ID code: '1F7F' 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' A A 4 alpha beta 106 128 112 109 144 C1' G A 5 alpha beta 139 162 145 142 178 C1' U A 6 alpha beta 173 193 179 176 208 C1' C A 7 alpha beta 203 223 209 206 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' G A 9 alpha beta 265 288 271 268 304 C1' G A 10 alpha beta 299 322 305 302 338 C1' U A 11 alpha beta 333 353 339 336 368 C1' C A 12 alpha beta 363 383 369 366 399 C1' U A 13 alpha beta 394 414 400 397 429 C1' U A 14 alpha beta 424 444 430 427 459 C1' C A 15 alpha beta 454 474 460 457 490 C1' G A 16 alpha beta 485 508 491 488 524 C1' G A 17 alpha beta 519 542 525 522 558 C1' A A 18 alpha beta 553 575 559 556 591 C1' C A 19 alpha beta 586 606 592 589 622 C1' C A 20 alpha beta 617 637 623 620 653 C1' G A 21 alpha beta 648 671 654 651 687 C1' G A 22 alpha beta 682 705 688 685 721 C1' C A 23 alpha beta 716 736 722 719 752 C1' U A 24 alpha beta 747 767 753 750 782 C1' U A 25 alpha beta 777 797 783 780 812 C1' C A 26 alpha beta 807 827 813 810 843 C1' C A 27 alpha beta 838 859 844 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 4 OK OK 111 107 126 110 142 C2' G A 5 OK OK 144 140 160 143 176 C2' U A 6 OK OK 178 174 191 177 206 C2' C A 7 OK OK 208 204 221 207 237 C2' C A 8 OK OK 239 235 252 238 268 C2' G A 9 OK OK 270 266 286 269 302 C2' G A 10 OK OK 304 300 320 303 336 C2' U A 11 OK OK 338 334 351 337 366 C2' C A 12 OK OK 368 364 381 367 397 C2' U A 13 OK OK 399 395 412 398 427 C2' U A 14 OK OK 429 425 442 428 457 C2' C A 15 OK OK 459 455 472 458 488 C2' G A 16 OK OK 490 486 506 489 522 C2' G A 17 OK OK 524 520 540 523 556 C2' A A 18 OK OK 558 554 573 557 589 C2' C A 19 OK OK 591 587 604 590 620 C2' C A 20 OK OK 622 618 635 621 651 C2' G A 21 OK OK 653 649 669 652 685 C2' G A 22 OK OK 687 683 703 686 719 C2' C A 23 OK OK 721 717 734 720 750 C2' U A 24 OK OK 752 748 765 751 780 C2' U A 25 OK OK 782 778 795 781 810 C2' C A 26 OK OK 812 808 825 811 841 C2' C A 27 OK OK 843 839 857 842 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 105 125 108 109 140 C3' G A 5 OK OK 138 159 141 142 174 C3' U A 6 OK OK 172 190 175 176 204 C3' C A 7 OK OK 202 220 205 206 235 C3' C A 8 OK OK 233 251 236 237 266 C3' G A 9 OK OK 264 285 267 268 300 C3' G A 10 OK OK 298 319 301 302 334 C3' U A 11 OK OK 332 350 335 336 364 C3' C A 12 OK OK 362 380 365 366 395 C3' U A 13 OK OK 393 411 396 397 425 C3' U A 14 OK OK 423 441 426 427 455 C3' C A 15 OK OK 453 471 456 457 486 C3' G A 16 OK OK 484 505 487 488 520 C3' G A 17 OK OK 518 539 521 522 554 C3' A A 18 OK OK 552 572 555 556 587 C3' C A 19 OK OK 585 603 588 589 618 C3' C A 20 OK OK 616 634 619 620 649 C3' G A 21 OK OK 647 668 650 651 683 C3' G A 22 OK OK 681 702 684 685 717 C3' C A 23 OK OK 715 733 718 719 748 C3' U A 24 OK OK 746 764 749 750 778 C3' U A 25 OK OK 776 794 779 780 808 C3' C A 26 OK OK 806 824 809 810 839 C3' C A 27 OK OK 837 855 840 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 107 124 104 106 138 C4' G A 5 OK OK 140 158 137 139 172 