ID code: '1Q2T' 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' MCY A 1 alpha beta 13 21 1 10 42 C1' DC A 2 alpha beta 38 57 43 41 73 C1' DT A 3 alpha beta 69 89 74 72 105 C1' DC A 4 alpha beta 101 120 106 104 136 C1' DT A 5 alpha beta 132 152 137 135 168 C1' DC A 6 alpha beta 164 183 169 167 199 C1' DC A 7 alpha beta 195 215 200 198 230 C1' MCY B 1 alpha beta 234 242 222 231 263 C1' DC B 2 alpha beta 259 278 264 262 294 C1' DT B 3 alpha beta 290 310 295 293 326 C1' DC B 4 alpha beta 322 341 327 325 357 C1' DT B 5 alpha beta 353 373 358 356 389 C1' DC B 6 alpha beta 385 404 390 388 420 C1' DC B 7 alpha beta 416 436 421 419 451 C1' MCY C 1 alpha beta 455 463 443 452 484 C1' DC C 2 alpha beta 480 499 485 483 514 C1' DT C 3 alpha beta 510 530 515 513 546 C1' DC C 4 alpha beta 542 561 547 545 576 C1' DT C 5 alpha beta 572 592 577 575 608 C1' DC C 6 alpha beta 604 623 609 607 638 C1' DC C 7 alpha beta 634 654 639 637 668 C1' MCY D 1 alpha beta 672 680 660 669 701 C1' DC D 2 alpha beta 697 716 702 700 731 C1' DT D 3 alpha beta 727 747 732 730 763 C1' DC D 4 alpha beta 759 778 764 762 793 C1' DT D 5 alpha beta 789 809 794 792 825 C1' DC D 6 alpha beta 821 840 826 824 855 C1' DC D 7 alpha beta 851 871 856 854 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' MCY A 1 OK OK 9 11 22 23 41 C2' DC A 2 OK OK 42 39 55 56 72 C2' DT A 3 OK OK 73 70 87 88 104 C2' DC A 4 OK OK 105 102 118 119 135 C2' DT A 5 OK OK 136 133 150 151 167 C2' DC A 6 OK OK 168 165 181 182 198 C2' DC A 7 OK OK 199 196 213 214 231 C2' MCY B 1 OK OK 230 232 243 244 262 C2' DC B 2 OK OK 263 260 276 277 293 C2' DT B 3 OK OK 294 291 308 309 325 C2' DC B 4 OK OK 326 323 339 340 356 C2' DT B 5 OK OK 357 354 371 372 388 C2' DC B 6 OK OK 389 386 402 403 419 C2' DC B 7 OK OK 420 417 434 435 452 C2' MCY C 1 OK OK 451 453 464 465 483 C2' DC C 2 OK OK 484 481 497 498 513 C2' DT C 3 OK OK 514 511 528 529 545 C2' DC C 4 OK OK 546 543 559 560 575 C2' DT C 5 OK OK 576 573 590 591 607 C2' DC C 6 OK OK 608 605 621 622 637 C2' DC C 7 OK OK 638 635 652 653 669 C2' MCY D 1 OK OK 668 670 681 682 700 C2' DC D 2 OK OK 701 698 714 715 730 C2' DT D 3 OK OK 731 728 745 746 762 C2' DC D 4 OK OK 763 760 776 777 792 C2' DT D 5 OK OK 793 790 807 808 824 C2' DC D 6 OK OK 825 822 838 839 854 C2' DC D 7 OK OK 855 852 869 870 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 11 C3' MCY A 1 OK OK 12 24 14 10 39 C3' DC A 2 OK OK 37 54 40 41 70 C3' DT A 3 OK OK 68 86 71 72 102 C3' DC A 4 OK OK 100 117 103 104 133 C3' DT A 5 OK OK 131 149 134 135 165 C3' DC A 6 OK OK 163 180 166 167 196 C3' DC A 7 OK OK 194 211 197 198 232 C3' MCY B 1 OK OK 233 245 235 231 260 C3' DC B 2 OK OK 258 275 261 262 291 C3' DT B 3 OK OK 289 307 292 293 323 C3' DC B 4 OK OK 321 338 324 325 354 C3' DT B 5 OK OK 352 370 355 356 386 C3' DC B 6 OK OK 384 401 387 388 417 C3' DC B 7 OK OK 415 432 418 419 453 C3' MCY C 1 OK OK 454 466 456 452 481 C3' DC C 2 OK OK 479 496 482 483 511 C3' DT C 3 OK OK 509 527 512 513 543 C3' DC C 4 OK OK 541 558 544 545 573 C3' DT C 5 OK OK 571 589 574 575 605 C3' DC C 6 OK OK 603 620 606 607 635 C3' DC C 7 OK OK 633 650 636 637 670 C3' MCY D 1 OK OK 671 683 673 669 698 C3' DC D 2 OK OK 696 713 699 700 728 C3' DT D 3 OK OK 726 744 729 730 760 C3' DC D 4 OK OK 758 775 761 762 790 C3' DT D 5 OK OK 788 806 791 792 822 C3' DC D 6 OK OK 820 837 823 824 852 C3' DC D 7 OK OK 850 867 853 854 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 