ID code: '1OUQ' 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' --------------------------------------------------------------------------------- 8 C1' T X 116 beta 4 9 7 28 C1' G X 117 beta 24 29 27 50 C1' T X 118 beta 46 51 49 70 C1' A X 119 beta 66 71 69 91 C1' T X 120 beta 87 92 90 111 C1' G X 121 beta 107 112 110 133 C1' C X 122 beta 129 134 132 152 C1' T X 123 beta 148 153 151 172 C1' A X 124 beta 168 173 171 193 C1' T X 125 beta 189 194 192 213 C1' A X 126 beta 209 214 212 234 C1' C X 127 beta 230 235 233 253 C1' G X 128 beta 249 254 252 275 C1' A X 129 beta 271 276 274 296 C1' A X 130 beta 292 297 295 317 C1' G X 131 beta 313 318 316 339 C1' T X 132 beta 335 340 338 359 C1' T X 133 beta 355 360 358 379 C1' A X 134 beta 375 380 378 400 C1' T X 135 beta 396 401 399 420 C1' C X 136 beta 416 421 419 440 C1' G D 101 beta 436 441 439 462 C1' A D 102 beta 458 463 461 483 C1' T D 103 beta 479 484 482 503 C1' A D 104 beta 499 504 502 524 C1' A D 105 beta 520 525 523 545 C1' C D 106 beta 541 546 544 564 C1' T D 107 beta 560 565 563 584 C1' T D 108 beta 580 585 583 604 C1' C D 109 beta 600 605 603 623 C1' G D 110 beta 619 624 622 645 C1' T D 111 beta 641 646 644 665 C1' A D 112 beta 661 666 664 686 C1' T D 113 beta 682 687 685 706 C1' A D 114 beta 702 707 705 727 C1' G D 115 beta 723 728 726 749 C1' C D 116 beta 745 750 748 768 C1' A D 117 beta 764 769 767 789 C1' T D 118 beta 785 790 788 809 C1' A D 119 beta 805 810 808 830 C1' C D 120 beta 826 831 829 849 C1' A D 121 beta 845 850 848 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' T X 116 8 5 27 C2' G X 117 28 25 49 C2' T X 118 50 47 69 C2' A X 119 70 67 90 C2' T X 120 91 88 110 C2' G X 121 111 108 132 C2' C X 122 133 130 151 C2' T X 123 152 149 171 C2' A X 124 172 169 192 C2' T X 125 193 190 212 C2' A X 126 213 210 233 C2' C X 127 234 231 252 C2' G X 128 253 250 274 C2' A X 129 275 272 295 C2' A X 130 296 293 316 C2' G X 131 317 314 338 C2' T X 132 339 336 358 C2' T X 133 359 356 378 C2' A X 134 379 376 399 C2' T X 135 400 397 419 C2' C X 136 420 417 439 C2' G D 101 440 437 461 C2' A D 102 462 459 482 C2' T D 103 483 480 502 C2' A D 104 503 500 523 C2' A D 105 524 521 544 C2' C D 106 545 542 563 C2' T D 107 564 561 583 C2' T D 108 584 581 603 C2' C D 109 604 601 622 C2' G D 110 623 620 644 C2' T D 111 645 642 664 C2' A D 112 665 662 685 C2' T D 113 686 683 705 C2' A D 114 706 703 726 C2' G D 115 727 724 748 C2' C D 116 749 746 767 C2' A D 117 768 765 788 C2' T D 118 789 786 808 C2' A D 119 809 806 829 C2' C D 120 830 827 848 C2' A D 121 849 846 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' T X 116 OK 3 6 7 25 C3' G X 117 OK 23 26 27 47 C3' T X 118 OK 45 48 49 67 C3' A X 119 OK 65 68 69 88 C3' T X 120 OK 86 89 90 108 C3' G X 121 OK 106 109 110 130 C3' C X 122 OK 128 131 132 149 C3' T X 123 OK 147 150 151 169 C3' A X 124 OK 167 170 171 190 C3' T X 125 OK 188 191 192 210 C3' A X 126 OK 208 211 212 231 C3' C X 127 OK 229 232 233 250 C3' G X 128 OK 248 251 252 272 C3' A X 129 OK 270 273 274 293 C3' A X 130 OK 291 294 295 314 C3' G X 131 OK 312 315 316 336 C3' T X 132 OK 334 337 338 356 C3' T X 133 OK 354 357 358 376 C3' A X 134 OK 374 377 378 397 C3' T X 135 OK 395 398 399 417 C3' C X 136 OK 415 418 419 437 C3' G D 101 OK 435 438 439 459 C3' A D 102 OK 457 460 461 480 C3' T D 103 OK 478 481 482 500 C3' A D 104 OK 498 501 502 521 C3' A D 105 OK 519 522 523 542 C3' C D 106 OK 540 543 544 561 C3' T D 107 OK 559 562 563 581 C3' T D 108 OK 579 582 583 601 C3' C D 109 OK 599 602 603 620 C3' G D 110 OK 618 621 622 642 C3' T D 111 OK 640 643 644 662 C3' A D 112 OK 660 663 664 683 C3' T D 113 OK 681 684 685 703 C3' A D 114 OK 701 704 705 724 C3' G D 115 OK 722 725 726 746 C3' C D 116 OK 744 747 748 765 C3' A D 117 OK 763 766 767 786 C3' T D 118 OK 784 787 788 806 C3' A D 119 OK 804 807 808 827 C3' C D 120 OK 825 828 829 846 C3' A D 121 OK 844 847 848 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' T X 116 OK 5 2 4 23 C4' G X 117 OK 25 22 24 45 C4' T X 118 OK 47 44 46 65 C4' A X 119 OK 67 64 66 86 C4' T X 120 OK 88 85 87 106 C4' G X 121 OK 108 105 107 128 C4' C X 122 OK 130 127 129 147 C4' T X 123 OK 149 146 148 167 C4' A X 124 OK 169 166 168 