ID code: '4F8U' 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' --------------------------------------------------------------------------------- 13 C1' U A 2 beta 8 14 11 33 C1' G A 3 beta 28 34 31 56 C1' C A 4 beta 51 57 54 76 C1' G A 5 beta 71 77 74 99 C1' U A 6 beta 94 100 97 119 C1' C A 7 beta 114 120 117 139 C1' A A 8 beta 134 140 137 161 C1' C A 9 beta 156 162 159 181 C1' A A 10 beta 176 182 179 203 C1' C A 11 beta 198 204 201 223 C1' C A 12 beta 218 224 221 243 C1' G A 13 beta 238 244 241 266 C1' G A 14 beta 261 267 264 289 C1' U A 15 beta 284 290 287 309 C1' G A 16 beta 304 310 307 332 C1' A A 17 beta 327 333 330 354 C1' A A 18 beta 349 355 352 376 C1' G A 19 beta 371 377 374 399 C1' U A 20 beta 394 400 397 419 C1' C A 21 beta 414 420 417 439 C1' G A 22 beta 434 440 437 462 C1' C A 23 beta 457 463 460 484 C1' G B 26 beta 479 485 482 507 C1' C B 27 beta 502 508 505 527 C1' G B 28 beta 522 528 525 550 C1' U B 29 beta 545 551 548 570 C1' C B 30 beta 565 571 568 590 C1' A B 31 beta 585 591 588 612 C1' C B 32 beta 607 613 610 632 C1' A B 33 beta 627 633 630 654 C1' C B 34 beta 649 655 652 674 C1' C B 35 beta 669 675 672 694 C1' G B 36 beta 689 695 692 717 C1' G B 37 beta 712 718 715 740 C1' U B 38 beta 735 741 738 760 C1' G B 39 beta 755 761 758 783 C1' A B 40 beta 778 784 781 805 C1' A B 41 beta 800 806 803 827 C1' G B 42 beta 822 828 825 850 C1' U B 43 beta 845 851 848 870 C1' C B 44 beta 865 871 868 890 C1' G B 45 beta 885 891 888 913 C1' C B 46 beta 908 914 911 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' U A 2 OK 13 9 12 31 C2' G A 3 OK 33 29 32 54 C2' C A 4 OK 56 52 55 74 C2' G A 5 OK 76 72 75 97 C2' U A 6 OK 99 95 98 117 C2' C A 7 OK 119 115 118 137 C2' A A 8 OK 139 135 138 159 C2' C A 9 OK 161 157 160 179 C2' A A 10 OK 181 177 180 201 C2' C A 11 OK 203 199 202 221 C2' C A 12 OK 223 219 222 241 C2' G A 13 OK 243 239 242 264 C2' G A 14 OK 266 262 265 287 C2' U A 15 OK 289 285 288 307 C2' G A 16 OK 309 305 308 330 C2' A A 17 OK 332 328 331 352 C2' A A 18 OK 354 350 353 374 C2' G A 19 OK 376 372 375 397 C2' U A 20 OK 399 395 398 417 C2' C A 21 OK 419 415 418 437 C2' G A 22 OK 439 435 438 460 C2' C A 23 OK 462 458 461 482 C2' G B 26 OK 484 480 483 505 C2' C B 27 OK 507 503 506 525 C2' G B 28 OK 527 523 526 548 C2' U B 29 OK 550 546 549 568 C2' C B 30 OK 570 566 569 588 C2' A B 31 OK 590 586 589 610 C2' C B 32 OK 612 608 611 630 C2' A B 33 OK 632 628 631 652 C2' C B 34 OK 654 650 653 672 C2' C B 35 OK 674 670 673 692 C2' G B 36 OK 694 690 693 715 C2' G B 37 OK 717 713 716 738 C2' U B 38 OK 740 736 739 758 C2' G B 39 OK 760 756 759 781 C2' A B 40 OK 783 779 782 803 C2' A B 41 OK 805 801 804 825 C2' G B 42 OK 827 823 826 848 C2' U B 43 OK 850 846 849 868 C2' C B 44 OK 870 866 869 888 C2' G B 45 OK 890 886 889 911 C2' C B 46 OK 913 909 912 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' U A 2 OK 