ID code: '2M24' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' A A 6 alpha beta 170 192 176 173 208 C1' U A 7 alpha beta 203 223 209 206 238 C1' G A 8 alpha beta 233 256 239 236 272 C1' U A 9 alpha beta 267 287 273 270 302 C1' A A 10 alpha beta 297 319 303 300 335 C1' U A 11 alpha beta 330 350 336 333 365 C1' U A 12 alpha beta 360 380 366 363 395 C1' G A 13 alpha beta 390 413 396 393 429 C1' G A 14 alpha beta 424 447 430 427 463 C1' C A 15 alpha beta 458 478 464 461 494 C1' A A 16 alpha beta 489 511 495 492 527 C1' C A 17 alpha beta 522 542 528 525 558 C1' U A 18 alpha beta 553 573 559 556 588 C1' G A 19 alpha beta 583 606 589 586 622 C1' A A 20 alpha beta 617 639 623 620 655 C1' G A 21 alpha beta 650 673 656 653 689 C1' C A 22 alpha beta 684 704 690 687 720 C1' A A 23 alpha beta 715 737 721 718 753 C1' U A 24 alpha beta 748 768 754 751 783 C1' A A 25 alpha beta 778 800 784 781 816 C1' C A 26 alpha beta 811 831 817 814 847 C1' U A 27 alpha beta 842 862 848 845 877 C1' C A 28 alpha beta 872 892 878 875 908 C1' C A 29 alpha beta 903 923 909 906 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' U A 5 OK OK 145 141 158 144 173 C2' A A 6 OK OK 175 171 190 174 206 C2' U A 7 OK OK 208 204 221 207 236 C2' G A 8 OK OK 238 234 254 237 270 C2' U A 9 OK OK 272 268 285 271 300 C2' A A 10 OK OK 302 298 317 301 333 C2' U A 11 OK OK 335 331 348 334 363 C2' U A 12 OK OK 365 361 378 364 393 C2' G A 13 OK OK 395 391 411 394 427 C2' G A 14 OK OK 429 425 445 428 461 C2' C A 15 OK OK 463 459 476 462 492 C2' A A 16 OK OK 494 490 509 493 525 C2' C A 17 OK OK 527 523 540 526 556 C2' U A 18 OK OK 558 554 571 557 586 C2' G A 19 OK OK 588 584 604 587 620 C2' A A 20 OK OK 622 618 637 621 653 C2' G A 21 OK OK 655 651 671 654 687 C2' C A 22 OK OK 689 685 702 688 718 C2' A A 23 OK OK 720 716 735 719 751 C2' U A 24 OK OK 753 749 766 752 781 C2' A A 25 OK OK 783 779 798 782 814 C2' C A 26 OK OK 816 812 829 815 845 C2' U A 27 OK OK 847 843 860 846 875 C2' C A 28 OK OK 877 873 890 876 906 C2' C A 29 OK OK 908 904 921 907 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' U A 5 OK OK 139 157 142 143 171 C3' A A 6 OK OK 169 189 172 173 204 C3' U A 7 OK OK 202 220 205 206 234 C3' G A 8 OK OK 232 253 235 236 268 C3' U A 9 OK OK 266 284 269 270 298 C3' A A 10 OK OK 296 316 299 300 331 C3' U A 11 OK OK 329 347 332 333 361 C3' U A 12 OK OK 359 377 362 363 391 C3' G A 13 OK OK 389 410 392 393 425 C3' G A 14 OK OK 423 444 426 427 459 C3' C A 15 OK OK 457 475 460 461 490 C3' A A 16 OK OK 488 508 491 492 523 C3' C A 17 OK OK 521 539 524 525 554 C3' U A 18 OK OK 552 570 555 556 584 C3' G A 19 OK OK 582 603 585 586 618 C3' A A 20 OK OK 616 636 619 620 651 C3' G A 21 OK OK 649 670 652 653 685 C3' C A 22 OK OK 683 701 686 687 716 C3' A A 23 OK OK 714 734 717 718 749 C3' U A 24 OK OK 747 765 750 751 779 C3' A A 25 OK OK 777 797 780 781 812 C3' C A 26 OK OK 810 828 813 814 843 C3' U A 27 OK OK 841 859 844 845 873 C3' C A 28 OK OK 871 889 874 875 904 C3' C A 29 OK OK 902 920 905 906 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' U A 5 OK OK 141 156 138 140 169 C4' A A 6 OK OK 171 188 168 170 202 C4' U A 7 OK OK 204 