ID code: '1JUW' 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' --------------------------------------------------------------------------------- 8 C1' A B 1 beta 4 9 7 29 C1' A B 2 beta 25 30 28 50 C1' A B 3 beta 46 51 49 71 C1' A B 4 beta 67 72 70 92 C1' A B 5 beta 88 93 91 113 C1' G B 6 beta 109 114 112 135 C1' A B 7 beta 131 136 134 156 C1' C B 8 beta 152 157 155 175 C1' T B 9 beta 171 176 174 195 C1' T B 10 beta 191 196 194 215 C1' A B 11 beta 211 216 214 236 C1' G B 12 beta 232 237 235 258 C1' A B 13 beta 254 259 257 279 C1' A B 14 beta 275 280 278 300 C1' A B 15 beta 296 301 299 321 C1' A B 16 beta 317 322 320 342 C1' A B 17 beta 338 343 341 363 C1' T B 18 beta 359 364 362 383 C1' T B 19 beta 379 384 382 403 C1' T B 20 beta 399 404 402 423 C1' T B 21 beta 419 424 422 443 C1' T B 22 beta 439 444 442 461 C1' A C 101 beta 457 462 460 482 C1' A C 102 beta 478 483 481 503 C1' A C 103 beta 499 504 502 524 C1' A C 104 beta 520 525 523 545 C1' A C 105 beta 541 546 544 566 C1' T C 106 beta 562 567 565 586 C1' T C 107 beta 582 587 585 606 C1' T C 108 beta 602 607 605 626 C1' T C 109 beta 622 627 625 646 C1' T C 110 beta 642 647 645 666 C1' C C 111 beta 662 667 665 685 C1' T C 112 beta 681 686 684 705 C1' A C 113 beta 701 706 704 726 C1' A C 114 beta 722 727 725 747 C1' G C 115 beta 743 748 746 769 C1' T C 116 beta 765 770 768 789 C1' C C 117 beta 785 790 788 808 C1' T C 118 beta 804 809 807 828 C1' T C 119 beta 824 829 827 848 C1' T C 120 beta 844 849 847 868 C1' T C 121 beta 864 869 867 888 C1' T C 122 beta 884 889 887 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A B 1 8 5 28 C2' A B 2 29 26 49 C2' A B 3 50 47 70 C2' A B 4 71 68 91 C2' A B 5 92 89 112 C2' G B 6 113 110 134 C2' A B 7 135 132 155 C2' C B 8 156 153 174 C2' T B 9 175 172 194 C2' T B 10 195 192 214 C2' A B 11 215 212 235 C2' G B 12 236 233 257 C2' A B 13 258 255 278 C2' A B 14 279 276 299 C2' A B 15 300 297 320 C2' A B 16 321 318 341 C2' A B 17 342 339 362 C2' T B 18 363 360 382 C2' T B 19 383 380 402 C2' T B 20 403 400 422 C2' T B 21 423 420 442 C2' T B 22 443 440 460 C2' A C 101 461 458 481 C2' A C 102 482 479 502 C2' A C 103 503 500 523 C2' A C 104 524 521 544 C2' A C 105 545 542 565 C2' T C 106 566 563 585 C2' T C 107 586 583 605 C2' T C 108 606 603 625 C2' T C 109 626 623 645 C2' T C 110 646 643 665 C2' C C 111 666 663 684 C2' T C 112 685 682 704 C2' A C 113 705 702 725 C2' A C 114 726 723 746 C2' G C 115 747 744 768 C2' T C 116 769 766 788 C2' C C 117 789 786 807 C2' T C 118 808 805 827 C2' T C 119 828 825 847 C2' T C 120 848 845 867 C2' T C 121 868 865 887 C2' T C 122 888 885 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A B 1 OK 3 6 7 26 C3' A B 2 OK 24 27 28 47 C3' A B 3 OK 45 48 49 68 C3' A B 4 OK 66 69 70 89 C3' A B 5 OK 87 90 91 110 C3' G B 6 OK 108 111 112 132 C3' A B 7 OK 130 133 134 153 C3' C B 8 OK 151 