ID code: '2O3Y' 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' --------------------------------------------------------------------------------- 12 C1' U A 2 beta 7 13 10 32 C1' G A 3 beta 27 33 30 55 C1' C A 4 beta 50 56 53 75 C1' G A 5 beta 70 76 73 98 C1' U A 6 beta 93 99 96 118 C1' C A 7 beta 113 119 116 138 C1' G A 8 beta 133 139 136 161 C1' C A 9 beta 156 162 159 181 C1' U A 10 beta 176 182 179 201 C1' C A 11 beta 196 202 199 221 C1' C A 12 beta 216 222 219 241 C1' G A 13 beta 236 242 239 264 C1' G A 14 beta 259 265 262 287 C1' A A 15 beta 282 288 285 309 C1' A A 16 beta 304 310 307 331 C1' A A 17 beta 326 332 329 353 C1' A A 18 beta 348 354 351 375 C1' G A 19 beta 370 376 373 398 C1' U A 20 beta 393 399 396 418 C1' C A 21 beta 413 419 416 438 C1' G A 22 beta 433 439 436 461 C1' C A 23 beta 456 462 459 482 C1' G B 26 beta 477 483 480 505 C1' C B 27 beta 500 506 503 525 C1' G B 28 beta 520 526 523 548 C1' U B 29 beta 543 549 546 568 C1' C B 30 beta 563 569 566 588 C1' G B 31 beta 583 589 586 611 C1' C B 32 beta 606 612 609 631 C1' U B 33 beta 626 632 629 651 C1' C B 34 beta 646 652 649 671 C1' C B 35 beta 666 672 669 691 C1' G B 36 beta 686 692 689 714 C1' G B 37 beta 709 715 712 737 C1' A B 38 beta 732 738 735 759 C1' A B 39 beta 754 760 757 781 C1' A B 40 beta 776 782 779 803 C1' A B 41 beta 798 804 801 825 C1' G B 42 beta 820 826 823 848 C1' U B 43 beta 843 849 846 868 C1' C B 44 beta 863 869 866 888 C1' G B 45 beta 883 889 886 911 C1' C B 46 beta 906 912 909 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U A 2 OK 12 8 11 30 C2' G A 3 OK 32 28 31 53 C2' C A 4 OK 55 51 54 73 C2' G A 5 OK 75 71 74 96 C2' U A 6 OK 98 94 97 116 C2' C A 7 OK 118 114 117 136 C2' G A 8 OK 138 134 137 159 C2' C A 9 OK 161 157 160 179 C2' U A 10 OK 181 177 180 199 C2' C A 11 OK 201 197 200 219 C2' C A 12 OK 221 217 220 239 C2' G A 13 OK 241 237 240 262 C2' G A 14 OK 264 260 263 285 C2' A A 15 OK 287 283 286 307 C2' A A 16 OK 309 305 308 329 C2' A A 17 OK 331 327 330 351 C2' A A 18 OK 353 349 352 373 C2' G A 19 OK 375 371 374 396 C2' U A 20 OK 398 394 397 416 C2' C A 21 OK 418 414 417 436 C2' G A 22 OK 438 434 437 459 C2' C A 23 OK 461 457 460 480 C2' G B 26 OK 482 478 481 503 C2' C B 27 OK 505 501 504 523 C2' G B 28 OK 525 521 524 546 C2' U B 29 OK 548 544 547 566 C2' C B 30 OK 568 564 567 586 C2' G B 31 OK 588 584 587 609 C2' C B 32 OK 611 607 610 629 C2' U B 33 OK 631 627 630 649 C2' C B 34 OK 651 647 650 669 C2' C B 35 OK 671 667 670 689 C2' G B 36 OK 691 687 690 712 C2' G B 37 OK 714 710 713 735 C2' A B 38 OK 737 733 736 757 C2' A B 39 OK 759 755 758 779 C2' A B 40 OK 781 777 780 801 C2' A B 41 OK 803 799 802 823 C2' G B 42 OK 825 821 824 846 C2' U B 43 OK 848 844 847 866 C2' C B 44 OK 868 864 867 886 C2' G B 45 OK 888 884 887 909 C2' C B 46 OK 911 907 910 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U A 2 OK 6 9 