ID code: '1OUZ' 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' --------------------------------------------------------------------------------- 11 C1' G C 49 beta 7 12 10 33 C1' G C 48 beta 29 34 32 55 C1' T C 47 beta 51 56 54 75 C1' G C 46 beta 71 76 74 97 C1' C C 45 beta 93 98 96 116 C1' T C 44 beta 112 117 115 136 C1' A C 43 beta 132 137 135 157 C1' C C 42 beta 153 158 156 176 C1' A C 41 beta 172 177 175 197 C1' A C 40 beta 193 198 196 218 C1' A C 39 beta 214 219 217 239 C1' T C 38 beta 235 240 238 259 C1' T C 37 beta 255 260 258 279 C1' G C 36 beta 275 280 278 301 C1' A C 35 beta 297 302 300 322 C1' T C 34 beta 318 323 321 342 C1' A C 33 beta 338 343 341 363 C1' A C 32 beta 359 364 362 384 C1' G C 31 beta 380 385 383 406 C1' C C 30 beta 402 407 405 423 C1' G E 30 beta 419 424 422 445 C1' C E 31 beta 441 446 444 464 C1' T E 32 beta 460 465 463 484 C1' T E 33 beta 480 485 483 504 C1' A E 34 beta 500 505 503 525 C1' T E 35 beta 521 526 524 545 C1' C E 36 beta 541 546 544 564 C1' A E 37 beta 560 565 563 585 C1' A E 38 beta 581 586 584 606 C1' T E 39 beta 602 607 605 626 C1' T E 40 beta 622 627 625 646 C1' T E 41 beta 642 647 645 666 C1' G E 42 beta 662 667 665 688 C1' T E 43 beta 684 689 687 708 C1' A E 44 beta 704 709 707 729 C1' G E 45 beta 725 730 728 751 C1' C E 46 beta 747 752 750 770 C1' A E 47 beta 766 771 769 791 C1' C E 48 beta 787 792 790 810 C1' C E 49 beta 806 811 809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G C 49 11 8 32 C2' G C 48 33 30 54 C2' T C 47 55 52 74 C2' G C 46 75 72 96 C2' C C 45 97 94 115 C2' T C 44 116 113 135 C2' A C 43 136 133 156 C2' C C 42 157 154 175 C2' A C 41 176 173 196 C2' A C 40 197 194 217 C2' A C 39 218 215 238 C2' T C 38 239 236 258 C2' T C 37 259 256 278 C2' G C 36 279 276 300 C2' A C 35 301 298 321 C2' T C 34 322 319 341 C2' A C 33 342 339 362 C2' A C 32 363 360 383 C2' G C 31 384 381 405 C2' C C 30 406 403 422 C2' G E 30 423 420 444 C2' C E 31 445 442 463 C2' T E 32 464 461 483 C2' T E 33 484 481 503 C2' A E 34 504 501 524 C2' T E 35 525 522 544 C2' C E 36 545 542 563 C2' A E 37 564 561 584 C2' A E 38 585 582 605 C2' T E 39 606 603 625 C2' T E 40 626 623 645 C2' T E 41 646 643 665 C2' G E 42 666 663 687 C2' T E 43 688 685 707 C2' A E 44 708 705 728 C2' G E 45 729 726 750 C2' C E 46 751 748 769 C2' A E 47 770 767 790 C2' C E 48 791 788 809 C2' C E 49 810 807 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G C 49 OK 6 9 10 30 C3' G C 48 OK 28 31 32 52 C3' T C 47 OK 50 53 54 72 C3' G C 46 OK 70 73 74 94 C3' C C 45 OK 92 95 96 113 C3' T C 44 OK 111 114 115 133 C3' A C 43 OK 131 134 135 154 C3' C C 42 OK 152 155 156 173 C3' A C 41 OK 171 174 175 194 C3' A C 40 OK 192 195 196 215 C3' A C 39 OK 213 216 217 236 C3' T C 38 OK 234 237 238 256 C3' T C 37 OK 254 257 258 276 C3' G C 36 OK 274 277 278 298 C3' A C 35 OK 296 299 300 319 C3' T C 34 OK 317 320 321 339 C3' A C 33 OK 337 340 341 360 C3' A C 32 OK 358 361 362 381 C3' G C 31 OK 379 382 383 403 C3' C C 30 OK 401 404 405 420 C3' G E 30 OK 418 421 422 442 C3' C E 31 OK 440 443 444 461 C3' T E 32 OK 459 462 463 481 C3' T E 33 OK 479 482 483 501 C3' A E 34 OK 499 502 503 522 C3' T E 35 OK 520 523 524 542 C3' C E 36 OK 540 543 544 561 C3' A E 37 OK 559 562 563 582 C3' A E 38 OK 580 583 584 603 C3' T E 39 OK 601 604 605 623 C3' T E 40 OK 621 624 625 643 C3' T E 41 OK 641 644 645 663 C3' G E 42 OK 661 664 665 685 C3' T E 43 OK 683 686 687 705 C3' A E 44 OK 703 706 707 726 C3' G E 45 OK 724 727 728 748 C3' C E 46 OK 746 749 750 767 C3' A E 47 OK 765 768 769 788 C3' C E 48 OK 786 789 790 807 C3' C E 49 OK 805 808 809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G C 49 OK 8 5 7 28 C4' G C 48 OK 30 27 29 50 C4' T C 47 OK 52 49 51 70 C4' G C 46 OK 72 69 71 92 C4' C C 45 OK 94 91 93 111 C4' T C 44 OK 113 110 112 131 C4' A C 43 OK 133 130 132 152 C4' C C 42 OK 154 151 153 171 C4' A C 41 OK 173 170 172 192 