12 C4' MCY A 1 OK OK 11 25 15 13 37 C4' DC A 2 OK OK 39 53 36 38 68 C4' DT A 3 OK OK 70 85 67 69 100 C4' DC A 4 OK OK 102 116 99 101 131 C4' DT A 5 OK OK 133 148 130 132 163 C4' DC A 6 OK OK 165 179 162 164 194 C4' DC A 7 OK OK 196 210 193 195 233 C4' MCY B 1 OK OK 232 246 236 234 258 C4' DC B 2 OK OK 260 274 257 259 289 C4' DT B 3 OK OK 291 306 288 290 321 C4' DC B 4 OK OK 323 337 320 322 352 C4' DT B 5 OK OK 354 369 351 353 384 C4' DC B 6 OK OK 386 400 383 385 415 C4' DC B 7 OK OK 417 431 414 416 454 C4' MCY C 1 OK OK 453 467 457 455 479 C4' DC C 2 OK OK 481 495 478 480 509 C4' DT C 3 OK OK 511 526 508 510 541 C4' DC C 4 OK OK 543 557 540 542 571 C4' DT C 5 OK OK 573 588 570 572 603 C4' DC C 6 OK OK 605 619 602 604 633 C4' DC C 7 OK OK 635 649 632 634 671 C4' MCY D 1 OK OK 670 684 674 672 696 C4' DC D 2 OK OK 698 712 695 697 726 C4' DT D 3 OK OK 728 743 725 727 758 C4' DC D 4 OK OK 760 774 757 759 788 C4' DT D 5 OK OK 790 805 787 789 820 C4' DC D 6 OK OK 822 836 819 821 850 C4' DC D 7 OK OK 852 866 849 851 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 15 C5' MCY A 1 OK OK 16 26 27 12 36 C5' DC A 2 OK OK 35 51 52 37 67 C5' DT A 3 OK OK 66 83 84 68 99 C5' DC A 4 OK OK 98 114 115 100 130 C5' DT A 5 OK OK 129 146 147 131 162 C5' DC A 6 OK OK 161 177 178 163 193 C5' DC A 7 OK OK 192 208 209 194 236 C5' MCY B 1 OK OK 237 247 248 233 257 C5' DC B 2 OK OK 256 272 273 258 288 C5' DT B 3 OK OK 287 304 305 289 320 C5' DC B 4 OK OK 319 335 336 321 351 C5' DT B 5 OK OK 350 367 368 352 383 C5' DC B 6 OK OK 382 398 399 384 414 C5' DC B 7 OK OK 413 429 430 415 457 C5' MCY C 1 OK OK 458 468 469 454 478 C5' DC C 2 OK OK 477 493 494 479 508 C5' DT C 3 OK OK 507 524 525 509 540 C5' DC C 4 OK OK 539 555 556 541 570 C5' DT C 5 OK OK 569 586 587 571 602 C5' DC C 6 OK OK 601 617 618 603 632 C5' DC C 7 OK OK 631 647 648 633 674 C5' MCY D 1 OK OK 675 685 686 671 695 C5' DC D 2 OK OK 694 710 711 696 725 C5' DT D 3 OK OK 724 741 742 726 757 C5' DC D 4 OK OK 756 772 773 758 787 C5' DT D 5 OK OK 786 803 804 788 819 C5' DC D 6 OK OK 818 834 835 820 849 C5' DC D 7 OK OK 848 864 865 850 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P DC A 2 distorted distorted 14 33 34 35 63 P DT A 3 distorted distorted 40 64 65 66 95 P DC A 4 distorted distorted 71 96 97 98 126 P DT A 5 distorted distorted 103 127 128 129 158 P DC A 6 distorted distorted 134 159 160 161 189 P DC A 7 distorted distorted 166 190 191 192 253 P DC B 2 distorted distorted 235 254 255 256 284 P DT B 3 distorted distorted 261 285 286 287 316 P DC B 4 distorted distorted 292 317 318 319 347 P DT B 5 distorted distorted 324 348 349 350 379 P DC B 6 distorted distorted 355 380 381 382 410 P DC B 7 distorted distorted 387 411 412 413 474 P DC C 2 distorted distorted 456 475 476 477 504 P DT C 3 distorted distorted 482 505 506 507 536 P DC C 4 distorted distorted 512 537 538 539 566 P DT C 5 distorted distorted 544 567 568 569 598 P DC C 6 distorted distorted 574 599 600 601 628 P DC C 7 distorted distorted 606 629 630 631 691 P DC D 2 distorted distorted 673 692 693 694 721 P DT D 3 distorted distorted 699 722 723 724 753 P DC D 4 distorted distorted 729 754 755 756 783 P DT D 5 distorted distorted 761 784 785 786 815 P DC D 6 distorted distorted 791 816 817 818 845 P DC D 7 distorted distorted 823 846 847 848 ---------------------------------------------------------------------------------