ID code: '1F7I' 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' U A 7 alpha beta 203 223 209 206 238 C1' C A 8 alpha beta 233 253 239 236 269 C1' G A 9 alpha beta 264 287 270 267 303 C1' G A 10 alpha beta 298 321 304 301 337 C1' U A 11 alpha beta 332 352 338 335 367 C1' C A 12 alpha beta 362 382 368 365 398 C1' U A 13 alpha beta 393 413 399 396 428 C1' U A 14 alpha beta 423 443 429 426 458 C1' C A 15 alpha beta 453 473 459 456 489 C1' G A 16 alpha beta 484 507 490 487 523 C1' G A 17 alpha beta 518 541 524 521 557 C1' A A 18 alpha beta 552 574 558 555 590 C1' C A 19 alpha beta 585 605 591 588 621 C1' C A 20 alpha beta 616 636 622 619 652 C1' G A 21 alpha beta 647 670 653 650 686 C1' G A 22 alpha beta 681 704 687 684 720 C1' C A 23 alpha beta 715 735 721 718 751 C1' U A 24 alpha beta 746 766 752 749 781 C1' U A 25 alpha beta 776 796 782 779 811 C1' C A 26 alpha beta 806 826 812 809 842 C1' C A 27 alpha beta 837 858 843 840 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 7 OK OK 208 204 221 207 236 C2' C A 8 OK OK 238 234 251 237 267 C2' G A 9 OK OK 269 265 285 268 301 C2' G A 10 OK OK 303 299 319 302 335 C2' U A 11 OK OK 337 333 350 336 365 C2' C A 12 OK OK 367 363 380 366 396 C2' U A 13 OK OK 398 394 411 397 426 C2' U A 14 OK OK 428 424 441 427 456 C2' C A 15 OK OK 458 454 471 457 487 C2' G A 16 OK OK 489 485 505 488 521 C2' G A 17 OK OK 523 519 539 522 555 C2' A A 18 OK OK 557 553 572 556 588 C2' C A 19 OK OK 590 586 603 589 619 C2' C A 20 OK OK 621 617 634 620 650 C2' G A 21 OK OK 652 648 668 651 684 C2' G A 22 OK OK 686 682 702 685 718 C2' C A 23 OK OK 720 716 733 719 749 C2' U A 24 OK OK 751 747 764 750 779 C2' U A 25 OK OK 781 777 794 780 809 C2' C A 26 OK OK 811 807 824 810 840 C2' C A 27 OK OK 842 838 856 841 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 7 OK OK 202 220 205 206 234 C3' C A 8 OK OK 232 250 235 236 265 C3' G A 9 OK OK 263 284 266 267 299 C3' G A 10 OK OK 297 318 300 301 333 C3' U A 11 OK OK 331 349 334 335 363 C3' C A 12 OK OK 361 379 364 365 394 C3' U A 13 OK OK 392 410 395 396 424 C3' U A 14 OK OK 422 440 425 426 454 C3' C A 15 OK OK 452 470 455 456 485 C3' G A 16 OK OK 483 504 486 487 519 C3' G A 17 OK OK 517 538 520 521 553 C3' A A 18 OK OK 551 571 554 555 586 C3' C A 19 OK OK 584 602 587 588 617 C3' C A 20 OK OK 615 633 618 619 648 C3' G A 21 OK OK 646 667 649 650 682 C3' G A 22 OK OK 680 701 683 684 716 C3' C A 23 OK OK 714 732 717 718 747 C3' U A 24 OK OK 745 763 748 749 777 C3' U A 25 OK OK 775 793 778 779 807 C3' C A 26 OK OK 805 823 808 809 838 C3' C A 27 OK OK 836 854 839 840 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 7 OK OK 204 219 201 203 232 C4' C A 8 OK OK 234 249 231 233 263 C4' G A 9 OK OK 265 283 262 264 297 C4' G A 10 OK OK 299 317 296 298 331 C4' U A 11 OK OK 333 348 330 332 361 C4' C A 12 OK OK 363 378 360 362 392 C4' U A 13 OK OK 394 409 391 393 422 C4' U A 14 OK OK 424 439 421 423 452 C4' C A 15 OK OK 454 469 451 453 483 C4' G A 16 OK OK 485 503 482 484 517 C4' G A 17 OK OK 519 537 516 518 551 C4' A A 18 OK OK 553 570 550 552 584 C4' C A 19 OK OK 586 601 583 585 615 C4' C A 20 OK OK 617 632 614 616 646 C4' G A 21 OK OK 648 666 645 647 680 C4' G A 22 OK OK 682 700 679 681 714 C4' C A 23 OK OK 716 731 713 715 745 C4' U A 24 OK OK 747 762 744 746 775 C4' U A 25 OK OK 777 792 774 776 805 C4' C A 26 OK OK 807 822 804 806 836 C4' C A 27 OK OK 838 853 835 837 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 7 OK OK 200 217 218 202 231 C5' C A 8 OK OK 230 247 248 232 262 C5' G A 9 OK OK 261 281 282 263 296 C5' G A 10 OK OK 295 315 316 297 330 C5' U A 11 OK OK 329 346 347 331 360 C5' C A 12 OK OK 359 376 377 361 391 C5' U A 13 OK OK 390 407 408 392 421 C5' U A 14 OK OK 420 437 438 422 451 C5' C A 15 OK OK 450 467 468 452 482 C5' G A 16 OK OK 481 501 502 483 516 C5' G A 17 OK OK 515 535 536 517 550 C5' A A 18 OK OK 549 568 569 551 583 C5' C A 19 OK OK 582 599 600 584 614 C5' C A 20 OK OK 613 630 631 615 645 C5' G A 21 OK OK 644 664 665 646 679 C5' G A 22 OK OK 678 698 699 680 713 C5' C A 23 OK OK 712 729 730 714 744 C5' U A 24 OK OK 743 760 761 745 774 C5' U A 25 OK OK 773 790 791 775 804 C5' C A 26 OK OK 803 820 821 805 835 C5' C A 27 OK OK 834 851 852 836 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 7 distorted distorted 175 198 199 200 227 P C A 8 distorted distorted 205 228 229 230 258 P G A 9 distorted distorted 235 259 260 261 292 P G A 10 distorted distorted 266 293 294 295 326 P U A 11 distorted distorted 300 327 328 329 356 P C A 12 distorted distorted 334 357 358 359 387 P U A 13 distorted distorted 364 388 389 390 417 P U A 14 distorted distorted 395 418 419 420 447 P C A 15 distorted distorted 425 448 449 450 478 P G A 16 distorted distorted 455 479 480 481 512 P G A 17 distorted distorted 486 513 514 515 546 P A A 18 distorted distorted 520 547 548 549 579 P C A 19 distorted distorted 554 580 581 582 610 P C A 20 distorted distorted 587 611 612 613 641 P G A 21 distorted distorted 618 642 643 644 675 P G A 22 distorted distorted 649 676 677 678 709 P C A 23 distorted distorted 683 710 711 712 740 P U A 24 distorted distorted 717 741 742 743 770 P U A 25 distorted distorted 748 771 772 773 800 P C A 26 distorted distorted 778 801 802 803 831 P C A 27 distorted distorted 808 832 833 834 ---------------------------------------------------------------------------------