ID code: '2M4Q' 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 1 1 alpha beta 4 27 10 7 44 C1' G 1 2 alpha beta 39 62 45 42 78 C1' C 1 3 alpha beta 73 93 79 76 109 C1' G 1 4 alpha beta 104 127 110 107 143 C1' U 1 5 alpha beta 138 158 144 141 173 C1' C 1 6 alpha beta 168 188 174 171 204 C1' A 1 7 alpha beta 199 221 205 202 237 C1' C 1 8 alpha beta 232 252 238 235 268 C1' A 1 9 alpha beta 263 285 269 266 301 C1' C 1 10 alpha beta 296 316 302 299 332 C1' C 1 11 alpha beta 327 347 333 330 363 C1' U 1 12 alpha beta 358 378 364 361 393 C1' U 1 13 alpha beta 388 408 394 391 423 C1' C 1 14 alpha beta 418 438 424 421 454 C1' G 1 15 alpha beta 449 472 455 452 488 C1' G 1 16 alpha beta 483 506 489 486 522 C1' G 1 17 alpha beta 517 540 523 520 556 C1' U 1 18 alpha beta 551 571 557 554 586 C1' G 1 19 alpha beta 581 604 587 584 620 C1' A 1 20 alpha beta 615 637 621 618 653 C1' A 1 21 alpha beta 648 670 654 651 686 C1' G 1 22 alpha beta 681 704 687 684 720 C1' U 1 23 alpha beta 715 735 721 718 750 C1' C 1 24 alpha beta 745 765 751 748 781 C1' G 1 25 alpha beta 776 799 782 779 815 C1' C 1 26 alpha beta 810 830 816 813 846 C1' C 1 27 alpha beta 841 862 847 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G 1 1 OK OK 9 5 25 8 42 C2' G 1 2 OK OK 44 40 60 43 76 C2' C 1 3 OK OK 78 74 91 77 107 C2' G 1 4 OK OK 109 105 125 108 141 C2' U 1 5 OK OK 143 139 156 142 171 C2' C 1 6 OK OK 173 169 186 172 202 C2' A 1 7 OK OK 204 200 219 203 235 C2' C 1 8 OK OK 237 233 250 236 266 C2' A 1 9 OK OK 268 264 283 267 299 C2' C 1 10 OK OK 301 297 314 300 330 C2' C 1 11 OK OK 332 328 345 331 361 C2' U 1 12 OK OK 363 359 376 362 391 C2' U 1 13 OK OK 393 389 406 392 421 C2' C 1 14 OK OK 423 419 436 422 452 C2' G 1 15 OK OK 454 450 470 453 486 C2' G 1 16 OK OK 488 484 504 487 520 C2' G 1 17 OK OK 522 518 538 521 554 C2' U 1 18 OK OK 556 552 569 555 584 C2' G 1 19 OK OK 586 582 602 585 618 C2' A 1 20 OK OK 620 616 635 619 651 C2' A 1 21 OK OK 653 649 668 652 684 C2' G 1 22 OK OK 686 682 702 685 718 C2' U 1 23 OK OK 720 716 733 719 748 C2' C 1 24 OK OK 750 746 763 749 779 C2' G 1 25 OK OK 781 777 797 780 813 C2' C 1 26 OK OK 815 811 828 814 844 C2' C 1 27 OK OK 846 842 860 845 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G 1 1 OK OK 3 24 6 7 40 C3' G 1 2 OK OK 38 59 41 42 74 C3' C 1 3 OK OK 72 90 75 76 105 C3' G 1 4 OK OK 103 124 106 107 139 C3' U 1 5 OK OK 137 155 140 141 169 C3' C 1 6 OK OK 167 185 170 171 200 C3' A 1 7 OK OK 198 218 201 202 233 C3' C 1 8 OK OK 231 249 234 235 264 C3' A 1 9 OK OK 262 282 265 266 297 C3' C 1 10 OK OK 295 313 298 299 328 C3' C 1 11 OK OK 326 344 329 330 359 C3' U 1 12 OK OK 357 375 360 361 389 C3' U 1 13 OK OK 387 405 390 391 419 C3' C 1 14 OK OK 417 435 420 421 450 C3' G 1 15 OK OK 448 469 451 452 484 C3' G 1 16 OK OK 482 503 485 486 518 C3' G 1 17 OK OK 516 537 519 520 552 C3' U 1 18 OK OK 550 568 553 554 582 C3' G 1 19 OK OK 580 601 583 584 616 C3' A 1 20 OK OK 614 634 617 618 649 C3' A 1 21 OK OK 647 667 650 651 682 C3' G 1 22 OK OK 680 701 683 684 716 C3' U 1 23 OK OK 714 732 717 718 746 C3' C 1 24 OK OK 744 762 747 748 777 C3' G 1 25 OK OK 775 796 778 779 811 C3' C 1 26 OK OK 809 827 812 813 842 C3' C 1 27 OK OK 840 858 843 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G 1 1 OK OK 5 23 2 4 38 C4' G 1 2 OK OK 40 58 37 39 72 