7 10 11 29 C3' G A 3 OK 27 30 31 52 C3' C A 4 OK 50 53 54 72 C3' G A 5 OK 70 73 74 95 C3' U A 6 OK 93 96 97 115 C3' C A 7 OK 113 116 117 135 C3' A A 8 OK 133 136 137 157 C3' C A 9 OK 155 158 159 177 C3' A A 10 OK 175 178 179 199 C3' C A 11 OK 197 200 201 219 C3' C A 12 OK 217 220 221 239 C3' G A 13 OK 237 240 241 262 C3' G A 14 OK 260 263 264 285 C3' U A 15 OK 283 286 287 305 C3' G A 16 OK 303 306 307 328 C3' A A 17 OK 326 329 330 350 C3' A A 18 OK 348 351 352 372 C3' G A 19 OK 370 373 374 395 C3' U A 20 OK 393 396 397 415 C3' C A 21 OK 413 416 417 435 C3' G A 22 OK 433 436 437 458 C3' C A 23 OK 456 459 460 480 C3' G B 26 OK 478 481 482 503 C3' C B 27 OK 501 504 505 523 C3' G B 28 OK 521 524 525 546 C3' U B 29 OK 544 547 548 566 C3' C B 30 OK 564 567 568 586 C3' A B 31 OK 584 587 588 608 C3' C B 32 OK 606 609 610 628 C3' A B 33 OK 626 629 630 650 C3' C B 34 OK 648 651 652 670 C3' C B 35 OK 668 671 672 690 C3' G B 36 OK 688 691 692 713 C3' G B 37 OK 711 714 715 736 C3' U B 38 OK 734 737 738 756 C3' G B 39 OK 754 757 758 779 C3' A B 40 OK 777 780 781 801 C3' A B 41 OK 799 802 803 823 C3' G B 42 OK 821 824 825 846 C3' U B 43 OK 844 847 848 866 C3' C B 44 OK 864 867 868 886 C3' G B 45 OK 884 887 888 909 C3' C B 46 OK 907 910 911 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' U A 2 OK 9 6 8 27 C4' G A 3 OK 29 26 28 50 C4' C A 4 OK 52 49 51 70 C4' G A 5 OK 72 69 71 93 C4' U A 6 OK 95 92 94 113 C4' C A 7 OK 115 112 114 133 C4' A A 8 OK 135 132 134 155 C4' C A 9 OK 157 154 156 175 C4' A A 10 OK 177 174 176 197 C4' C A 11 OK 199 196 198 217 C4' C A 12 OK 219 216 218 237 C4' G A 13 OK 239 236 238 260 C4' G A 14 OK 262 259 261 283 C4' U A 15 OK 285 282 284 303 C4' G A 16 OK 305 302 304 326 C4' A A 17 OK 328 325 327 348 C4' A A 18 OK 350 347 349 370 C4' G A 19 OK 372 369 371 393 C4' U A 20 OK 395 392 394 413 C4' C A 21 OK 415 412 414 433 C4' G A 22 OK 435 432 434 456 C4' C A 23 OK 458 455 457 478 C4' G B 26 OK 480 477 479 501 C4' C B 27 OK 503 500 502 521 C4' G B 28 OK 523 520 522 544 C4' U B 29 OK 546 543 545 564 C4' C B 30 OK 566 563 565 584 C4' A B 31 OK 586 583 585 606 C4' C B 32 OK 608 605 607 626 C4' A B 33 OK 628 625 627 648 C4' C B 34 OK 650 647 649 668 C4' C B 35 OK 670 667 669 688 C4' G B 36 OK 690 687 689 711 C4' G B 37 OK 713 710 712 734 C4' U B 38 OK 736 733 735 754 C4' G B 39 OK 756 753 755 777 C4' A B 40 OK 779 776 778 799 C4' A B 41 OK 801 798 800 821 C4' G B 42 OK 823 820 822 844 C4' U B 43 OK 846 843 845 864 C4' C B 44 OK 866 863 865 884 C4' G B 45 OK 886 883 885 907 C4' C B 46 OK 909 906 908 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' U A 2 5 7 26 C5' G A 3 25 27 49 C5' C A 4 48 50 69 C5' G A 5 68 70 92 C5' U A 6 91 93 112 C5' C A 7 111 113 132 C5' A A 8 131 133 154 C5' C A 9 153 155 174 C5' A A 10 173 175 196 C5' C A 11 195 197 216 C5' C A 12 215 217 236 C5' G A 13 235 237 259 C5' G A 14 258 