ID code: '4F8V' 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' G A 3 beta 8 14 11 36 C1' C A 4 beta 31 37 34 56 C1' G A 5 beta 51 57 54 79 C1' U A 6 beta 74 80 77 99 C1' C A 7 beta 94 100 97 119 C1' A A 8 beta 114 120 117 141 C1' C A 9 beta 136 142 139 161 C1' A A 10 beta 156 162 159 183 C1' C A 11 beta 178 184 181 203 C1' C A 12 beta 198 204 201 223 C1' G A 13 beta 218 224 221 246 C1' G A 14 beta 241 247 244 269 C1' U A 15 beta 264 270 267 289 C1' G A 16 beta 284 290 287 312 C1' A A 17 beta 307 313 310 334 C1' A A 18 beta 329 335 332 356 C1' G A 19 beta 351 357 354 379 C1' U A 20 beta 374 380 377 399 C1' C A 21 beta 394 400 397 419 C1' G A 22 beta 414 420 417 442 C1' C A 23 beta 437 443 440 464 C1' G B 26 beta 459 465 462 487 C1' C B 27 beta 482 488 485 507 C1' G B 28 beta 502 508 505 530 C1' U B 29 beta 525 531 528 550 C1' C B 30 beta 545 551 548 570 C1' A B 31 beta 565 571 568 592 C1' C B 32 beta 587 593 590 612 C1' A B 33 beta 607 613 610 634 C1' C B 34 beta 629 635 632 654 C1' C B 35 beta 649 655 652 674 C1' G B 36 beta 669 675 672 697 C1' G B 37 beta 692 698 695 720 C1' U B 38 beta 715 721 718 740 C1' G B 39 beta 735 741 738 763 C1' A B 40 beta 758 764 761 785 C1' A B 41 beta 780 786 783 807 C1' G B 42 beta 802 808 805 830 C1' U B 43 beta 825 831 828 850 C1' C B 44 beta 845 851 848 870 C1' G B 45 beta 865 871 868 893 C1' C B 46 beta 888 894 891 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 3 OK 13 9 12 34 C2' C A 4 OK 36 32 35 54 C2' G A 5 OK 56 52 55 77 C2' U A 6 OK 79 75 78 97 C2' C A 7 OK 99 95 98 117 C2' A A 8 OK 119 115 118 139 C2' C A 9 OK 141 137 140 159 C2' A A 10 OK 161 157 160 181 C2' C A 11 OK 183 179 182 201 C2' C A 12 OK 203 199 202 221 C2' G A 13 OK 223 219 222 244 C2' G A 14 OK 246 242 245 267 C2' U A 15 OK 269 265 268 287 C2' G A 16 OK 289 285 288 310 C2' A A 17 OK 312 308 311 332 C2' A A 18 OK 334 330 333 354 C2' G A 19 OK 356 352 355 377 C2' U A 20 OK 379 375 378 397 C2' C A 21 OK 399 395 398 417 C2' G A 22 OK 419 415 418 440 C2' C A 23 OK 442 438 441 462 C2' G B 26 OK 464 460 463 485 C2' C B 27 OK 487 483 486 505 C2' G B 28 OK 507 503 506 528 C2' U B 29 OK 530 526 529 548 C2' C B 30 OK 550 546 549 568 C2' A B 31 OK 570 566 569 590 C2' C B 32 OK 592 588 591 610 C2' A B 33 OK 612 608 611 632 C2' C B 34 OK 634 630 633 652 C2' C B 35 OK 654 650 653 672 C2' G B 36 OK 674 670 673 695 C2' G B 37 OK 697 693 696 718 C2' U B 38 OK 720 716 719 738 C2' G B 39 OK 740 736 739 761 C2' A B 40 OK 763 759 762 783 C2' A B 41 OK 785 781 784 805 C2' G B 42 OK 807 803 806 828 C2' U B 43 OK 830 826 829 848 C2' C B 44 OK 850 846 849 868 C2' G B 45 OK 870 866 869 891 C2' C B 46 OK 893 889 892 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 3 OK 7 10 11 32 C3' C A 4 OK 30 33 34 52 C3' G A 5 OK 50 53 54 75 