C4' C 1 3 OK OK 74 89 71 73 103 C4' G 1 4 OK OK 105 123 102 104 137 C4' U 1 5 OK OK 139 154 136 138 167 C4' C 1 6 OK OK 169 184 166 168 198 C4' A 1 7 OK OK 200 217 197 199 231 C4' C 1 8 OK OK 233 248 230 232 262 C4' A 1 9 OK OK 264 281 261 263 295 C4' C 1 10 OK OK 297 312 294 296 326 C4' C 1 11 OK OK 328 343 325 327 357 C4' U 1 12 OK OK 359 374 356 358 387 C4' U 1 13 OK OK 389 404 386 388 417 C4' C 1 14 OK OK 419 434 416 418 448 C4' G 1 15 OK OK 450 468 447 449 482 C4' G 1 16 OK OK 484 502 481 483 516 C4' G 1 17 OK OK 518 536 515 517 550 C4' U 1 18 OK OK 552 567 549 551 580 C4' G 1 19 OK OK 582 600 579 581 614 C4' A 1 20 OK OK 616 633 613 615 647 C4' A 1 21 OK OK 649 666 646 648 680 C4' G 1 22 OK OK 682 700 679 681 714 C4' U 1 23 OK OK 716 731 713 715 744 C4' C 1 24 OK OK 746 761 743 745 775 C4' G 1 25 OK OK 777 795 774 776 809 C4' C 1 26 OK OK 811 826 808 810 840 C4' C 1 27 OK OK 842 857 839 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G 1 1 OK OK 1 21 22 3 37 C5' G 1 2 OK OK 36 56 57 38 71 C5' C 1 3 OK OK 70 87 88 72 102 C5' G 1 4 OK OK 101 121 122 103 136 C5' U 1 5 OK OK 135 152 153 137 166 C5' C 1 6 OK OK 165 182 183 167 197 C5' A 1 7 OK OK 196 215 216 198 230 C5' C 1 8 OK OK 229 246 247 231 261 C5' A 1 9 OK OK 260 279 280 262 294 C5' C 1 10 OK OK 293 310 311 295 325 C5' C 1 11 OK OK 324 341 342 326 356 C5' U 1 12 OK OK 355 372 373 357 386 C5' U 1 13 OK OK 385 402 403 387 416 C5' C 1 14 OK OK 415 432 433 417 447 C5' G 1 15 OK OK 446 466 467 448 481 C5' G 1 16 OK OK 480 500 501 482 515 C5' G 1 17 OK OK 514 534 535 516 549 C5' U 1 18 OK OK 548 565 566 550 579 C5' G 1 19 OK OK 578 598 599 580 613 C5' A 1 20 OK OK 612 631 632 614 646 C5' A 1 21 OK OK 645 664 665 647 679 C5' G 1 22 OK OK 678 698 699 680 713 C5' U 1 23 OK OK 712 729 730 714 743 C5' C 1 24 OK OK 742 759 760 744 774 C5' G 1 25 OK OK 773 793 794 775 808 C5' C 1 26 OK OK 807 824 825 809 839 C5' C 1 27 OK OK 838 855 856 840 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G 1 2 distorted distorted 6 34 35 36 67 P C 1 3 distorted distorted 41 68 69 70 98 P G 1 4 distorted distorted 75 99 100 101 132 P U 1 5 distorted distorted 106 133 134 135 162 P C 1 6 distorted distorted 140 163 164 165 193 P A 1 7 distorted distorted 170 194 195 196 226 P C 1 8 distorted distorted 201 227 228 229 257 P A 1 9 distorted distorted 234 258 259 260 290 P C 1 10 distorted distorted 265 291 292 293 321 P C 1 11 distorted distorted 298 322 323 324 352 P U 1 12 distorted distorted 329 353 354 355 382 P U 1 13 distorted distorted 360 383 384 385 412 P C 1 14 distorted distorted 390 413 414 415 443 P G 1 15 distorted distorted 420 444 445 446 477 P G 1 16 distorted distorted 451 478 479 480 511 P G 1 17 distorted distorted 485 512 513 514 545 P U 1 18 distorted distorted 519 546 547 548 575 P G 1 19 distorted distorted 553 576 577 578 609 P A 1 20 distorted distorted 583 610 611 612 642 P A 1 21 distorted distorted 617 643 644 645 675 P G 1 22 distorted distorted 650 676 677 678 709 P U 1 23 distorted distorted 683 710 711 712 739 P C 1 24 distorted distorted 717 740 741 742 770 P G 1 25 distorted distorted 747 771 772 773 804 P C 1 26 distorted distorted 778 805 806 807 835 P C 1 27 distorted distorted 812 836 837 838 ---------------------------------------------------------------------------------