10 28 C3' G A 3 OK 26 29 30 51 C3' C A 4 OK 49 52 53 71 C3' G A 5 OK 69 72 73 94 C3' U A 6 OK 92 95 96 114 C3' C A 7 OK 112 115 116 134 C3' G A 8 OK 132 135 136 157 C3' C A 9 OK 155 158 159 177 C3' U A 10 OK 175 178 179 197 C3' C A 11 OK 195 198 199 217 C3' C A 12 OK 215 218 219 237 C3' G A 13 OK 235 238 239 260 C3' G A 14 OK 258 261 262 283 C3' A A 15 OK 281 284 285 305 C3' A A 16 OK 303 306 307 327 C3' A A 17 OK 325 328 329 349 C3' A A 18 OK 347 350 351 371 C3' G A 19 OK 369 372 373 394 C3' U A 20 OK 392 395 396 414 C3' C A 21 OK 412 415 416 434 C3' G A 22 OK 432 435 436 457 C3' C A 23 OK 455 458 459 478 C3' G B 26 OK 476 479 480 501 C3' C B 27 OK 499 502 503 521 C3' G B 28 OK 519 522 523 544 C3' U B 29 OK 542 545 546 564 C3' C B 30 OK 562 565 566 584 C3' G B 31 OK 582 585 586 607 C3' C B 32 OK 605 608 609 627 C3' U B 33 OK 625 628 629 647 C3' C B 34 OK 645 648 649 667 C3' C B 35 OK 665 668 669 687 C3' G B 36 OK 685 688 689 710 C3' G B 37 OK 708 711 712 733 C3' A B 38 OK 731 734 735 755 C3' A B 39 OK 753 756 757 777 C3' A B 40 OK 775 778 779 799 C3' A B 41 OK 797 800 801 821 C3' G B 42 OK 819 822 823 844 C3' U B 43 OK 842 845 846 864 C3' C B 44 OK 862 865 866 884 C3' G B 45 OK 882 885 886 907 C3' C B 46 OK 905 908 909 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U A 2 OK 8 5 7 26 C4' G A 3 OK 28 25 27 49 C4' C A 4 OK 51 48 50 69 C4' G A 5 OK 71 68 70 92 C4' U A 6 OK 94 91 93 112 C4' C A 7 OK 114 111 113 132 C4' G A 8 OK 134 131 133 155 C4' C A 9 OK 157 154 156 175 C4' U A 10 OK 177 174 176 195 C4' C A 11 OK 197 194 196 215 C4' C A 12 OK 217 214 216 235 C4' G A 13 OK 237 234 236 258 C4' G A 14 OK 260 257 259 281 C4' A A 15 OK 283 280 282 303 C4' A A 16 OK 305 302 304 325 C4' A A 17 OK 327 324 326 347 C4' A A 18 OK 349 346 348 369 C4' G A 19 OK 371 368 370 392 C4' U A 20 OK 394 391 393 412 C4' C A 21 OK 414 411 413 432 C4' G A 22 OK 434 431 433 455 C4' C A 23 OK 457 454 456 476 C4' G B 26 OK 478 475 477 499 C4' C B 27 OK 501 498 500 519 C4' G B 28 OK 521 518 520 542 C4' U B 29 OK 544 541 543 562 C4' C B 30 OK 564 561 563 582 C4' G B 31 OK 584 581 583 605 C4' C B 32 OK 607 604 606 625 C4' U B 33 OK 627 624 626 645 C4' C B 34 OK 647 644 646 665 C4' C B 35 OK 667 664 666 685 C4' G B 36 OK 687 684 686 708 C4' G B 37 OK 710 707 709 731 C4' A B 38 OK 733 730 732 753 C4' A B 39 OK 755 752 754 775 C4' A B 40 OK 777 774 776 797 C4' A B 41 OK 799 796 798 819 C4' G B 42 OK 821 818 820 842 C4' U B 43 OK 844 841 843 862 C4' C B 44 OK 864 861 863 882 C4' G B 45 OK 884 881 883 905 C4' C B 46 OK 907 904 906 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U A 2 4 6 25 C5' G A 3 24 26 48 C5' C A 4 47 49 68 C5' G A 5 67 69 91 C5' U A 6 90 92 111 C5' C A 7 110 112 131 C5' G A 8 130 132 154 C5' C A 9 153 155 174 C5' U A 10 173 175 194 C5' C A 11 193 195 214 C5' C A 12 213 215 234 C5' G A 13 233 235 257 C5' G A 14 256 258 280 C5' A