ID code: '1K61' 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' C E 2 beta 7 12 10 30 C1' A E 3 beta 26 31 29 51 C1' T E 4 beta 47 52 50 71 C1' G E 5 beta 67 72 70 93 C1' T E 6 beta 89 94 92 113 C1' A E 7 beta 109 114 112 134 C1' A E 8 beta 130 135 133 155 C1' T E 9 beta 151 156 154 175 C1' T E 10 beta 171 176 174 195 C1' C E 11 beta 191 196 194 214 C1' A E 12 beta 210 215 213 235 C1' T E 13 beta 231 236 234 255 C1' T E 14 beta 251 256 254 275 C1' T E 15 beta 271 276 274 295 C1' A E 16 beta 291 296 294 316 C1' C E 17 beta 312 317 315 335 C1' A E 18 beta 331 336 334 356 C1' C E 19 beta 352 357 355 375 C1' G E 20 beta 371 376 374 397 C1' C E 21 beta 393 398 396 417 C1' G F 23 beta 413 418 416 439 C1' C F 24 beta 435 440 438 458 C1' G F 25 beta 454 459 457 480 C1' T F 26 beta 476 481 479 500 C1' G F 27 beta 496 501 499 522 C1' T F 28 beta 518 523 521 542 C1' A F 29 beta 538 543 541 563 C1' A F 30 beta 559 564 562 584 C1' A F 31 beta 580 585 583 605 C1' T F 32 beta 601 606 604 625 C1' G F 33 beta 621 626 624 647 C1' A F 34 beta 643 648 646 668 C1' A F 35 beta 664 669 667 689 C1' T F 36 beta 685 690 688 709 C1' T F 37 beta 705 710 708 729 C1' A F 38 beta 725 730 728 750 C1' C F 39 beta 746 751 749 769 C1' A F 40 beta 765 770 768 790 C1' T F 41 beta 786 791 789 810 C1' G F 42 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' C E 2 11 8 29 C2' A E 3 30 27 50 C2' T E 4 51 48 70 C2' G E 5 71 68 92 C2' T E 6 93 90 112 C2' A E 7 113 110 133 C2' A E 8 134 131 154 C2' T E 9 155 152 174 C2' T E 10 175 172 194 C2' C E 11 195 192 213 C2' A E 12 214 211 234 C2' T E 13 235 232 254 C2' T E 14 255 252 274 C2' T E 15 275 272 294 C2' A E 16 295 292 315 C2' C E 17 316 313 334 C2' A E 18 335 332 355 C2' C E 19 356 353 374 C2' G E 20 375 372 396 C2' C E 21 397 394 416 C2' G F 23 417 414 438 C2' C F 24 439 436 457 C2' G F 25 458 455 479 C2' T F 26 480 477 499 C2' G F 27 500 497 521 C2' T F 28 522 519 541 C2' A F 29 542 539 562 C2' A F 30 563 560 583 C2' A F 31 584 581 604 C2' T F 32 605 602 624 C2' G F 33 625 622 646 C2' A F 34 647 644 667 C2' A F 35 668 665 688 C2' T F 36 689 686 708 C2' T F 37 709 706 728 C2' A F 38 729 726 749 C2' C F 39 750 747 768 C2' A F 40 769 766 789 C2' T F 41 790 787 809 C2' G F 42 810 807 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C E 2 OK 6 9 10 27 C3' A E 3 OK 25 28 29 48 C3' T E 4 OK 46 49 50 68 C3' G E 5 OK 66 69 70 90 C3' T E 6 OK 88 91 92 110 C3' A E 7 OK 108 111 112 131 C3' A E 8 OK 129 132 133 152 C3' T E 9 OK 150 153 154 172 C3' T E 10 OK 170 173 174 192 C3' C E 11 OK 190 193 194 211 C3' A E 12 OK 209 212 213 232 C3' T E 13 OK 230 233 234 252 C3' T E 14 OK 250 253 254 272 C3' T E 15 OK 270 273 274 292 C3' A E 16 OK 290 293 294 313 C3' C E 17 OK 311 314 315 332 C3' A E 18 OK 330 333 334 353 C3' C E 19 OK 351 354 355 372 C3' G E 20 OK 370 373 374 394 C3' C E 21 OK 392 395 396 414 C3' G F 23 OK 412 415 416 436 C3' C F 24 OK 434 437 438 455 C3' G F 25 OK 453 456 457 477 C3' T F 26 OK 475 478 479 497 C3' G F 27 OK 495 498 499 519 C3' T F 28 OK 517 520 521 539 C3' A F 29 OK 537 540 541 560 C3' A F 30 OK 558 561 562 581 C3' A F 31 OK 579 582 583 602 C3' T F 32 OK 600 603 604 622 C3' G F 33 OK 620 623 624 644 C3' A F 34 OK 642 645 646 665 C3' A F 35 OK 663 666 667 686 C3' T F 36 OK 684 687 688 706 C3' T F 37 OK 704 707 708 726 C3' A F 38 OK 724 727 728 747 C3' C F 39 OK 745 748 749 766 C3' A F 40 OK 764 767 768 787 C3' T F 41 OK 785 788 789 807 C3' G F 42 OK 805 808 809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C E 2 OK 8 5 7 25 C4' A E 3 OK 27 24 26 46 C4' T E 4 OK 48 45 47 66 C4' G E 5 OK 68 65 67 88 C4' T E 6 OK 90 87 89 108 C4' A E 7 OK 110 107 109 129 C4' A E 8 OK 131 128 130 150 C4' T E 9 OK 152 149 151 170 C4' T E 10 OK 172 169 171 190 C4' C E 11 OK 192 189 191 209 C4' A E 12 OK 211 208 210 230 C4' T E 13 OK 232 229 