ID code: '1TKD' 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' DC P 807 beta 7 12 10 30 C1' DG P 808 beta 26 31 29 52 C1' DA P 809 beta 48 53 51 73 C1' DC P 810 beta 69 74 72 92 C1' DG P 811 beta 88 93 91 114 C1' DG P 812 beta 110 115 113 136 C1' DC P 813 beta 132 137 135 155 C1' DC P 814 beta 151 156 154 174 C1' DA P 815 beta 170 175 173 195 C1' DG P 816 beta 191 196 194 217 C1' DT P 817 beta 213 218 216 237 C1' DG P 818 beta 233 238 236 259 C1' DC P 819 beta 255 260 258 278 C1' DC P 820 beta 274 279 277 297 C1' DA P 821 beta 293 298 296 316 C1' DOC P 822 beta 320 308 317 337 C1' DC T 853 beta 333 338 336 356 C1' DA T 854 beta 352 357 355 377 C1' 8OG T 855 beta 373 378 376 400 C1' DT T 856 beta 396 401 399 420 C1' DG T 857 beta 416 421 419 442 C1' DG T 858 beta 438 443 441 464 C1' DC T 859 beta 460 465 463 483 C1' DA T 860 beta 479 484 482 504 C1' DC T 861 beta 500 505 503 523 C1' DT T 862 beta 519 524 522 543 C1' DG T 863 beta 539 544 542 565 C1' DG T 864 beta 561 566 564 587 C1' DC T 865 beta 583 588 586 606 C1' DC T 866 beta 602 607 605 625 C1' DG T 867 beta 621 626 624 647 C1' DT T 868 beta 643 648 646 667 C1' DC T 869 beta 663 668 666 686 C1' DG T 870 beta 682 687 685 708 C1' DT T 871 beta 704 709 707 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' DC P 807 11 8 29 C2' DG P 808 30 27 51 C2' DA P 809 52 49 72 C2' DC P 810 73 70 91 C2' DG P 811 92 89 113 C2' DG P 812 114 111 135 C2' DC P 813 136 133 154 C2' DC P 814 155 152 173 C2' DA P 815 174 171 194 C2' DG P 816 195 192 216 C2' DT P 817 217 214 236 C2' DG P 818 237 234 258 C2' DC P 819 259 256 277 C2' DC P 820 278 275 296 C2' DA P 821 297 294 317 C2' DOC P 822 316 318 336 C2' DC T 853 337 334 355 C2' DA T 854 356 353 376 C2' 8OG T 855 377 374 399 C2' DT T 856 400 397 419 C2' DG T 857 420 417 441 C2' DG T 858 442 439 463 C2' DC T 859 464 461 482 C2' DA T 860 483 480 503 C2' DC T 861 504 501 522 C2' DT T 862 523 520 542 C2' DG T 863 543 540 564 C2' DG T 864 565 562 586 C2' DC T 865 587 584 605 C2' DC T 866 606 603 624 C2' DG T 867 625 622 646 C2' DT T 868 647 644 666 C2' DC T 869 667 664 685 C2' DG T 870 686 683 707 C2' DT T 871 708 705 7092 C2' D3T A 823 7082 7093 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DC P 807 OK 6 9 10 27 C3' DG P 808 OK 25 28 29 49 C3' DA P 809 OK 47 50 51 70 C3' DC P 810 OK 68 71 72 89 C3' DG P 811 OK 87 90 91 111 C3' DG P 812 OK 109 112 113 133 C3' DC P 813 OK 131 134 135 152 C3' DC P 814 OK 150 153 154 171 C3' DA P 815 OK 169 172 173 192 C3' DG P 816 OK 190 193 194 214 C3' DT P 817 OK 212 215 216 234 C3' DG P 818 OK 232 235 236 256 C3' DC P 819 OK 254 257 258 275 C3' DC P 820 OK 273 276 277 294 C3' DA P 821 OK 292 295 296 318 C3' DOC P 822 319 317 334 C3' DC T 853 OK 332 335 336 353 C3' DA T 854 OK 351 354 355 374 C3' 8OG T 855 OK 372 375 376 397 C3' DT T 856 OK 395 398 399 417 C3' DG T 857 OK 415 418 419 439 C3' DG T 858 OK 437 440 441 461 C3' DC T 859 OK 459 462 463 480 C3' DA T 860 OK 478 481 482 501 C3' DC T 861 OK 499 502 503 520 C3' DT T 862 OK 518 521 522 540 C3' DG T 863 OK 538 541 542 562 C3' DG T 864 OK 560 563 564 584 C3' DC T 865 OK 582 585 586 603 C3' DC T 866 OK 601 604 605 622 C3' DG T 867 OK 620 623 624 644 C3' DT T 868 OK 642 645 646 664 C3' DC T 869 OK 662 665 666 683 C3' DG T 870 OK 681 684 685 705 C3' DT T 871 OK 703 706 707 7093 C3' D3T A 823 7080 7092 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DC P 807 OK 8 5 7 25 C4' DG P 808 OK 27 24 26 47 C4' DA P 809 OK 49 46 48 68 C4' DC P 810 OK 70 67 69 87 C4' DG P 811 OK 89 86 88 109 C4' DG P 812 OK 111 108 110 131 C4' DC P 813 OK 133 130 132 150 C4' DC P 814 OK 152 149 151 169 C4' DA P 815 OK 171 