ID code: '1H6F' 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' A C 3 beta 7 12 10 32 C1' T C 4 beta 28 33 31 52 C1' T C 5 beta 48 53 51 72 C1' T C 6 beta 68 73 71 92 C1' C C 7 beta 88 93 91 111 C1' A C 8 beta 107 112 110 132 C1' C C 9 beta 128 133 131 151 C1' A C 10 beta 147 152 150 172 C1' C C 11 beta 168 173 171 191 C1' C C 12 beta 187 192 190 210 C1' T C 13 beta 206 211 209 230 C1' A C 14 beta 226 231 229 251 C1' G C 15 beta 247 252 250 273 C1' G C 16 beta 269 274 272 295 C1' T C 17 beta 291 296 294 315 C1' G C 18 beta 311 316 314 337 C1' T C 19 beta 333 338 336 357 C1' G C 20 beta 353 358 356 379 C1' A C 21 beta 375 380 378 400 C1' A C 22 beta 396 401 399 421 C1' A C 23 beta 417 422 420 442 C1' T C 24 beta 438 443 441 463 C1' A D 3 beta 459 464 462 484 C1' T D 4 beta 480 485 483 504 C1' T D 5 beta 500 505 503 524 C1' T D 6 beta 520 525 523 544 C1' C D 7 beta 540 545 543 563 C1' A D 8 beta 559 564 562 584 C1' C D 9 beta 580 585 583 603 C1' A D 10 beta 599 604 602 624 C1' C D 11 beta 620 625 623 643 C1' C D 12 beta 639 644 642 662 C1' T D 13 beta 658 663 661 682 C1' A D 14 beta 678 683 681 703 C1' G D 15 beta 699 704 702 725 C1' G D 16 beta 721 726 724 747 C1' T D 17 beta 743 748 746 767 C1' G D 18 beta 763 768 766 789 C1' T D 19 beta 785 790 788 809 C1' G D 20 beta 805 810 808 831 C1' A D 21 beta 827 832 830 852 C1' A D 22 beta 848 853 851 873 C1' A D 23 beta 869 874 872 894 C1' T D 24 beta 890 895 893 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A C 3 11 8 31 C2' T C 4 32 29 51 C2' T C 5 52 49 71 C2' T C 6 72 69 91 C2' C C 7 92 89 110 C2' A C 8 111 108 131 C2' C C 9 132 129 150 C2' A C 10 151 148 171 C2' C C 11 172 169 190 C2' C C 12 191 188 209 C2' T C 13 210 207 229 C2' A C 14 230 227 250 C2' G C 15 251 248 272 C2' G C 16 273 270 294 C2' T C 17 295 292 314 C2' G C 18 315 312 336 C2' T C 19 337 334 356 C2' G C 20 357 354 378 C2' A C 21 379 376 399 C2' A C 22 400 397 420 C2' A C 23 421 418 441 C2' T C 24 442 439 462 C2' A D 3 463 460 483 C2' T D 4 484 481 503 C2' T D 5 504 501 523 C2' T D 6 524 521 543 C2' C D 7 544 541 562 C2' A D 8 563 560 583 C2' C D 9 584 581 602 C2' A D 10 603 600 623 C2' C D 11 624 621 642 C2' C D 12 643 640 661 C2' T D 13 662 659 681 C2' A D 14 682 679 702 C2' G D 15 703 700 724 C2' G D 16 725 722 746 C2' T D 17 747 744 766 C2' G D 18 767 764 788 C2' T D 19 789 786 808 C2' G D 20 809 806 830 C2' A D 21 831 828 851 C2' A D 22 852 849 872 C2' A D 23 873 870 893 C2' T D 24 894 891 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A C 3 OK 6 9 10 29 C3' T C 4 OK 27 30 31 49 C3' T C 5 OK 47 50 51 69 C3' T C 6 OK 67 70 71 89 C3' C C 7 OK 87 90 91 108 C3' A C 8 OK 106 109 110 129 C3' C C 9 OK 127 130 131 148 C3' A C 10 OK 146 149 150 169 C3' C C 11 OK 167 170 171 188 C3' C C 12 OK 186 189 190 207 C3' T C 