C4' A C 40 OK 194 191 193 213 C4' A C 39 OK 215 212 214 234 C4' T C 38 OK 236 233 235 254 C4' T C 37 OK 256 253 255 274 C4' G C 36 OK 276 273 275 296 C4' A C 35 OK 298 295 297 317 C4' T C 34 OK 319 316 318 337 C4' A C 33 OK 339 336 338 358 C4' A C 32 OK 360 357 359 379 C4' G C 31 OK 381 378 380 401 C4' C C 30 OK 403 400 402 418 C4' G E 30 OK 420 417 419 440 C4' C E 31 OK 442 439 441 459 C4' T E 32 OK 461 458 460 479 C4' T E 33 OK 481 478 480 499 C4' A E 34 OK 501 498 500 520 C4' T E 35 OK 522 519 521 540 C4' C E 36 OK 542 539 541 559 C4' A E 37 OK 561 558 560 580 C4' A E 38 OK 582 579 581 601 C4' T E 39 OK 603 600 602 621 C4' T E 40 OK 623 620 622 641 C4' T E 41 OK 643 640 642 661 C4' G E 42 OK 663 660 662 683 C4' T E 43 OK 685 682 684 703 C4' A E 44 OK 705 702 704 724 C4' G E 45 OK 726 723 725 746 C4' C E 46 OK 748 745 747 765 C4' A E 47 OK 767 764 766 786 C4' C E 48 OK 788 785 787 805 C4' C E 49 OK 807 804 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G C 49 4 6 27 C5' G C 48 26 28 49 C5' T C 47 48 50 69 C5' G C 46 68 70 91 C5' C C 45 90 92 110 C5' T C 44 109 111 130 C5' A C 43 129 131 151 C5' C C 42 150 152 170 C5' A C 41 169 171 191 C5' A C 40 190 192 212 C5' A C 39 211 213 233 C5' T C 38 232 234 253 C5' T C 37 252 254 273 C5' G C 36 272 274 295 C5' A C 35 294 296 316 C5' T C 34 315 317 336 C5' A C 33 335 337 357 C5' A C 32 356 358 378 C5' G C 31 377 379 400 C5' C C 30 399 401 417 C5' G E 30 416 418 439 C5' C E 31 438 440 458 C5' T E 32 457 459 478 C5' T E 33 477 479 498 C5' A E 34 497 499 519 C5' T E 35 518 520 539 C5' C E 36 538 540 558 C5' A E 37 557 559 579 C5' A E 38 578 580 600 C5' T E 39 599 601 620 C5' T E 40 619 621 640 C5' T E 41 639 641 660 C5' G E 42 659 661 682 C5' T E 43 681 683 702 C5' A E 44 701 703 723 C5' G E 45 722 724 745 C5' C E 46 744 746 764 C5' A E 47 763 765 785 C5' C E 48 784 786 804 C5' C E 49 803 805 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G C 49 distorted distorted 2 3 4 23 P G C 48 distorted distorted 9 24 25 26 45 P T C 47 distorted distorted 31 46 47 48 65 P G C 46 distorted distorted 53 66 67 68 87 P C C 45 distorted distorted 73 88 89 90 106 P T C 44 distorted distorted 95 107 108 109 126 P A C 43 distorted distorted 114 127 128 129 147 P C C 42 distorted distorted 134 148 149 150 166 P A C 41 distorted distorted 155 167 168 169 187 P A C 40 distorted distorted 174 188 189 190 208 P A C 39 distorted distorted 195 209 210 211 229 P T C 38 distorted distorted 216 230 231 232 249 P T C 37 distorted distorted 237 250 251 252 269 P G C 36 distorted distorted 257 270 271 272 291 P A C 35 distorted distorted 277 292 293 294 312 P T C 34 distorted distorted 299 313 314 315 332 P A C 33 distorted distorted 320 333 334 335 353 P A C 32 distorted distorted 340 354 355 356 374 P G C 31 distorted distorted 361 375 376 377 396 P C C 30 distorted distorted 382 397 398 399 435 P C E 31 distorted distorted 421 436 437 438 454 P T E 32 distorted distorted 443 455 456 457 474 P T E 33 distorted distorted 462 475 476 477 494 P A E 34 distorted distorted 482 495 496 497 515 P T E 35 distorted distorted 502 516 517 518 535 P C E 36 distorted distorted 523 536 537 538 554 P A E 37 distorted distorted 543 555 556 557 575 P A E 38 distorted distorted 562 576 577 578 596 P T E 39 distorted distorted 583 597 598 599 616 P T E 40 distorted distorted 604 617 618 619 636 P T E 41 distorted distorted 624 637 638 639 656 P G E 42 distorted distorted 644 657 658 659 678 P T E 43 distorted distorted 664 679 680 681 698 P A E 44 distorted distorted 686 699 700 701 719 P G E 45 distorted distorted 706 720 721 722 741 P C E 46 distorted distorted 727 742 743 744 760 P A E 47 distorted distorted 749 761 762 763 781 P C E 48 distorted distorted 768 782 783 784 800 P C E 49 distorted distorted 789 801 802 803 ---------------------------------------------------------------------------------