ID code: '2G5K' 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' U B 25 beta 477 483 480 502 C1' G B 26 beta 497 503 500 525 C1' C B 27 beta 520 526 523 545 C1' G B 28 beta 540 546 543 568 C1' U B 29 beta 563 569 566 588 C1' C B 30 beta 583 589 586 608 C1' G B 31 beta 603 609 606 631 C1' C B 32 beta 626 632 629 651 C1' U B 33 beta 646 652 649 671 C1' C B 34 beta 666 672 669 691 C1' C B 35 beta 686 692 689 711 C1' G B 36 beta 706 712 709 734 C1' G B 37 beta 729 735 732 757 C1' A B 38 beta 752 758 755 779 C1' A B 39 beta 774 780 777 801 C1' A B 40 beta 796 802 799 823 C1' A B 41 beta 818 824 821 845 C1' G B 42 beta 840 846 843 868 C1' U B 43 beta 863 869 866 888 C1' C B 44 beta 883 889 886 908 C1' G B 45 beta 903 909 906 931 C1' C B 46 beta 926 932 929 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U B 25 OK 482 478 481 500 C2' G B 26 OK 502 498 501 523 C2' C B 27 OK 525 521 524 543 C2' G B 28 OK 545 541 544 566 C2' U B 29 OK 568 564 567 586 C2' C B 30 OK 588 584 587 606 C2' G B 31 OK 608 604 607 629 C2' C B 32 OK 631 627 630 649 C2' U B 33 OK 651 647 650 669 C2' C B 34 OK 671 667 670 689 C2' C B 35 OK 691 687 690 709 C2' G B 36 OK 711 707 710 732 C2' G B 37 OK 734 730 733 755 C2' A B 38 OK 757 753 756 777 C2' A B 39 OK 779 775 778 799 C2' A B 40 OK 801 797 800 821 C2' A B 41 OK 823 819 822 843 C2' G B 42 OK 845 841 844 866 C2' U B 43 OK 868 864 867 886 C2' C B 44 OK 888 884 887 906 C2' G B 45 OK 908 904 907 929 C2' C B 46 OK 931 927 930 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U B 25 OK 476 479 480 498 C3' G B 26 OK 496 499 500 521 C3' C B 27 OK 519 522 523 541 C3' G B 28 OK 539 542 543 564 C3' U B 29 OK 562 565 566 584 C3' C B 30 OK 582 585 586 604 C3' G B 31 OK 602 605 606 627 C3' C B 32 OK 625 628 629 647 C3' U B 33 OK 645 648 649 667 C3' C B 34 OK 665 668 669 687 C3' C B 35 OK 685 688 689 707 C3' G B 36 OK 705 708 709 730 C3' G B 37 OK 728 731 732 753 C3' A B 38 OK 751 754 755 775 C3' A B 39 OK 773 776 777 797 C3' A B 40 OK 795 798 799 819 C3' A B 41 OK 817 820 821 841 C3' G B 42 OK 839 842 843 864 C3' U B 43 OK 862 865 866 884 C3' C B 44 OK 882 885 886 904 C3' G B 45 OK 902 905 906 927 C3' C B 46 OK 925 928 929 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U B 25 OK 478 475 477 496 C4' G B 26 OK 498 495 497 519 C4' C B 27 OK 521 518 520 539 C4' G B 28 OK 541 538 540 562 C4' U B 29 OK 564 561 563 582 C4' C B 30 OK 584 581 583 602 C4' G B 31 OK 604 601 603 625 C4' C B 32 OK 627 624 626 645 C4' U B 33 OK 647 644 646 665 C4' C B 34 OK 667 664 666 685 C4' C B 35 OK 687 684 686 705 C4' G B 36 OK 707 704 706 728 C4' G B 37 OK 730 727 729 751 C4' A B 38 OK 753 750 752 773 C4' A B 39 OK 775 772 774 795 C4' A B 40 OK 797 794 796 817 C4' A B 41 OK 819 816 818 839 C4' G B 42 OK 841 838 840 862 C4' U B 43 OK 864 861 863 882 C4' C B 44 OK 884 881 883 902 C4' G B 45 OK 904 901 903 925 C4' C B 46 OK 927 924 926 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U B 25 474 476 495 C5' G B 26 494 496 518 C5' C B 27 517 519 538 C5' G B 28 537 539 561 C5' U B 29 560 562 581 C5' C B 30 580 582 601 C5' G B 31 600 602 624 C5' C B 32 623 625 644 C5' U B 33 643 645 664 C5' C B 34 663 665 684 C5' C B 35 683 685 704 C5' G B 36 703 705 727 C5' G B 37 726 728 750 C5' A B 38 749 751 772 C5' A B 39 771 773 794 C5' A B 40 793 795 816 C5' A B 41 815 817 838 C5' G B 42 837 839 861 C5' U B 43 860 862 881 C5' C B 44 880 882 901 C5' G B 45 900 902 924 C5' C B 46 923 925 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U B 25 distorted distorted 472 473 474 491 P G B 26 distorted distorted 479 492 493 494 514 P C B 27 distorted distorted 499 515 516 517 534 P G B 28 distorted distorted 522 535 536 537 557 P U B 29 distorted distorted 542 558 559 560 577 P C B 30 distorted distorted 565 578 579 580 597 P G B 31 distorted distorted 585 598 599 600 620 P C B 32 distorted distorted 605 621 622 623 640 P U B 33 distorted distorted 628 641 642 643 660 P C B 34 distorted distorted 648 661 662 663 680 P C B 35 distorted distorted 668 681 682 683 700 P G B 36 distorted distorted 688 701 702 703 723 P G B 37 distorted distorted 708 724 725 726 746 P A B 38 distorted distorted 731 747 748 749 768 P A B 39 distorted distorted 754 769 770 771 790 P A B 40 distorted distorted 776 791 792 793 812 P A B 41 distorted distorted 798 813 814 815 834 P G B 42 distorted distorted 820 835 836 837 857 P U B 43 distorted distorted 842 858 859 860 877 P C B 44 distorted distorted 865 878 879 880 897 P G B 45 distorted distorted 885 898 899 900 920 P C B 46 distorted distorted 905 921 922 923 ---------------------------------------------------------------------------------