260 282 C5' U A 15 281 283 302 C5' G A 16 301 303 325 C5' A A 17 324 326 347 C5' A A 18 346 348 369 C5' G A 19 368 370 392 C5' U A 20 391 393 412 C5' C A 21 411 413 432 C5' G A 22 431 433 455 C5' C A 23 454 456 477 C5' G B 26 476 478 500 C5' C B 27 499 501 520 C5' G B 28 519 521 543 C5' U B 29 542 544 563 C5' C B 30 562 564 583 C5' A B 31 582 584 605 C5' C B 32 604 606 625 C5' A B 33 624 626 647 C5' C B 34 646 648 667 C5' C B 35 666 668 687 C5' G B 36 686 688 710 C5' G B 37 709 711 733 C5' U B 38 732 734 753 C5' G B 39 752 754 776 C5' A B 40 775 777 798 C5' A B 41 797 799 820 C5' G B 42 819 821 843 C5' U B 43 842 844 863 C5' C B 44 862 864 883 C5' G B 45 882 884 906 C5' C B 46 905 907 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P U A 2 OK OK 3 4 5 22 P G A 3 distorted distorted 10 23 24 25 45 P C A 4 distorted distorted 30 46 47 48 65 P G A 5 distorted distorted 53 66 67 68 88 P U A 6 distorted distorted 73 89 90 91 108 P C A 7 distorted distorted 96 109 110 111 128 P A A 8 distorted distorted 116 129 130 131 150 P C A 9 distorted distorted 136 151 152 153 170 P A A 10 distorted distorted 158 171 172 173 192 P C A 11 distorted distorted 178 193 194 195 212 P C A 12 distorted distorted 200 213 214 215 232 P G A 13 distorted distorted 220 233 234 235 255 P G A 14 distorted distorted 240 256 257 258 278 P U A 15 distorted distorted 263 279 280 281 298 P G A 16 distorted distorted 286 299 300 301 321 P A A 17 distorted distorted 306 322 323 324 343 P A A 18 distorted distorted 329 344 345 346 365 P G A 19 distorted distorted 351 366 367 368 388 P U A 20 distorted distorted 373 389 390 391 408 P C A 21 distorted distorted 396 409 410 411 428 P G A 22 distorted distorted 416 429 430 431 451 P C A 23 distorted distorted 436 452 453 454 473 P G B 26 distorted distorted 474 475 476 496 P C B 27 distorted distorted 481 497 498 499 516 P G B 28 distorted distorted 504 517 518 519 539 P U B 29 distorted distorted 524 540 541 542 559 P C B 30 distorted distorted 547 560 561 562 579 P A B 31 distorted distorted 567 580 581 582 601 P C B 32 distorted distorted 587 602 603 604 621 P A B 33 distorted distorted 609 622 623 624 643 P C B 34 distorted distorted 629 644 645 646 663 P C B 35 distorted distorted 651 664 665 666 683 P G B 36 distorted distorted 671 684 685 686 706 P G B 37 distorted distorted 691 707 708 709 729 P U B 38 distorted distorted 714 730 731 732 749 P G B 39 distorted distorted 737 750 751 752 772 P A B 40 distorted distorted 757 773 774 775 794 P A B 41 distorted distorted 780 795 796 797 816 P G B 42 distorted distorted 802 817 818 819 839 P U B 43 distorted distorted 824 840 841 842 859 P C B 44 distorted distorted 847 860 861 862 879 P G B 45 distorted distorted 867 880 881 882 902 P C B 46 distorted distorted 887 903 904 905 ---------------------------------------------------------------------------------