219 201 203 232 C4' G A 8 OK OK 234 252 231 233 266 C4' U A 9 OK OK 268 283 265 267 296 C4' A A 10 OK OK 298 315 295 297 329 C4' U A 11 OK OK 331 346 328 330 359 C4' U A 12 OK OK 361 376 358 360 389 C4' G A 13 OK OK 391 409 388 390 423 C4' G A 14 OK OK 425 443 422 424 457 C4' C A 15 OK OK 459 474 456 458 488 C4' A A 16 OK OK 490 507 487 489 521 C4' C A 17 OK OK 523 538 520 522 552 C4' U A 18 OK OK 554 569 551 553 582 C4' G A 19 OK OK 584 602 581 583 616 C4' A A 20 OK OK 618 635 615 617 649 C4' G A 21 OK OK 651 669 648 650 683 C4' C A 22 OK OK 685 700 682 684 714 C4' A A 23 OK OK 716 733 713 715 747 C4' U A 24 OK OK 749 764 746 748 777 C4' A A 25 OK OK 779 796 776 778 810 C4' C A 26 OK OK 812 827 809 811 841 C4' U A 27 OK OK 843 858 840 842 871 C4' C A 28 OK OK 873 888 870 872 902 C4' C A 29 OK OK 904 919 901 903 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' U A 5 OK OK 137 154 155 139 168 C5' A A 6 OK OK 167 186 187 169 201 C5' U A 7 OK OK 200 217 218 202 231 C5' G A 8 OK OK 230 250 251 232 265 C5' U A 9 OK OK 264 281 282 266 295 C5' A A 10 OK OK 294 313 314 296 328 C5' U A 11 OK OK 327 344 345 329 358 C5' U A 12 OK OK 357 374 375 359 388 C5' G A 13 OK OK 387 407 408 389 422 C5' G A 14 OK OK 421 441 442 423 456 C5' C A 15 OK OK 455 472 473 457 487 C5' A A 16 OK OK 486 505 506 488 520 C5' C A 17 OK OK 519 536 537 521 551 C5' U A 18 OK OK 550 567 568 552 581 C5' G A 19 OK OK 580 600 601 582 615 C5' A A 20 OK OK 614 633 634 616 648 C5' G A 21 OK OK 647 667 668 649 682 C5' C A 22 OK OK 681 698 699 683 713 C5' A A 23 OK OK 712 731 732 714 746 C5' U A 24 OK OK 745 762 763 747 776 C5' A A 25 OK OK 775 794 795 777 809 C5' C A 26 OK OK 808 825 826 810 840 C5' U A 27 OK OK 839 856 857 841 870 C5' C A 28 OK OK 869 886 887 871 901 C5' C A 29 OK OK 900 917 918 902 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P U A 5 distorted distorted 108 135 136 137 164 P A A 6 distorted distorted 142 165 166 167 197 P U A 7 distorted distorted 172 198 199 200 227 P G A 8 distorted distorted 205 228 229 230 261 P U A 9 distorted distorted 235 262 263 264 291 P A A 10 distorted distorted 269 292 293 294 324 P U A 11 distorted distorted 299 325 326 327 354 P U A 12 distorted distorted 332 355 356 357 384 P G A 13 distorted distorted 362 385 386 387 418 P G A 14 distorted distorted 392 419 420 421 452 P C A 15 distorted distorted 426 453 454 455 483 P A A 16 distorted distorted 460 484 485 486 516 P C A 17 distorted distorted 491 517 518 519 547 P U A 18 distorted distorted 524 548 549 550 577 P G A 19 distorted distorted 555 578 579 580 611 P A A 20 distorted distorted 585 612 613 614 644 P G A 21 distorted distorted 619 645 646 647 678 P C A 22 distorted distorted 652 679 680 681 709 P A A 23 distorted distorted 686 710 711 712 742 P U A 24 distorted distorted 717 743 744 745 772 P A A 25 distorted distorted 750 773 774 775 805 P C A 26 distorted distorted 780 806 807 808 836 P U A 27 distorted distorted 813 837 838 839 866 P C A 28 distorted distorted 844 867 868 869 897 P C A 29 distorted distorted 874 898 899 900 ---------------------------------------------------------------------------------