA P 809 beta 69 74 72 94 C1' DC P 810 beta 90 95 93 113 C1' DG P 811 beta 109 114 112 135 C1' DG P 812 beta 131 136 134 157 C1' DC P 813 beta 153 158 156 176 C1' DC P 814 beta 172 177 175 195 C1' DA P 815 beta 191 196 194 216 C1' DG P 816 beta 212 217 215 238 C1' DT P 817 beta 234 239 237 258 C1' DG P 818 beta 254 259 257 280 C1' DC P 819 beta 276 281 279 299 C1' DC P 820 beta 295 300 298 318 C1' DA P 821 beta 314 319 317 338 C1' 2DA P 822 beta 335 339 337 360 C1' DC T 853 beta 356 361 359 379 C1' DA T 854 beta 375 380 378 400 C1' 8OG T 855 beta 396 401 399 423 C1' DT T 856 beta 419 424 422 443 C1' DG T 857 beta 439 444 442 465 C1' DG T 858 beta 461 466 464 487 C1' DC T 859 beta 483 488 486 506 C1' DA T 860 beta 502 507 505 527 C1' DC T 861 beta 523 528 526 546 C1' DT T 862 beta 542 547 545 566 C1' DG T 863 beta 562 567 565 588 C1' DG T 864 beta 584 589 587 610 C1' DC T 865 beta 606 611 609 629 C1' DC T 866 beta 625 630 628 648 C1' DG T 867 beta 644 649 647 669 C1' DT T 868 beta 665 670 668 689 C1' DC T 869 beta 685 690 688 708 C1' DG T 870 beta 704 709 707 730 C1' DT T 871 beta 726 731 729 750 C1' DT T 872 beta 746 751 749 7082 C1' D3T A 823 beta 7081 7083 7092 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' DA P 806 11 8 31 C2' DC P 807 32 29 50 C2' DG P 808 51 48 72 C2' DA P 809 73 70 93 C2' DC P 810 94 91 112 C2' DG P 811 113 110 134 C2' DG P 812 135 132 156 C2' DC P 813 157 154 175 C2' DC P 814 176 173 194 C2' DA P 815 195 192 215 C2' DG P 816 216 213 237 C2' DT P 817 238 235 257 C2' DG P 818 258 255 279 C2' DC P 819 280 277 298 C2' DC P 820 299 296 317 C2' DA P 821 318 315 337 C2' 2DA P 822 338 336 359 C2' DC T 853 360 357 378 C2' DA T 854 379 376 399 C2' 8OG T 855 400 397 422 C2' DT T 856 423 420 442 C2' DG T 857 443 440 464 C2' DG T 858 465 462 486 C2' DC T 859 487 484 505 C2' DA T 860 506 503 526 C2' DC T 861 527 524 545 C2' DT T 862 546 543 565 C2' DG T 863 566 563 587 C2' DG T 864 588 585 609 C2' DC T 865 610 607 628 C2' DC T 866 629 626 647 C2' DG T 867 648 645 668 C2' DT T 868 669 666 688 C2' DC T 869 689 686 707 C2' DG T 870 708 705 729 C2' DT T 871 730 727 749 C2' DT T 872 750 747 7092 C2' D3T A 823 7082 7093 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DA P 806 OK 6 9 10 29 C3' DC P 807 OK 27 30 31 48 C3' DG P 808 OK 46 49 50 70 C3' DA P 809 OK 68 71 72 91 C3' DC P 810 OK 89 92 93 110 C3' DG P 811 OK 108 111 112 132 C3' DG P 812 OK 130 133 134 154 C3' DC P 813 OK 152 155 156 173 C3' DC P 814 OK 171 174 175 192 C3' DA P 815 OK 190 193 194 213 C3' DG P 816 OK 211 214 215 235 C3' DT P 817 OK 233 236 237 255 C3' DG P 818 OK 253 256 257 277 C3' DC P 819 OK 275 278 279 296 C3' DC P 820 OK 294 297 298 315 C3' DA P 821 OK 313 316 317 336 C3' 2DA P 822 334 337 357 C3' DC T 853 OK 355 358 359 376 C3' DA T 854 OK 374 377 378 397 C3' 8OG T 855 OK 395 398 399 420 C3' DT T 856 OK 418 421 422 440 C3' DG T 857 OK 438 441 442 462 C3' DG T 858 OK 460 463 464 484 C3' DC T 859 OK 482 485 486 503 C3' DA T 860 OK 501 504 505 524 C3' DC T 861 OK 522 525 526 543 C3' DT T 862 OK 541 544 545 563 C3' DG T 863 OK 561 564 565 585 C3' DG T 864 OK 583 586 587 607 C3' DC T 865 OK 605 608 609 626 C3' DC T 866 OK 624 627 628 645 C3' DG T 867 OK 643 646 647 666 C3' DT T 868 OK 664 667 668 686 C3' DC T 869 OK 684 687 688 705 C3' DG T 870 OK 703 706 707 727 C3' DT T 871 OK 725 728 729 747 C3' DT T 872 OK 745 748 749 7093 C3' D3T A 823 7080 7092 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DA P 806 OK 8 5 7 27 C4' DC P 807 OK 29 26 28 46 C4' DG P 808 OK 48 45 47 68 C4' DA P 809 OK 70 67 69 89 C4' DC P 810 OK 91 88 90 108 C4' DG P 811 OK 110 107 109 130 C4' DG P 812 OK 132 129 131 152 C4' DC P 813 OK 154 151 153 171 C4' DC P 814 OK 173 170 172 190 C4' DA P 815 OK 192 189 191 211 C4' DG P 816 OK 213 210 212 233 C4' DT