A 15 279 281 302 C5' A A 16 301 303 324 C5' A A 17 323 325 346 C5' A A 18 345 347 368 C5' G A 19 367 369 391 C5' U A 20 390 392 411 C5' C A 21 410 412 431 C5' G A 22 430 432 454 C5' C A 23 453 455 475 C5' G B 26 474 476 498 C5' C B 27 497 499 518 C5' G B 28 517 519 541 C5' U B 29 540 542 561 C5' C B 30 560 562 581 C5' G B 31 580 582 604 C5' C B 32 603 605 624 C5' U B 33 623 625 644 C5' C B 34 643 645 664 C5' C B 35 663 665 684 C5' G B 36 683 685 707 C5' G B 37 706 708 730 C5' A B 38 729 731 752 C5' A B 39 751 753 774 C5' A B 40 773 775 796 C5' A B 41 795 797 818 C5' G B 42 817 819 841 C5' U B 43 840 842 861 C5' C B 44 860 862 881 C5' G B 45 880 882 904 C5' C B 46 903 905 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U A 2 distorted distorted 2 3 4 21 P G A 3 distorted distorted 9 22 23 24 44 P C A 4 distorted distorted 29 45 46 47 64 P G A 5 distorted distorted 52 65 66 67 87 P U A 6 distorted distorted 72 88 89 90 107 P C A 7 distorted distorted 95 108 109 110 127 P G A 8 distorted distorted 115 128 129 130 150 P C A 9 distorted distorted 135 151 152 153 170 P U A 10 distorted distorted 158 171 172 173 190 P C A 11 distorted distorted 178 191 192 193 210 P C A 12 distorted distorted 198 211 212 213 230 P G A 13 distorted distorted 218 231 232 233 253 P G A 14 distorted distorted 238 254 255 256 276 P A A 15 distorted distorted 261 277 278 279 298 P A A 16 distorted distorted 284 299 300 301 320 P A A 17 distorted distorted 306 321 322 323 342 P A A 18 distorted distorted 328 343 344 345 364 P G A 19 distorted distorted 350 365 366 367 387 P U A 20 distorted distorted 372 388 389 390 407 P C A 21 distorted distorted 395 408 409 410 427 P G A 22 distorted distorted 415 428 429 430 450 P C A 23 distorted distorted 435 451 452 453 471 P G B 26 distorted distorted 472 473 474 494 P C B 27 distorted distorted 479 495 496 497 514 P G B 28 distorted distorted 502 515 516 517 537 P U B 29 distorted distorted 522 538 539 540 557 P C B 30 distorted distorted 545 558 559 560 577 P G B 31 distorted distorted 565 578 579 580 600 P C B 32 distorted distorted 585 601 602 603 620 P U B 33 distorted distorted 608 621 622 623 640 P C B 34 distorted distorted 628 641 642 643 660 P C B 35 distorted distorted 648 661 662 663 680 P G B 36 distorted distorted 668 681 682 683 703 P G B 37 distorted distorted 688 704 705 706 726 P A B 38 distorted distorted 711 727 728 729 748 P A B 39 distorted distorted 734 749 750 751 770 P A B 40 distorted distorted 756 771 772 773 792 P A B 41 distorted distorted 778 793 794 795 814 P G B 42 distorted distorted 800 815 816 817 837 P U B 43 distorted distorted 822 838 839 840 857 P C B 44 distorted distorted 845 858 859 860 877 P G B 45 distorted distorted 865 878 879 880 900 P C B 46 distorted distorted 885 901 902 903 ---------------------------------------------------------------------------------