ID code: '2ESJ' 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' G A 2 beta 7 13 10 35 C1' C A 3 beta 30 36 33 55 C1' G A 4 beta 50 56 53 78 C1' U A 5 beta 73 79 76 98 C1' C A 6 beta 93 99 96 118 C1' A A 7 beta 113 119 116 140 C1' C A 8 beta 135 141 138 160 C1' A A 9 beta 155 161 158 182 C1' C A 10 beta 177 183 180 202 C1' C A 11 beta 197 203 200 222 C1' G A 12 beta 217 223 220 245 C1' G A 13 beta 240 246 243 268 C1' U A 14 beta 263 269 266 288 C1' G A 15 beta 283 289 286 311 C1' A A 16 beta 306 312 309 333 C1' A A 17 beta 328 334 331 355 C1' G A 18 beta 350 356 353 378 C1' U A 19 beta 373 379 376 398 C1' C A 20 beta 393 399 396 418 C1' G A 21 beta 413 419 416 441 C1' C A 22 beta 436 442 439 462 C1' G B 25 beta 457 463 460 485 C1' C B 26 beta 480 486 483 505 C1' G B 27 beta 500 506 503 528 C1' U B 28 beta 523 529 526 548 C1' C B 29 beta 543 549 546 568 C1' A B 30 beta 563 569 566 590 C1' C B 31 beta 585 591 588 610 C1' A B 32 beta 605 611 608 632 C1' C B 33 beta 627 633 630 652 C1' C B 34 beta 647 653 650 672 C1' G B 35 beta 667 673 670 695 C1' G B 36 beta 690 696 693 718 C1' U B 37 beta 713 719 716 738 C1' G B 38 beta 733 739 736 761 C1' A B 39 beta 756 762 759 783 C1' A B 40 beta 778 784 781 805 C1' G B 41 beta 800 806 803 828 C1' U B 42 beta 823 829 826 848 C1' C B 43 beta 843 849 846 868 C1' G B 44 beta 863 869 866 891 C1' C B 45 beta 886 892 889 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 2 OK 12 8 11 33 C2' C A 3 OK 35 31 34 53 C2' G A 4 OK 55 51 54 76 C2' U A 5 OK 78 74 77 96 C2' C A 6 OK 98 94 97 116 C2' A A 7 OK 118 114 117 138 C2' C A 8 OK 140 136 139 158 C2' A A 9 OK 160 156 159 180 C2' C A 10 OK 182 178 181 200 C2' C A 11 OK 202 198 201 220 C2' G A 12 OK 222 218 221 243 C2' G A 13 OK 245 241 244 266 C2' U A 14 OK 268 264 267 286 C2' G A 15 OK 288 284 287 309 C2' A A 16 OK 311 307 310 331 C2' A A 17 OK 333 329 332 353 C2' G A 18 OK 355 351 354 376 C2' U A 19 OK 378 374 377 396 C2' C A 20 OK 398 394 397 416 C2' G A 21 OK 418 414 417 439 C2' C A 22 OK 441 437 440 460 C2' G B 25 OK 462 458 461 483 C2' C B 26 OK 485 481 484 503 C2' G B 27 OK 505 501 504 526 C2' U B 28 OK 528 524 527 546 C2' C B 29 OK 548 544 547 566 C2' A B 30 OK 568 564 567 588 C2' C B 31 OK 590 586 589 608 C2' A B 32 OK 610 606 609 630 C2' C B 33 OK 632 628 631 650 C2' C B 34 OK 652 648 651 670 C2' G B 35 OK 672 668 671 693 C2' G B 36 OK 695 691 694 716 C2' U B 37 OK 718 714 717 736 C2' G B 38 OK 738 734 737 759 C2' A B 39 OK 761 757 760 781 C2' A B 40 OK 783 779 782 803 C2' G B 41 OK 805 801 804 826 C2' U B 42 OK 828 824 827 846 C2' C B 43 OK 848 844 847 866 C2' G B 44 OK 868 864 867 889 C2' C B 45 OK 891 887 890 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 2 OK 6 9 10 31 C3' C A 3 OK 29 32 33 51 C3' G A 4 OK 49 52 53 