C4' U A 6 OK OK 174 189 171 173 202 C4' C A 7 OK OK 204 219 201 203 233 C4' C A 8 OK OK 235 250 232 234 264 C4' G A 9 OK OK 266 284 263 265 298 C4' G A 10 OK OK 300 318 297 299 332 C4' U A 11 OK OK 334 349 331 333 362 C4' C A 12 OK OK 364 379 361 363 393 C4' U A 13 OK OK 395 410 392 394 423 C4' U A 14 OK OK 425 440 422 424 453 C4' C A 15 OK OK 455 470 452 454 484 C4' G A 16 OK OK 486 504 483 485 518 C4' G A 17 OK OK 520 538 517 519 552 C4' A A 18 OK OK 554 571 551 553 585 C4' C A 19 OK OK 587 602 584 586 616 C4' C A 20 OK OK 618 633 615 617 647 C4' G A 21 OK OK 649 667 646 648 681 C4' G A 22 OK OK 683 701 680 682 715 C4' C A 23 OK OK 717 732 714 716 746 C4' U A 24 OK OK 748 763 745 747 776 C4' U A 25 OK OK 778 793 775 777 806 C4' C A 26 OK OK 808 823 805 807 837 C4' C A 27 OK OK 839 854 836 838 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 103 122 123 105 137 C5' G A 5 OK OK 136 156 157 138 171 C5' U A 6 OK OK 170 187 188 172 201 C5' C A 7 OK OK 200 217 218 202 232 C5' C A 8 OK OK 231 248 249 233 263 C5' G A 9 OK OK 262 282 283 264 297 C5' G A 10 OK OK 296 316 317 298 331 C5' U A 11 OK OK 330 347 348 332 361 C5' C A 12 OK OK 360 377 378 362 392 C5' U A 13 OK OK 391 408 409 393 422 C5' U A 14 OK OK 421 438 439 423 452 C5' C A 15 OK OK 451 468 469 453 483 C5' G A 16 OK OK 482 502 503 484 517 C5' G A 17 OK OK 516 536 537 518 551 C5' A A 18 OK OK 550 569 570 552 584 C5' C A 19 OK OK 583 600 601 585 615 C5' C A 20 OK OK 614 631 632 616 646 C5' G A 21 OK OK 645 665 666 647 680 C5' G A 22 OK OK 679 699 700 681 714 C5' C A 23 OK OK 713 730 731 715 745 C5' U A 24 OK OK 744 761 762 746 775 C5' U A 25 OK OK 774 791 792 776 805 C5' C A 26 OK OK 804 821 822 806 836 C5' C A 27 OK OK 835 852 853 837 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 4 distorted distorted 75 101 102 103 133 P G A 5 distorted distorted 108 134 135 136 167 P U A 6 distorted distorted 141 168 169 170 197 P C A 7 distorted distorted 175 198 199 200 228 P C A 8 distorted distorted 205 229 230 231 259 P G A 9 distorted distorted 236 260 261 262 293 P G A 10 distorted distorted 267 294 295 296 327 P U A 11 distorted distorted 301 328 329 330 357 P C A 12 distorted distorted 335 358 359 360 388 P U A 13 distorted distorted 365 389 390 391 418 P U A 14 distorted distorted 396 419 420 421 448 P C A 15 distorted distorted 426 449 450 451 479 P G A 16 distorted distorted 456 480 481 482 513 P G A 17 distorted distorted 487 514 515 516 547 P A A 18 distorted distorted 521 548 549 550 580 P C A 19 distorted distorted 555 581 582 583 611 P C A 20 distorted distorted 588 612 613 614 642 P G A 21 distorted distorted 619 643 644 645 676 P G A 22 distorted distorted 650 677 678 679 710 P C A 23 distorted distorted 684 711 712 713 741 P U A 24 distorted distorted 718 742 743 744 771 P U A 25 distorted distorted 749 772 773 774 801 P C A 26 distorted distorted 779 802 803 804 832 P C A 27 distorted distorted 809 833 834 835 ---------------------------------------------------------------------------------