13 OK 205 208 209 227 C3' A C 14 OK 225 228 229 248 C3' G C 15 OK 246 249 250 270 C3' G C 16 OK 268 271 272 292 C3' T C 17 OK 290 293 294 312 C3' G C 18 OK 310 313 314 334 C3' T C 19 OK 332 335 336 354 C3' G C 20 OK 352 355 356 376 C3' A C 21 OK 374 377 378 397 C3' A C 22 OK 395 398 399 418 C3' A C 23 OK 416 419 420 439 C3' T C 24 OK 437 440 441 460 C3' A D 3 OK 458 461 462 481 C3' T D 4 OK 479 482 483 501 C3' T D 5 OK 499 502 503 521 C3' T D 6 OK 519 522 523 541 C3' C D 7 OK 539 542 543 560 C3' A D 8 OK 558 561 562 581 C3' C D 9 OK 579 582 583 600 C3' A D 10 OK 598 601 602 621 C3' C D 11 OK 619 622 623 640 C3' C D 12 OK 638 641 642 659 C3' T D 13 OK 657 660 661 679 C3' A D 14 OK 677 680 681 700 C3' G D 15 OK 698 701 702 722 C3' G D 16 OK 720 723 724 744 C3' T D 17 OK 742 745 746 764 C3' G D 18 OK 762 765 766 786 C3' T D 19 OK 784 787 788 806 C3' G D 20 OK 804 807 808 828 C3' A D 21 OK 826 829 830 849 C3' A D 22 OK 847 850 851 870 C3' A D 23 OK 868 871 872 891 C3' T D 24 OK 889 892 893 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A C 3 OK 8 5 7 27 C4' T C 4 OK 29 26 28 47 C4' T C 5 OK 49 46 48 67 C4' T C 6 OK 69 66 68 87 C4' C C 7 OK 89 86 88 106 C4' A C 8 OK 108 105 107 127 C4' C C 9 OK 129 126 128 146 C4' A C 10 OK 148 145 147 167 C4' C C 11 OK 169 166 168 186 C4' C C 12 OK 188 185 187 205 C4' T C 13 OK 207 204 206 225 C4' A C 14 OK 227 224 226 246 C4' G C 15 OK 248 245 247 268 C4' G C 16 OK 270 267 269 290 C4' T C 17 OK 292 289 291 310 C4' G C 18 OK 312 309 311 332 C4' T C 19 OK 334 331 333 352 C4' G C 20 OK 354 351 353 374 C4' A C 21 OK 376 373 375 395 C4' A C 22 OK 397 394 396 416 C4' A C 23 OK 418 415 417 437 C4' T C 24 OK 439 436 438 458 C4' A D 3 OK 460 457 459 479 C4' T D 4 OK 481 478 480 499 C4' T D 5 OK 501 498 500 519 C4' T D 6 OK 521 518 520 539 C4' C D 7 OK 541 538 540 558 C4' A D 8 OK 560 557 559 579 C4' C D 9 OK 581 578 580 598 C4' A D 10 OK 600 597 599 619 C4' C D 11 OK 621 618 620 638 C4' C D 12 OK 640 637 639 657 C4' T D 13 OK 659 656 658 677 C4' A D 14 OK 679 676 678 698 C4' G D 15 OK 700 697 699 720 C4' G D 16 OK 722 719 721 742 C4' T D 17 OK 744 741 743 762 C4' G D 18 OK 764 761 763 784 C4' T D 19 OK 786 783 785 804 C4' G D 20 OK 806 803 805 826 C4' A D 21 OK 828 825 827 847 C4' A D 22 OK 849 846 848 868 C4' A D 23 OK 870 867 869 889 C4' T D 24 OK 891 888 890 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A C 3 4 6 26 C5' T C 4 25 27 46 C5' T C 5 45 47 66 C5' T C 6 65 67 86 C5' C C 7 85 87 105 C5' A C 8 104 106 126 C5' C C 9 125 127 145 C5' A C 10 144 146 166 C5' C C 11 165 167 185 C5' C C 12 184 186 204 C5' T C 13 203 205 224 C5' A C 14 223 225 245 C5' G C 15 244 246 267 C5' G C 16 266 268 289 C5' T C 17 288 290 309 C5' G C 18 308 310 331 C5' T C 19 330 332 351 C5' G C 20 350 352 373 C5' A C 21 372 374 394 