C3' U A 6 OK 73 76 77 95 C3' C A 7 OK 93 96 97 115 C3' A A 8 OK 113 116 117 137 C3' C A 9 OK 135 138 139 157 C3' A A 10 OK 155 158 159 179 C3' C A 11 OK 177 180 181 199 C3' C A 12 OK 197 200 201 219 C3' G A 13 OK 217 220 221 242 C3' G A 14 OK 240 243 244 265 C3' U A 15 OK 263 266 267 285 C3' G A 16 OK 283 286 287 308 C3' A A 17 OK 306 309 310 330 C3' A A 18 OK 328 331 332 352 C3' G A 19 OK 350 353 354 375 C3' U A 20 OK 373 376 377 395 C3' C A 21 OK 393 396 397 415 C3' G A 22 OK 413 416 417 438 C3' C A 23 OK 436 439 440 460 C3' G B 26 OK 458 461 462 483 C3' C B 27 OK 481 484 485 503 C3' G B 28 OK 501 504 505 526 C3' U B 29 OK 524 527 528 546 C3' C B 30 OK 544 547 548 566 C3' A B 31 OK 564 567 568 588 C3' C B 32 OK 586 589 590 608 C3' A B 33 OK 606 609 610 630 C3' C B 34 OK 628 631 632 650 C3' C B 35 OK 648 651 652 670 C3' G B 36 OK 668 671 672 693 C3' G B 37 OK 691 694 695 716 C3' U B 38 OK 714 717 718 736 C3' G B 39 OK 734 737 738 759 C3' A B 40 OK 757 760 761 781 C3' A B 41 OK 779 782 783 803 C3' G B 42 OK 801 804 805 826 C3' U B 43 OK 824 827 828 846 C3' C B 44 OK 844 847 848 866 C3' G B 45 OK 864 867 868 889 C3' C B 46 OK 887 890 891 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 3 OK 9 6 8 30 C4' C A 4 OK 32 29 31 50 C4' G A 5 OK 52 49 51 73 C4' U A 6 OK 75 72 74 93 C4' C A 7 OK 95 92 94 113 C4' A A 8 OK 115 112 114 135 C4' C A 9 OK 137 134 136 155 C4' A A 10 OK 157 154 156 177 C4' C A 11 OK 179 176 178 197 C4' C A 12 OK 199 196 198 217 C4' G A 13 OK 219 216 218 240 C4' G A 14 OK 242 239 241 263 C4' U A 15 OK 265 262 264 283 C4' G A 16 OK 285 282 284 306 C4' A A 17 OK 308 305 307 328 C4' A A 18 OK 330 327 329 350 C4' G A 19 OK 352 349 351 373 C4' U A 20 OK 375 372 374 393 C4' C A 21 OK 395 392 394 413 C4' G A 22 OK 415 412 414 436 C4' C A 23 OK 438 435 437 458 C4' G B 26 OK 460 457 459 481 C4' C B 27 OK 483 480 482 501 C4' G B 28 OK 503 500 502 524 C4' U B 29 OK 526 523 525 544 C4' C B 30 OK 546 543 545 564 C4' A B 31 OK 566 563 565 586 C4' C B 32 OK 588 585 587 606 C4' A B 33 OK 608 605 607 628 C4' C B 34 OK 630 627 629 648 C4' C B 35 OK 650 647 649 668 C4' G B 36 OK 670 667 669 691 C4' G B 37 OK 693 690 692 714 C4' U B 38 OK 716 713 715 734 C4' G B 39 OK 736 733 735 757 C4' A B 40 OK 759 756 758 779 C4' A B 41 OK 781 778 780 801 C4' G B 42 OK 803 800 802 824 C4' U B 43 OK 826 823 825 844 C4' C B 44 OK 846 843 845 864 C4' G B 45 OK 866 863 865 887 C4' C B 46 OK 889 886 888 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 3 5 7 29 C5' C A 4 28 30 49 C5' G A 5 48 50 72 C5' U A 6 71 73 92 C5' C A 7 91 93 112 C5' A A 8 111 113 134 C5' C A 9 133 135 154 C5' A A 10 153 155 176 C5' C A 11 175 177 196 C5' C A 12 195 197 216 C5' G A 13 215 217 239 C5' G A 14 238 240 262 C5' U A 15 261 263 282 C5' G A 16 281 283 305 C5' A