ID code: '1FYP' 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' G A 7 alpha beta 199 222 205 202 238 C1' C A 8 alpha beta 233 253 239 236 269 C1' A A 9 alpha beta 264 286 270 267 302 C1' C A 10 alpha beta 297 317 303 300 333 C1' C A 11 alpha beta 328 348 334 331 364 C1' U A 12 alpha beta 359 379 365 362 394 C1' U A 13 alpha beta 389 409 395 392 424 C1' C A 14 alpha beta 419 439 425 422 455 C1' G A 15 alpha beta 450 473 456 453 489 C1' G A 16 alpha beta 484 507 490 487 523 C1' G A 17 alpha beta 518 541 524 521 557 C1' U A 18 alpha beta 552 572 558 555 587 C1' G A 19 alpha beta 582 605 588 585 621 C1' A A 20 alpha beta 616 638 622 619 654 C1' A A 21 alpha beta 649 671 655 652 687 C1' G A 22 alpha beta 682 705 688 685 721 C1' U A 23 alpha beta 716 736 722 719 751 C1' C A 24 alpha beta 746 766 752 749 782 C1' G A 25 alpha beta 777 800 783 780 816 C1' C A 26 alpha beta 811 831 817 814 847 C1' C A 27 alpha beta 842 863 848 845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 7 OK OK 204 200 220 203 236 C2' C A 8 OK OK 238 234 251 237 267 C2' A A 9 OK OK 269 265 284 268 300 C2' C A 10 OK OK 302 298 315 301 331 C2' C A 11 OK OK 333 329 346 332 362 C2' U A 12 OK OK 364 360 377 363 392 C2' U A 13 OK OK 394 390 407 393 422 C2' C A 14 OK OK 424 420 437 423 453 C2' G A 15 OK OK 455 451 471 454 487 C2' G A 16 OK OK 489 485 505 488 521 C2' G A 17 OK OK 523 519 539 522 555 C2' U A 18 OK OK 557 553 570 556 585 C2' G A 19 OK OK 587 583 603 586 619 C2' A A 20 OK OK 621 617 636 620 652 C2' A A 21 OK OK 654 650 669 653 685 C2' G A 22 OK OK 687 683 703 686 719 C2' U A 23 OK OK 721 717 734 720 749 C2' C A 24 OK OK 751 747 764 750 780 C2' G A 25 OK OK 782 778 798 781 814 C2' C A 26 OK OK 816 812 829 815 845 C2' C A 27 OK OK 847 843 861 846 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 7 OK OK 198 219 201 202 234 C3' C A 8 OK OK 232 250 235 236 265 C3' A A 9 OK OK 263 283 266 267 298 C3' C A 10 OK OK 296 314 299 300 329 C3' C A 11 OK OK 327 345 330 331 360 C3' U A 12 OK OK 358 376 361 362 390 C3' U A 13 OK OK 388 406 391 392 420 C3' C A 14 OK OK 418 436 421 422 451 C3' G A 15 OK OK 449 470 452 453 485 C3' G A 16 OK OK 483 504 486 487 519 C3' G A 17 OK OK 517 538 520 521 553 C3' U A 18 OK OK 551 569 554 555 583 C3' G A 19 OK OK 581 602 584 585 617 C3' A A 20 OK OK 615 635 618 619 650 C3' A A 21 OK OK 648 668 651 652 683 C3' G A 22 OK OK 681 702 684 685 717 C3' U A 23 OK OK 715 733 718 719 747 C3' C A 24 OK OK 745 763 748 749 778 C3' G A 25 OK OK 776 797 779 780 812 C3' C A 26 OK OK 810 828 813 814 843 C3' C A 27 OK OK 841 859 844 845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 7 OK OK 200 218 197 199 232 C4' C A 8 OK OK 234 249 231 233 263 C4' A A 9 OK OK 265 282 262 264 296 C4' C A 10 OK OK 298 313 295 297 327 C4' C A 11 OK OK 329 344 326 328 358 C4' U A 12 OK OK 360 375 357 359 388 C4' U A 13 OK OK 390 405 387 389 418 C4' C A 14 OK OK 420 435 417 419 449 C4' G A 15 OK OK 451 469 448 450 483 C4' G A 16 OK OK 485 503 482 484 517 C4' G A 17 OK OK 519 537 516 518 551 C4' U A 18 OK OK 553 568 550 552 581 C4' G A 19 OK OK 583 601 580 582 615 C4' A A 20 OK OK 617 634 614 616 648 C4' A A 21 OK OK 650 667 647 649 681 C4' G A 22 OK OK 683 701 680 682 715 C4' U A 23 OK OK 717 732 714 716 745 C4' C A 24 OK OK 747 762 744 746 776 C4' G A 25 OK OK 778 796 775 777 810 C4' C A 26 OK OK 812 827 809 811 841 C4' C A 27 OK OK 843 858 840 842 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 7 OK OK 196 216 217 198 231 C5' C A 8 OK OK 230 247 248 232 262 C5' A A 9 OK OK 261 280 281 263 295 C5' C A 10 OK OK 294 311 312 296 326 C5' C A 11 OK OK 325 342 343 327 357 C5' U A 12 OK OK 356 373 374 358 387 C5' U A 13 OK OK 386 403 404 388 417 C5' C A 14 OK OK 416 433 434 418 448 C5' G A 15 OK OK 447 467 468 449 482 C5' G A 16 OK OK 481 501 502 483 516 C5' G A 17 OK OK 515 535 536 517 550 C5' U A 18 OK OK 549 566 567 551 580 C5' G A 19 OK OK 579 599 600 581 614 C5' A A 20 OK OK 613 632 633 615 647 C5' A A 21 OK OK 646 665 666 648 680 C5' G A 22 OK OK 679 699 700 681 714 C5' U A 23 OK OK 713 730 731 715 744 C5' C A 24 OK OK 743 760 761 745 775 C5' G A 25 OK OK 774 794 795 776 809 C5' C A 26 OK OK 808 825 826 810 840 C5' C A 27 OK OK 839 856 857 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 7 distorted distorted 170 194 195 196 227 P C A 8 distorted distorted 201 228 229 230 258 P A A 9 distorted distorted 235 259 260 261 291 P C A 10 distorted distorted 266 292 293 294 322 P C A 11 distorted distorted 299 323 324 325 353 P U A 12 distorted distorted 330 354 355 356 383 P U A 13 distorted distorted 361 384 385 386 413 P C A 14 distorted distorted 391 414 415 416 444 P G A 15 distorted distorted 421 445 446 447 478 P G A 16 distorted distorted 452 479 480 481 512 P G A 17 distorted distorted 486 513 514 515 546 P U A 18 distorted distorted 520 547 548 549 576 P G A 19 distorted distorted 554 577 578 579 610 P A A 20 distorted distorted 584 611 612 613 643 P A A 21 distorted distorted 618 644 645 646 676 P G A 22 distorted distorted 651 677 678 679 710 P U A 23 distorted distorted 684 711 712 713 740 P C A 24 distorted distorted 718 741 742 743 771 P G A 25 distorted distorted 748 772 773 774 805 P C A 26 distorted distorted 779 806 807 808 836 P C A 27 distorted distorted 813 837 838 839 ---------------------------------------------------------------------------------