P 817 OK 235 232 234 253 C4' DG P 818 OK 255 252 254 275 C4' DC P 819 OK 277 274 276 294 C4' DC P 820 OK 296 293 295 313 C4' DA P 821 OK 315 312 314 334 C4' 2DA P 822 OK 336 333 335 355 C4' DC T 853 OK 357 354 356 374 C4' DA T 854 OK 376 373 375 395 C4' 8OG T 855 OK 397 394 396 418 C4' DT T 856 OK 420 417 419 438 C4' DG T 857 OK 440 437 439 460 C4' DG T 858 OK 462 459 461 482 C4' DC T 859 OK 484 481 483 501 C4' DA T 860 OK 503 500 502 522 C4' DC T 861 OK 524 521 523 541 C4' DT T 862 OK 543 540 542 561 C4' DG T 863 OK 563 560 562 583 C4' DG T 864 OK 585 582 584 605 C4' DC T 865 OK 607 604 606 624 C4' DC T 866 OK 626 623 625 643 C4' DG T 867 OK 645 642 644 664 C4' DT T 868 OK 666 663 665 684 C4' DC T 869 OK 686 683 685 703 C4' DG T 870 OK 705 702 704 725 C4' DT T 871 OK 727 724 726 745 C4' DT T 872 OK 747 744 746 7080 C4' D3T A 823 OK 7093 7079 7081 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' DA P 806 4 6 26 C5' DC P 807 25 27 45 C5' DG P 808 44 46 67 C5' DA P 809 66 68 88 C5' DC P 810 87 89 107 C5' DG P 811 106 108 129 C5' DG P 812 128 130 151 C5' DC P 813 150 152 170 C5' DC P 814 169 171 189 C5' DA P 815 188 190 210 C5' DG P 816 209 211 232 C5' DT P 817 231 233 252 C5' DG P 818 251 253 274 C5' DC P 819 273 275 293 C5' DC P 820 292 294 312 C5' DA P 821 311 313 333 C5' 2DA P 822 332 334 354 C5' DC T 853 353 355 373 C5' DA T 854 372 374 394 C5' 8OG T 855 393 395 417 C5' DT T 856 416 418 437 C5' DG T 857 436 438 459 C5' DG T 858 458 460 481 C5' DC T 859 480 482 500 C5' DA T 860 499 501 521 C5' DC T 861 520 522 540 C5' DT T 862 539 541 560 C5' DG T 863 559 561 582 C5' DG T 864 581 583 604 C5' DC T 865 603 605 623 C5' DC T 866 622 624 642 C5' DG T 867 641 643 663 C5' DT T 868 662 664 683 C5' DC T 869 682 684 702 C5' DG T 870 701 703 724 C5' DT T 871 723 725 744 C5' DT T 872 743 745 7079 C5' D3T A 823 7078 7080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DA P 806 distorted distorted 2 3 4 22 P DC P 807 distorted distorted 9 23 24 25 41 P DG P 808 distorted distorted 30 42 43 44 63 P DA P 809 distorted distorted 49 64 65 66 84 P DC P 810 distorted distorted 71 85 86 87 103 P DG P 811 distorted distorted 92 104 105 106 125 P DG P 812 distorted distorted 111 126 127 128 147 P DC P 813 distorted distorted 133 148 149 150 166 P DC P 814 distorted distorted 155 167 168 169 185 P DA P 815 distorted distorted 174 186 187 188 206 P DG P 816 distorted distorted 193 207 208 209 228 P DT P 817 distorted distorted 214 229 230 231 248 P DG P 818 distorted distorted 236 249 250 251 270 P DC P 819 distorted distorted 256 271 272 273 289 P DC P 820 distorted distorted 278 290 291 292 308 P DA P 821 distorted distorted 297 309 310 311 329 P 2DA P 822 distorted distorted 316 330 331 332 350 P DC T 853 OK OK 351 352 353 369 P DA T 854 distorted distorted 358 370 371 372 390 P 8OG T 855 distorted distorted 377 391 392 393 413 P DT T 856 distorted distorted 398 414 415 416 433 P DG T 857 distorted distorted 421 434 435 436 455 P DG T 858 distorted distorted 441 456 457 458 477 P DC T 859 distorted distorted 463 478 479 480 496 P DA T 860 distorted distorted 485 497 498 499 517 P DC T 861 distorted distorted 504 518 519 520 536 P DT T 862 distorted distorted 525 537 538 539 556 P DG T 863 distorted distorted 544 557 558 559 578 P DG T 864 distorted distorted 564 579 580 581 600 P DC T 865 distorted distorted 586 601 602 603 619 P DC T 866 distorted distorted 608 620 621 622 638 P DG T 867 distorted distorted 627 639 640 641 660 P DT T 868 646 661 662 679 P DC T 869 distorted distorted 667 680 681 682 698 P DG T 870 distorted distorted 687 699 700 701 720 P DT T 871 distorted distorted 706 721 722 723 740 P DT T 872 distorted distorted 728 741 742 743 ---------------------------------------------------------------------------------