ID code: '28SP' 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' C A 3 alpha beta 73 93 79 76 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' C A 6 alpha beta 168 188 174 171 204 C1' A A 7 alpha beta 199 221 205 202 237 C1' G A 8 alpha beta 232 255 238 235 271 C1' G A 9 alpha beta 266 289 272 269 305 C1' U A 10 alpha beta 300 320 306 303 335 C1' C A 11 alpha beta 330 350 336 333 366 C1' C A 12 alpha beta 361 381 367 364 397 C1' G A 13 alpha beta 392 415 398 395 431 C1' G A 14 alpha beta 426 449 432 429 465 C1' A A 15 alpha beta 460 482 466 463 498 C1' A A 16 alpha beta 493 515 499 496 531 C1' G A 17 alpha beta 526 549 532 529 565 C1' G A 18 alpha beta 560 583 566 563 599 C1' A A 19 alpha beta 594 616 600 597 632 C1' A A 20 alpha beta 627 649 633 630 665 C1' G A 21 alpha beta 660 683 666 663 699 C1' C A 22 alpha beta 694 714 700 697 730 C1' A A 23 alpha beta 725 747 731 728 763 C1' G A 24 alpha beta 758 781 764 761 797 C1' C A 25 alpha beta 792 812 798 795 828 C1' G A 26 alpha beta 823 846 829 826 862 C1' C A 27 alpha beta 857 877 863 860 893 C1' C A 28 alpha beta 888 909 894 891 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' G A 4 OK OK 109 105 125 108 141 C2' U A 5 OK OK 143 139 156 142 171 C2' C A 6 OK OK 173 169 186 172 202 C2' A A 7 OK OK 204 200 219 203 235 C2' G A 8 OK OK 237 233 253 236 269 C2' G A 9 OK OK 271 267 287 270 303 C2' U A 10 OK OK 305 301 318 304 333 C2' C A 11 OK OK 335 331 348 334 364 C2' C A 12 OK OK 366 362 379 365 395 C2' G A 13 OK OK 397 393 413 396 429 C2' G A 14 OK OK 431 427 447 430 463 C2' A A 15 OK OK 465 461 480 464 496 C2' A A 16 OK OK 498 494 513 497 529 C2' G A 17 OK OK 531 527 547 530 563 C2' G A 18 OK OK 565 561 581 564 597 C2' A A 19 OK OK 599 595 614 598 630 C2' A A 20 OK OK 632 628 647 631 663 C2' G A 21 OK OK 665 661 681 664 697 C2' C A 22 OK OK 699 695 712 698 728 C2' A A 23 OK OK 730 726 745 729 761 C2' G A 24 OK OK 763 759 779 762 795 C2' C A 25 OK OK 797 793 810 796 826 C2' G A 26 OK OK 828 824 844 827 860 C2' C A 27 OK OK 862 858 875 861 891 C2' C A 28 OK OK 893 889 907 892 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' G A 4 OK OK 103 124 106 107 139 C3' U A 5 OK OK 137 155 140 141 169 C3' C A 6 OK OK 167 185 170 171 200 C3' A A 7 OK OK 198 218 201 202 233 C3' G A 8 OK OK 231 252 234 235 267 C3' G A 9 OK OK 265 286 268 269 301 C3' U A 10 OK OK 299 317 302 303 331 C3' C A 11 OK OK 329 347 332 333 362 C3' C A 12 OK OK 360 378 363 364 393 C3' G A 13 OK OK 391 412 394 395 427 C3' G A 14 OK OK 425 446 428 429 461 C3' A A 15 OK OK 459 479 462 463 494 C3' A A 16 OK OK 492 512 495 496 527 C3' G A 17 OK OK 525 546 528 529 561 C3' G A 18 OK OK 559 580 562 563 595 C3' A A 19 OK OK 593 613 596 597 628 C3' A A 20 OK OK 626 646 629 630 661 C3' G A 21 OK OK 659 680 662 663 695 C3' C A 22 OK OK 693 711 696 697 726 C3' A A 23 OK OK 724 744 727 728 759 C3' G A 24 OK OK 757 778 760 761 793 C3' C A 25 OK OK 791 809 794 795 824 C3' G A 26 OK OK 822 843 825 826 858 C3' C A 27 OK OK 856 874 859 860 889 C3' C A 28 OK OK 887 905 890 891 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' G A 4 OK OK 105 123 102 104 137 C4' U A 5 OK OK 139 