154 155 172 C3' T B 9 OK 170 173 174 192 C3' T B 10 OK 190 193 194 212 C3' A B 11 OK 210 213 214 233 C3' G B 12 OK 231 234 235 255 C3' A B 13 OK 253 256 257 276 C3' A B 14 OK 274 277 278 297 C3' A B 15 OK 295 298 299 318 C3' A B 16 OK 316 319 320 339 C3' A B 17 OK 337 340 341 360 C3' T B 18 OK 358 361 362 380 C3' T B 19 OK 378 381 382 400 C3' T B 20 OK 398 401 402 420 C3' T B 21 OK 418 421 422 440 C3' T B 22 OK 438 441 442 458 C3' A C 101 OK 456 459 460 479 C3' A C 102 OK 477 480 481 500 C3' A C 103 OK 498 501 502 521 C3' A C 104 OK 519 522 523 542 C3' A C 105 OK 540 543 544 563 C3' T C 106 OK 561 564 565 583 C3' T C 107 OK 581 584 585 603 C3' T C 108 OK 601 604 605 623 C3' T C 109 OK 621 624 625 643 C3' T C 110 OK 641 644 645 663 C3' C C 111 OK 661 664 665 682 C3' T C 112 OK 680 683 684 702 C3' A C 113 OK 700 703 704 723 C3' A C 114 OK 721 724 725 744 C3' G C 115 OK 742 745 746 766 C3' T C 116 OK 764 767 768 786 C3' C C 117 OK 784 787 788 805 C3' T C 118 OK 803 806 807 825 C3' T C 119 OK 823 826 827 845 C3' T C 120 OK 843 846 847 865 C3' T C 121 OK 863 866 867 885 C3' T C 122 OK 883 886 887 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A B 1 OK 5 2 4 24 C4' A B 2 OK 26 23 25 45 C4' A B 3 OK 47 44 46 66 C4' A B 4 OK 68 65 67 87 C4' A B 5 OK 89 86 88 108 C4' G B 6 OK 110 107 109 130 C4' A B 7 OK 132 129 131 151 C4' C B 8 OK 153 150 152 170 C4' T B 9 OK 172 169 171 190 C4' T B 10 OK 192 189 191 210 C4' A B 11 OK 212 209 211 231 C4' G B 12 OK 233 230 232 253 C4' A B 13 OK 255 252 254 274 C4' A B 14 OK 276 273 275 295 C4' A B 15 OK 297 294 296 316 C4' A B 16 OK 318 315 317 337 C4' A B 17 OK 339 336 338 358 C4' T B 18 OK 360 357 359 378 C4' T B 19 OK 380 377 379 398 C4' T B 20 OK 400 397 399 418 C4' T B 21 OK 420 417 419 438 C4' T B 22 OK 440 437 439 456 C4' A C 101 OK 458 455 457 477 C4' A C 102 OK 479 476 478 498 C4' A C 103 OK 500 497 499 519 C4' A C 104 OK 521 518 520 540 C4' A C 105 OK 542 539 541 561 C4' T C 106 OK 563 560 562 581 C4' T C 107 OK 583 580 582 601 C4' T C 108 OK 603 600 602 621 C4' T C 109 OK 623 620 622 641 C4' T C 110 OK 643 640 642 661 C4' C C 111 OK 663 660 662 680 C4' T C 112 OK 682 679 681 700 C4' A C 113 OK 702 699 701 721 C4' A C 114 OK 723 720 722 742 C4' G C 115 OK 744 741 743 764 C4' T C 116 OK 766 763 765 784 C4' C C 117 OK 786 783 785 803 C4' T C 118 OK 805 802 804 823 C4' T C 119 OK 825 822 824 843 C4' T C 120 OK 845 842 844 863 C4' T C 121 OK 865 862 864 883 C4' T C 122 OK 885 882 884 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A B 1 1 3 23 C5' A B 2 22 24 44 C5' A B 3 43 45 65 C5' A B 4 64 66 86 C5' A B 5 85 87 107 C5' G B 6 106 108 129 C5' A B 7 128 130 150 C5' C B 8 149 151 169 C5' T B 9 168 170 189 C5' T B 10 188 190 209 C5' A B 11 208 210 230 C5' G B 12 229 231 252 C5' A B 13 251 253 273 C5' A B 14 272 274 294 C5' A B 15 293 295 315 C5' A B 16 314 