188 C4' T X 125 OK 190 187 189 208 C4' A X 126 OK 210 207 209 229 C4' C X 127 OK 231 228 230 248 C4' G X 128 OK 250 247 249 270 C4' A X 129 OK 272 269 271 291 C4' A X 130 OK 293 290 292 312 C4' G X 131 OK 314 311 313 334 C4' T X 132 OK 336 333 335 354 C4' T X 133 OK 356 353 355 374 C4' A X 134 OK 376 373 375 395 C4' T X 135 OK 397 394 396 415 C4' C X 136 OK 417 414 416 435 C4' G D 101 OK 437 434 436 457 C4' A D 102 OK 459 456 458 478 C4' T D 103 OK 480 477 479 498 C4' A D 104 OK 500 497 499 519 C4' A D 105 OK 521 518 520 540 C4' C D 106 OK 542 539 541 559 C4' T D 107 OK 561 558 560 579 C4' T D 108 OK 581 578 580 599 C4' C D 109 OK 601 598 600 618 C4' G D 110 OK 620 617 619 640 C4' T D 111 OK 642 639 641 660 C4' A D 112 OK 662 659 661 681 C4' T D 113 OK 683 680 682 701 C4' A D 114 OK 703 700 702 722 C4' G D 115 OK 724 721 723 744 C4' C D 116 OK 746 743 745 763 C4' A D 117 OK 765 762 764 784 C4' T D 118 OK 786 783 785 804 C4' A D 119 OK 806 803 805 825 C4' C D 120 OK 827 824 826 844 C4' A D 121 OK 846 843 845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' T X 116 1 3 22 C5' G X 117 21 23 44 C5' T X 118 43 45 64 C5' A X 119 63 65 85 C5' T X 120 84 86 105 C5' G X 121 104 106 127 C5' C X 122 126 128 146 C5' T X 123 145 147 166 C5' A X 124 165 167 187 C5' T X 125 186 188 207 C5' A X 126 206 208 228 C5' C X 127 227 229 247 C5' G X 128 246 248 269 C5' A X 129 268 270 290 C5' A X 130 289 291 311 C5' G X 131 310 312 333 C5' T X 132 332 334 353 C5' T X 133 352 354 373 C5' A X 134 372 374 394 C5' T X 135 393 395 414 C5' C X 136 413 415 434 C5' G D 101 433 435 456 C5' A D 102 455 457 477 C5' T D 103 476 478 497 C5' A D 104 496 498 518 C5' A D 105 517 519 539 C5' C D 106 538 540 558 C5' T D 107 557 559 578 C5' T D 108 577 579 598 C5' C D 109 597 599 617 C5' G D 110 616 618 639 C5' T D 111 638 640 659 C5' A D 112 658 660 680 C5' T D 113 679 681 700 C5' A D 114 699 701 721 C5' G D 115 720 722 743 C5' C D 116 742 744 762 C5' A D 117 761 763 783 C5' T D 118 782 784 803 C5' A D 119 802 804 824 C5' C D 120 823 825 843 C5' A D 121 842 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G X 117 distorted distorted 6 19 20 21 40 P T X 118 distorted distorted 26 41 42 43 60 P A X 119 distorted distorted 48 61 62 63 81 P T X 120 distorted distorted 68 82 83 84 101 P G X 121 distorted distorted 89 102 103 104 123 P C X 122 distorted distorted 109 124 125 126 142 P T X 123 distorted distorted 131 143 144 145 162 P A X 124 distorted distorted 150 163 164 165 183 P T X 125 distorted distorted 170 184 185 186 203 P A X 126 distorted distorted 191 204 205 206 224 P C X 127 distorted distorted 211 225 226 227 243 P G X 128 distorted distorted 232 244 245 246 265 P A X 129 distorted distorted 251 266 267 268 286 P A X 130 distorted distorted 273 287 288 289 307 P G X 131 distorted distorted 294 308 309 310 329 P T X 132 distorted distorted 315 330 331 332 349 P T X 133 distorted distorted 337 350 351 352 369 P A X 134 distorted distorted 357 370 371 372 390 P T X 135 distorted distorted 377 391 392 393 410 P C X 136 distorted distorted 398 411 412 413 430 P G D 101 distorted distorted 431 432 433 452 P A D 102 distorted distorted 438 453 454 455 473 P T D 103 distorted distorted 460 474 475 476 493 P A D 104 distorted distorted 481 494 495 496 514 P A D 105 distorted distorted 501 515 516 517 535 P C D 106 distorted distorted 522 536 537 538 554 P T D 107 distorted distorted 543 555 556 557 574 P T D 108 distorted distorted 562 575 576 577 594 P C D 109 distorted distorted 582 595 596 597 613 P G D 110 distorted distorted 602 614 615 616 635 P T D 111 distorted distorted 621 636 637 638 655 P A D 112 distorted distorted 643 656 657 658 676 P T D 113 distorted distorted 663 677 678 679 696 P A D 114 distorted distorted 684 697 698 699 717 P G D 115 distorted distorted 704 718 719 720 739 P C D 116 distorted distorted 725 740 741 742 758 P A D 117 distorted distorted 747 759 760 761 779 P T D 118 distorted distorted 766 780 781 782 799 P A D 119 distorted distorted 787 800 801 802 820 P C D 120 distorted distorted 807 821 822 823 839 P A D 121 distorted distorted 828 840 841 842 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