154 136 138 167 C4' C A 6 OK OK 169 184 166 168 198 C4' A A 7 OK OK 200 217 197 199 231 C4' G A 8 OK OK 233 251 230 232 265 C4' G A 9 OK OK 267 285 264 266 299 C4' U A 10 OK OK 301 316 298 300 329 C4' C A 11 OK OK 331 346 328 330 360 C4' C A 12 OK OK 362 377 359 361 391 C4' G A 13 OK OK 393 411 390 392 425 C4' G A 14 OK OK 427 445 424 426 459 C4' A A 15 OK OK 461 478 458 460 492 C4' A A 16 OK OK 494 511 491 493 525 C4' G A 17 OK OK 527 545 524 526 559 C4' G A 18 OK OK 561 579 558 560 593 C4' A A 19 OK OK 595 612 592 594 626 C4' A A 20 OK OK 628 645 625 627 659 C4' G A 21 OK OK 661 679 658 660 693 C4' C A 22 OK OK 695 710 692 694 724 C4' A A 23 OK OK 726 743 723 725 757 C4' G A 24 OK OK 759 777 756 758 791 C4' C A 25 OK OK 793 808 790 792 822 C4' G A 26 OK OK 824 842 821 823 856 C4' C A 27 OK OK 858 873 855 857 887 C4' C A 28 OK OK 889 904 886 888 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' G A 4 OK OK 101 121 122 103 136 C5' U A 5 OK OK 135 152 153 137 166 C5' C A 6 OK OK 165 182 183 167 197 C5' A A 7 OK OK 196 215 216 198 230 C5' G A 8 OK OK 229 249 250 231 264 C5' G A 9 OK OK 263 283 284 265 298 C5' U A 10 OK OK 297 314 315 299 328 C5' C A 11 OK OK 327 344 345 329 359 C5' C A 12 OK OK 358 375 376 360 390 C5' G A 13 OK OK 389 409 410 391 424 C5' G A 14 OK OK 423 443 444 425 458 C5' A A 15 OK OK 457 476 477 459 491 C5' A A 16 OK OK 490 509 510 492 524 C5' G A 17 OK OK 523 543 544 525 558 C5' G A 18 OK OK 557 577 578 559 592 C5' A A 19 OK OK 591 610 611 593 625 C5' A A 20 OK OK 624 643 644 626 658 C5' G A 21 OK OK 657 677 678 659 692 C5' C A 22 OK OK 691 708 709 693 723 C5' A A 23 OK OK 722 741 742 724 756 C5' G A 24 OK OK 755 775 776 757 790 C5' C A 25 OK OK 789 806 807 791 821 C5' G A 26 OK OK 820 840 841 822 855 C5' C A 27 OK OK 854 871 872 856 886 C5' C A 28 OK OK 885 902 903 887 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 75 99 100 101 132 P U A 5 distorted distorted 106 133 134 135 162 P C A 6 distorted distorted 140 163 164 165 193 P A A 7 distorted distorted 170 194 195 196 226 P G A 8 distorted distorted 201 227 228 229 260 P G A 9 distorted distorted 234 261 262 263 294 P U A 10 distorted distorted 268 295 296 297 324 P C A 11 distorted distorted 302 325 326 327 355 P C A 12 distorted distorted 332 356 357 358 386 P G A 13 distorted distorted 363 387 388 389 420 P G A 14 distorted distorted 394 421 422 423 454 P A A 15 distorted distorted 428 455 456 457 487 P A A 16 distorted distorted 462 488 489 490 520 P G A 17 distorted distorted 495 521 522 523 554 P G A 18 distorted distorted 528 555 556 557 588 P A A 19 distorted distorted 562 589 590 591 621 P A A 20 distorted distorted 596 622 623 624 654 P G A 21 distorted distorted 629 655 656 657 688 P C A 22 distorted distorted 662 689 690 691 719 P A A 23 distorted distorted 696 720 721 722 752 P G A 24 distorted distorted 727 753 754 755 786 P C A 25 distorted distorted 760 787 788 789 817 P G A 26 distorted distorted 794 818 819 820 851 P C A 27 distorted distorted 825 852 853 854 882 P C A 28 distorted distorted 859 883 884 885 ---------------------------------------------------------------------------------