74 C3' U A 5 OK 72 75 76 94 C3' C A 6 OK 92 95 96 114 C3' A A 7 OK 112 115 116 136 C3' C A 8 OK 134 137 138 156 C3' A A 9 OK 154 157 158 178 C3' C A 10 OK 176 179 180 198 C3' C A 11 OK 196 199 200 218 C3' G A 12 OK 216 219 220 241 C3' G A 13 OK 239 242 243 264 C3' U A 14 OK 262 265 266 284 C3' G A 15 OK 282 285 286 307 C3' A A 16 OK 305 308 309 329 C3' A A 17 OK 327 330 331 351 C3' G A 18 OK 349 352 353 374 C3' U A 19 OK 372 375 376 394 C3' C A 20 OK 392 395 396 414 C3' G A 21 OK 412 415 416 437 C3' C A 22 OK 435 438 439 458 C3' G B 25 OK 456 459 460 481 C3' C B 26 OK 479 482 483 501 C3' G B 27 OK 499 502 503 524 C3' U B 28 OK 522 525 526 544 C3' C B 29 OK 542 545 546 564 C3' A B 30 OK 562 565 566 586 C3' C B 31 OK 584 587 588 606 C3' A B 32 OK 604 607 608 628 C3' C B 33 OK 626 629 630 648 C3' C B 34 OK 646 649 650 668 C3' G B 35 OK 666 669 670 691 C3' G B 36 OK 689 692 693 714 C3' U B 37 OK 712 715 716 734 C3' G B 38 OK 732 735 736 757 C3' A B 39 OK 755 758 759 779 C3' A B 40 OK 777 780 781 801 C3' G B 41 OK 799 802 803 824 C3' U B 42 OK 822 825 826 844 C3' C B 43 OK 842 845 846 864 C3' G B 44 OK 862 865 866 887 C3' C B 45 OK 885 888 889 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 2 OK 8 5 7 29 C4' C A 3 OK 31 28 30 49 C4' G A 4 OK 51 48 50 72 C4' U A 5 OK 74 71 73 92 C4' C A 6 OK 94 91 93 112 C4' A A 7 OK 114 111 113 134 C4' C A 8 OK 136 133 135 154 C4' A A 9 OK 156 153 155 176 C4' C A 10 OK 178 175 177 196 C4' C A 11 OK 198 195 197 216 C4' G A 12 OK 218 215 217 239 C4' G A 13 OK 241 238 240 262 C4' U A 14 OK 264 261 263 282 C4' G A 15 OK 284 281 283 305 C4' A A 16 OK 307 304 306 327 C4' A A 17 OK 329 326 328 349 C4' G A 18 OK 351 348 350 372 C4' U A 19 OK 374 371 373 392 C4' C A 20 OK 394 391 393 412 C4' G A 21 OK 414 411 413 435 C4' C A 22 OK 437 434 436 456 C4' G B 25 OK 458 455 457 479 C4' C B 26 OK 481 478 480 499 C4' G B 27 OK 501 498 500 522 C4' U B 28 OK 524 521 523 542 C4' C B 29 OK 544 541 543 562 C4' A B 30 OK 564 561 563 584 C4' C B 31 OK 586 583 585 604 C4' A B 32 OK 606 603 605 626 C4' C B 33 OK 628 625 627 646 C4' C B 34 OK 648 645 647 666 C4' G B 35 OK 668 665 667 689 C4' G B 36 OK 691 688 690 712 C4' U B 37 OK 714 711 713 732 C4' G B 38 OK 734 731 733 755 C4' A B 39 OK 757 754 756 777 C4' A B 40 OK 779 776 778 799 C4' G B 41 OK 801 798 800 822 C4' U B 42 OK 824 821 823 842 C4' C B 43 OK 844 841 843 862 C4' G B 44 OK 864 861 863 885 C4' C B 45 OK 887 884 886 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 2 4 6 28 C5' C A 3 27 29 48 C5' G A 4 47 49 71 C5' U A 5 70 72 91 C5' C A 6 90 92 111 C5' A A 7 110 112 133 C5' C A 8 132 134 153 C5' A A 9 152 154 175 C5' C A 10 174 176 195 C5' C A 11 194 196 215 C5' G A 12 214 216 238 C5' G A 13 237 239 261 C5' U A 14 260 262 281 C5' G A 15 280 282 