C5' A C 22 393 395 415 C5' A C 23 414 416 436 C5' T C 24 435 437 457 C5' A D 3 456 458 478 C5' T D 4 477 479 498 C5' T D 5 497 499 518 C5' T D 6 517 519 538 C5' C D 7 537 539 557 C5' A D 8 556 558 578 C5' C D 9 577 579 597 C5' A D 10 596 598 618 C5' C D 11 617 619 637 C5' C D 12 636 638 656 C5' T D 13 655 657 676 C5' A D 14 675 677 697 C5' G D 15 696 698 719 C5' G D 16 718 720 741 C5' T D 17 740 742 761 C5' G D 18 760 762 783 C5' T D 19 782 784 803 C5' G D 20 802 804 825 C5' A D 21 824 826 846 C5' A D 22 845 847 867 C5' A D 23 866 868 888 C5' T D 24 887 889 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A C 3 distorted distorted 2 3 4 22 P T C 4 distorted distorted 9 23 24 25 42 P T C 5 distorted distorted 30 43 44 45 62 P T C 6 distorted distorted 50 63 64 65 82 P C C 7 distorted distorted 70 83 84 85 101 P A C 8 distorted distorted 90 102 103 104 122 P C C 9 distorted distorted 109 123 124 125 141 P A C 10 distorted distorted 130 142 143 144 162 P C C 11 distorted distorted 149 163 164 165 181 P C C 12 distorted distorted 170 182 183 184 200 P T C 13 distorted distorted 189 201 202 203 220 P A C 14 distorted distorted 208 221 222 223 241 P G C 15 distorted distorted 228 242 243 244 263 P G C 16 distorted distorted 249 264 265 266 285 P T C 17 distorted distorted 271 286 287 288 305 P G C 18 distorted distorted 293 306 307 308 327 P T C 19 distorted distorted 313 328 329 330 347 P G C 20 distorted distorted 335 348 349 350 369 P A C 21 distorted distorted 355 370 371 372 390 P A C 22 distorted distorted 377 391 392 393 411 P A C 23 distorted distorted 398 412 413 414 432 P T C 24 distorted distorted 419 433 434 435 453 P A D 3 distorted distorted 454 455 456 474 P T D 4 distorted distorted 461 475 476 477 494 P T D 5 distorted distorted 482 495 496 497 514 P T D 6 distorted distorted 502 515 516 517 534 P C D 7 distorted distorted 522 535 536 537 553 P A D 8 distorted distorted 542 554 555 556 574 P C D 9 distorted distorted 561 575 576 577 593 P A D 10 distorted distorted 582 594 595 596 614 P C D 11 distorted distorted 601 615 616 617 633 P C D 12 distorted distorted 622 634 635 636 652 P T D 13 distorted distorted 641 653 654 655 672 P A D 14 distorted distorted 660 673 674 675 693 P G D 15 distorted distorted 680 694 695 696 715 P G D 16 distorted distorted 701 716 717 718 737 P T D 17 distorted distorted 723 738 739 740 757 P G D 18 distorted distorted 745 758 759 760 779 P T D 19 distorted distorted 765 780 781 782 799 P G D 20 distorted distorted 787 800 801 802 821 P A D 21 distorted distorted 807 822 823 824 842 P A D 22 distorted distorted 829 843 844 845 863 P A D 23 distorted distorted 850 864 865 866 884 P T D 24 distorted distorted 871 885 886 887 ---------------------------------------------------------------------------------