168 170 190 C4' DG P 816 OK 192 189 191 212 C4' DT P 817 OK 214 211 213 232 C4' DG P 818 OK 234 231 233 254 C4' DC P 819 OK 256 253 255 273 C4' DC P 820 OK 275 272 274 292 C4' DA P 821 OK 294 291 293 319 C4' DOC P 822 OK 318 321 320 332 C4' DC T 853 OK 334 331 333 351 C4' DA T 854 OK 353 350 352 372 C4' 8OG T 855 OK 374 371 373 395 C4' DT T 856 OK 397 394 396 415 C4' DG T 857 OK 417 414 416 437 C4' DG T 858 OK 439 436 438 459 C4' DC T 859 OK 461 458 460 478 C4' DA T 860 OK 480 477 479 499 C4' DC T 861 OK 501 498 500 518 C4' DT T 862 OK 520 517 519 538 C4' DG T 863 OK 540 537 539 560 C4' DG T 864 OK 562 559 561 582 C4' DC T 865 OK 584 581 583 601 C4' DC T 866 OK 603 600 602 620 C4' DG T 867 OK 622 619 621 642 C4' DT T 868 OK 644 641 643 662 C4' DC T 869 OK 664 661 663 681 C4' DG T 870 OK 683 680 682 703 C4' DT T 871 OK 705 702 704 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' DC P 807 4 6 24 C5' DG P 808 23 25 46 C5' DA P 809 45 47 67 C5' DC P 810 66 68 86 C5' DG P 811 85 87 108 C5' DG P 812 107 109 130 C5' DC P 813 129 131 149 C5' DC P 814 148 150 168 C5' DA P 815 167 169 189 C5' DG P 816 188 190 211 C5' DT P 817 210 212 231 C5' DG P 818 230 232 253 C5' DC P 819 252 254 272 C5' DC P 820 271 273 291 C5' DA P 821 290 292 321 C5' DOC P 822 322 319 331 C5' DC T 853 330 332 350 C5' DA T 854 349 351 371 C5' 8OG T 855 370 372 394 C5' DT T 856 393 395 414 C5' DG T 857 413 415 436 C5' DG T 858 435 437 458 C5' DC T 859 457 459 477 C5' DA T 860 476 478 498 C5' DC T 861 497 499 517 C5' DT T 862 516 518 537 C5' DG T 863 536 538 559 C5' DG T 864 558 560 581 C5' DC T 865 580 582 600 C5' DC T 866 599 601 619 C5' DG T 867 618 620 641 C5' DT T 868 640 642 661 C5' DC T 869 660 662 680 C5' DG T 870 679 681 702 C5' DT T 871 701 703 7079 C5' D3T A 823 7078 7080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DC P 807 distorted distorted 2 3 4 20 P DG P 808 distorted distorted 9 21 22 23 42 P DA P 809 distorted distorted 28 43 44 45 63 P DC P 810 distorted distorted 50 64 65 66 82 P DG P 811 distorted distorted 71 83 84 85 104 P DG P 812 distorted distorted 90 105 106 107 126 P DC P 813 distorted distorted 112 127 128 129 145 P DC P 814 distorted distorted 134 146 147 148 164 P DA P 815 distorted distorted 153 165 166 167 185 P DG P 816 distorted distorted 172 186 187 188 207 P DT P 817 distorted distorted 193 208 209 210 227 P DG P 818 distorted distorted 215 228 229 230 249 P DC P 819 distorted distorted 235 250 251 252 268 P DC P 820 distorted distorted 257 269 270 271 287 P DA P 821 distorted distorted 276 288 289 290 323 P DOC P 822 distorted distorted 295 324 325 322 327 P DC T 853 OK OK 328 329 330 346 P DA T 854 distorted distorted 335 347 348 349 367 P 8OG T 855 distorted distorted 354 368 369 370 390 P DT T 856 distorted distorted 375 391 392 393 410 P DG T 857 distorted distorted 398 411 412 413 432 P DG T 858 distorted distorted 418 433 434 435 454 P DC T 859 distorted distorted 440 455 456 457 473 P DA T 860 distorted distorted 462 474 475 476 494 P DC T 861 distorted distorted 481 495 496 497 513 P DT T 862 distorted distorted 502 514 515 516 533 P DG T 863 distorted distorted 521 534 535 536 555 P DG T 864 distorted distorted 541 556 557 558 577 P DC T 865 distorted distorted 563 578 579 580 596 P DC T 866 distorted distorted 585 597 598 599 615 P DG T 867 distorted distorted 604 616 617 618 637 P DT T 868 distorted distorted 623 638 639 640 657 P DC T 869 distorted distorted 645 658 659 660 676 P DG T 870 distorted distorted 665 677 678 679 698 P DT T 871 distorted distorted 684 699 700 701 ---------------------------------------------------------------------------------