231 250 C4' T E 14 OK 252 249 251 270 C4' T E 15 OK 272 269 271 290 C4' A E 16 OK 292 289 291 311 C4' C E 17 OK 313 310 312 330 C4' A E 18 OK 332 329 331 351 C4' C E 19 OK 353 350 352 370 C4' G E 20 OK 372 369 371 392 C4' C E 21 OK 394 391 393 412 C4' G F 23 OK 414 411 413 434 C4' C F 24 OK 436 433 435 453 C4' G F 25 OK 455 452 454 475 C4' T F 26 OK 477 474 476 495 C4' G F 27 OK 497 494 496 517 C4' T F 28 OK 519 516 518 537 C4' A F 29 OK 539 536 538 558 C4' A F 30 OK 560 557 559 579 C4' A F 31 OK 581 578 580 600 C4' T F 32 OK 602 599 601 620 C4' G F 33 OK 622 619 621 642 C4' A F 34 OK 644 641 643 663 C4' A F 35 OK 665 662 664 684 C4' T F 36 OK 686 683 685 704 C4' T F 37 OK 706 703 705 724 C4' A F 38 OK 726 723 725 745 C4' C F 39 OK 747 744 746 764 C4' A F 40 OK 766 763 765 785 C4' T F 41 OK 787 784 786 805 C4' G F 42 OK 807 804 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C E 2 4 6 24 C5' A E 3 23 25 45 C5' T E 4 44 46 65 C5' G E 5 64 66 87 C5' T E 6 86 88 107 C5' A E 7 106 108 128 C5' A E 8 127 129 149 C5' T E 9 148 150 169 C5' T E 10 168 170 189 C5' C E 11 188 190 208 C5' A E 12 207 209 229 C5' T E 13 228 230 249 C5' T E 14 248 250 269 C5' T E 15 268 270 289 C5' A E 16 288 290 310 C5' C E 17 309 311 329 C5' A E 18 328 330 350 C5' C E 19 349 351 369 C5' G E 20 368 370 391 C5' C E 21 390 392 411 C5' G F 23 410 412 433 C5' C F 24 432 434 452 C5' G F 25 451 453 474 C5' T F 26 473 475 494 C5' G F 27 493 495 516 C5' T F 28 515 517 536 C5' A F 29 535 537 557 C5' A F 30 556 558 578 C5' A F 31 577 579 599 C5' T F 32 598 600 619 C5' G F 33 618 620 641 C5' A F 34 640 642 662 C5' A F 35 661 663 683 C5' T F 36 682 684 703 C5' T F 37 702 704 723 C5' A F 38 722 724 744 C5' C F 39 743 745 763 C5' A F 40 762 764 784 C5' T F 41 783 785 804 C5' G F 42 803 805 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C E 2 distorted distorted 2 3 4 20 P A E 3 distorted distorted 9 21 22 23 41 P T E 4 distorted distorted 28 42 43 44 61 P G E 5 distorted distorted 49 62 63 64 83 P T E 6 distorted distorted 69 84 85 86 103 P A E 7 distorted distorted 91 104 105 106 124 P A E 8 distorted distorted 111 125 126 127 145 P T E 9 distorted distorted 132 146 147 148 165 P T E 10 distorted distorted 153 166 167 168 185 P C E 11 distorted distorted 173 186 187 188 204 P A E 12 distorted distorted 193 205 206 207 225 P T E 13 distorted distorted 212 226 227 228 245 P T E 14 distorted distorted 233 246 247 248 265 P T E 15 distorted distorted 253 266 267 268 285 P A E 16 distorted distorted 273 286 287 288 306 P C E 17 distorted distorted 293 307 308 309 325 P A E 18 distorted distorted 314 326 327 328 346 P C E 19 distorted distorted 333 347 348 349 365 P G E 20 distorted distorted 354 366 367 368 387 P C E 21 distorted distorted 373 388 389 390 407 P G F 23 distorted distorted 408 409 410 429 P C F 24 distorted distorted 415 430 431 432 448 P G F 25 distorted distorted 437 449 450 451 470 P T F 26 distorted distorted 456 471 472 473 490 P G F 27 distorted distorted 478 491 492 493 512 P T F 28 distorted distorted 498 513 514 515 532 P A F 29 distorted distorted 520 533 534 535 553 P A F 30 distorted distorted 540 554 555 556 574 P A F 31 distorted distorted 561 575 576 577 595 P T F 32 distorted distorted 582 596 597 598 615 P G F 33 distorted distorted 603 616 617 618 637 P A F 34 distorted distorted 623 638 639 640 658 P A F 35 distorted distorted 645 659 660 661 679 P T F 36 distorted distorted 666 680 681 682 699 P T F 37 distorted distorted 687 700 701 702 719 P A F 38 distorted distorted 707 720 721 722 740 P C F 39 distorted distorted 727 741 742 743 759 P A F 40 distorted distorted 748 760 761 762 780 P T F 41 distorted distorted 767 781 782 783 800 P G F 42 distorted distorted 788 801 802 803 ---------------------------------------------------------------------------------