304 C5' A A 16 303 305 326 C5' A A 17 325 327 348 C5' G A 18 347 349 371 C5' U A 19 370 372 391 C5' C A 20 390 392 411 C5' G A 21 410 412 434 C5' C A 22 433 435 455 C5' G B 25 454 456 478 C5' C B 26 477 479 498 C5' G B 27 497 499 521 C5' U B 28 520 522 541 C5' C B 29 540 542 561 C5' A B 30 560 562 583 C5' C B 31 582 584 603 C5' A B 32 602 604 625 C5' C B 33 624 626 645 C5' C B 34 644 646 665 C5' G B 35 664 666 688 C5' G B 36 687 689 711 C5' U B 37 710 712 731 C5' G B 38 730 732 754 C5' A B 39 753 755 776 C5' A B 40 775 777 798 C5' G B 41 797 799 821 C5' U B 42 820 822 841 C5' C B 43 840 842 861 C5' G B 44 860 862 884 C5' C B 45 883 885 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 2 OK OK 2 3 4 24 P C A 3 distorted distorted 9 25 26 27 44 P G A 4 distorted distorted 32 45 46 47 67 P U A 5 distorted distorted 52 68 69 70 87 P C A 6 distorted distorted 75 88 89 90 107 P A A 7 distorted distorted 95 108 109 110 129 P C A 8 distorted distorted 115 130 131 132 149 P A A 9 distorted distorted 137 150 151 152 171 P C A 10 distorted distorted 157 172 173 174 191 P C A 11 distorted distorted 179 192 193 194 211 P G A 12 distorted distorted 199 212 213 214 234 P G A 13 distorted distorted 219 235 236 237 257 P U A 14 distorted distorted 242 258 259 260 277 P G A 15 distorted distorted 265 278 279 280 300 P A A 16 distorted distorted 285 301 302 303 322 P A A 17 distorted distorted 308 323 324 325 344 P G A 18 distorted distorted 330 345 346 347 367 P U A 19 distorted distorted 352 368 369 370 387 P C A 20 distorted distorted 375 388 389 390 407 P G A 21 distorted distorted 395 408 409 410 430 P C A 22 distorted distorted 415 431 432 433 451 P G B 25 distorted distorted 452 453 454 474 P C B 26 distorted distorted 459 475 476 477 494 P G B 27 distorted distorted 482 495 496 497 517 P U B 28 distorted distorted 502 518 519 520 537 P C B 29 distorted distorted 525 538 539 540 557 P A B 30 distorted distorted 545 558 559 560 579 P C B 31 distorted distorted 565 580 581 582 599 P A B 32 distorted distorted 587 600 601 602 621 P C B 33 distorted distorted 607 622 623 624 641 P C B 34 distorted distorted 629 642 643 644 661 P G B 35 distorted distorted 649 662 663 664 684 P G B 36 distorted distorted 669 685 686 687 707 P U B 37 distorted distorted 692 708 709 710 727 P G B 38 distorted distorted 715 728 729 730 750 P A B 39 distorted distorted 735 751 752 753 772 P A B 40 distorted distorted 758 773 774 775 794 P G B 41 distorted distorted 780 795 796 797 817 P U B 42 distorted distorted 802 818 819 820 837 P C B 43 distorted distorted 825 838 839 840 857 P G B 44 distorted distorted 845 858 859 860 880 P C B 45 distorted distorted 865 881 882 883 ---------------------------------------------------------------------------------