316 336 C5' A B 17 335 337 357 C5' T B 18 356 358 377 C5' T B 19 376 378 397 C5' T B 20 396 398 417 C5' T B 21 416 418 437 C5' T B 22 436 438 455 C5' A C 101 454 456 476 C5' A C 102 475 477 497 C5' A C 103 496 498 518 C5' A C 104 517 519 539 C5' A C 105 538 540 560 C5' T C 106 559 561 580 C5' T C 107 579 581 600 C5' T C 108 599 601 620 C5' T C 109 619 621 640 C5' T C 110 639 641 660 C5' C C 111 659 661 679 C5' T C 112 678 680 699 C5' A C 113 698 700 720 C5' A C 114 719 721 741 C5' G C 115 740 742 763 C5' T C 116 762 764 783 C5' C C 117 782 784 802 C5' T C 118 801 803 822 C5' T C 119 821 823 842 C5' T C 120 841 843 862 C5' T C 121 861 863 882 C5' T C 122 881 883 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P A B 2 distorted distorted 6 20 21 22 40 P A B 3 distorted distorted 27 41 42 43 61 P A B 4 distorted distorted 48 62 63 64 82 P A B 5 distorted distorted 69 83 84 85 103 P G B 6 distorted distorted 90 104 105 106 125 P A B 7 distorted distorted 111 126 127 128 146 P C B 8 distorted distorted 133 147 148 149 165 P T B 9 distorted distorted 154 166 167 168 185 P T B 10 distorted distorted 173 186 187 188 205 P A B 11 distorted distorted 193 206 207 208 226 P G B 12 distorted distorted 213 227 228 229 248 P A B 13 distorted distorted 234 249 250 251 269 P A B 14 distorted distorted 256 270 271 272 290 P A B 15 distorted distorted 277 291 292 293 311 P A B 16 distorted distorted 298 312 313 314 332 P A B 17 distorted distorted 319 333 334 335 353 P T B 18 distorted distorted 340 354 355 356 373 P T B 19 distorted distorted 361 374 375 376 393 P T B 20 distorted distorted 381 394 395 396 413 P T B 21 distorted distorted 401 414 415 416 433 P T B 22 distorted distorted 421 434 435 436 472 P A C 102 distorted distorted 459 473 474 475 493 P A C 103 distorted distorted 480 494 495 496 514 P A C 104 distorted distorted 501 515 516 517 535 P A C 105 distorted distorted 522 536 537 538 556 P T C 106 distorted distorted 543 557 558 559 576 P T C 107 distorted distorted 564 577 578 579 596 P T C 108 distorted distorted 584 597 598 599 616 P T C 109 distorted distorted 604 617 618 619 636 P T C 110 distorted distorted 624 637 638 639 656 P C C 111 distorted distorted 644 657 658 659 675 P T C 112 distorted distorted 664 676 677 678 695 P A C 113 distorted distorted 683 696 697 698 716 P A C 114 distorted distorted 703 717 718 719 737 P G C 115 distorted distorted 724 738 739 740 759 P T C 116 distorted distorted 745 760 761 762 779 P C C 117 distorted distorted 767 780 781 782 798 P T C 118 distorted distorted 787 799 800 801 818 P T C 119 distorted distorted 806 819 820 821 838 P T C 120 distorted distorted 826 839 840 841 858 P T C 121 distorted distorted 846 859 860 861 878 P T C 122 distorted distorted 866 879 880 881 ---------------------------------------------------------------------------------