A 17 304 306 327 C5' A A 18 326 328 349 C5' G A 19 348 350 372 C5' U A 20 371 373 392 C5' C A 21 391 393 412 C5' G A 22 411 413 435 C5' C A 23 434 436 457 C5' G B 26 456 458 480 C5' C B 27 479 481 500 C5' G B 28 499 501 523 C5' U B 29 522 524 543 C5' C B 30 542 544 563 C5' A B 31 562 564 585 C5' C B 32 584 586 605 C5' A B 33 604 606 627 C5' C B 34 626 628 647 C5' C B 35 646 648 667 C5' G B 36 666 668 690 C5' G B 37 689 691 713 C5' U B 38 712 714 733 C5' G B 39 732 734 756 C5' A B 40 755 757 778 C5' A B 41 777 779 800 C5' G B 42 799 801 823 C5' U B 43 822 824 843 C5' C B 44 842 844 863 C5' G B 45 862 864 886 C5' C B 46 885 887 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 3 distorted distorted 3 4 5 25 P C A 4 distorted distorted 10 26 27 28 45 P G A 5 distorted distorted 33 46 47 48 68 P U A 6 distorted distorted 53 69 70 71 88 P C A 7 distorted distorted 76 89 90 91 108 P A A 8 distorted distorted 96 109 110 111 130 P C A 9 distorted distorted 116 131 132 133 150 P A A 10 distorted distorted 138 151 152 153 172 P C A 11 distorted distorted 158 173 174 175 192 P C A 12 distorted distorted 180 193 194 195 212 P G A 13 distorted distorted 200 213 214 215 235 P G A 14 distorted distorted 220 236 237 238 258 P U A 15 distorted distorted 243 259 260 261 278 P G A 16 distorted distorted 266 279 280 281 301 P A A 17 distorted distorted 286 302 303 304 323 P A A 18 distorted distorted 309 324 325 326 345 P G A 19 distorted distorted 331 346 347 348 368 P U A 20 distorted distorted 353 369 370 371 388 P C A 21 distorted distorted 376 389 390 391 408 P G A 22 distorted distorted 396 409 410 411 431 P C A 23 distorted distorted 416 432 433 434 453 P G B 26 distorted distorted 454 455 456 476 P C B 27 distorted distorted 461 477 478 479 496 P G B 28 distorted distorted 484 497 498 499 519 P U B 29 distorted distorted 504 520 521 522 539 P C B 30 distorted distorted 527 540 541 542 559 P A B 31 distorted distorted 547 560 561 562 581 P C B 32 distorted distorted 567 582 583 584 601 P A B 33 distorted distorted 589 602 603 604 623 P C B 34 distorted distorted 609 624 625 626 643 P C B 35 distorted distorted 631 644 645 646 663 P G B 36 distorted distorted 651 664 665 666 686 P G B 37 distorted distorted 671 687 688 689 709 P U B 38 distorted distorted 694 710 711 712 729 P G B 39 distorted distorted 717 730 731 732 752 P A B 40 distorted distorted 737 753 754 755 774 P A B 41 distorted distorted 760 775 776 777 796 P G B 42 distorted distorted 782 797 798 799 819 P U B 43 distorted distorted 804 820 821 822 839 P C B 44 distorted distorted 827 840 841 842 859 P G B 45 distorted distorted 847 860 861 862 882 P C B 46 distorted distorted 867 883 884 885 ---------------------------------------------------------------------------------