ID code: '1JE8' 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' C G 1 beta 4 9 7 27 C1' G G 2 beta 23 28 26 49 C1' T G 3 beta 45 50 48 69 C1' A G 4 beta 65 70 68 90 C1' C G 5 beta 86 91 89 109 C1' C G 6 beta 105 110 108 128 C1' C G 7 beta 124 129 127 147 C1' A G 8 beta 143 148 146 168 C1' T G 9 beta 164 169 167 188 C1' T G 10 beta 184 189 187 208 C1' A G 11 beta 204 209 207 229 C1' A G 12 beta 225 230 228 250 C1' T G 13 beta 246 251 249 270 C1' G G 14 beta 266 271 269 292 C1' G G 15 beta 288 293 291 314 C1' G G 16 beta 310 315 313 336 C1' T G 17 beta 332 337 335 356 C1' A G 18 beta 352 357 355 377 C1' C G 19 beta 373 378 376 396 C1' G G 20 beta 392 397 395 416 C1' C H 21 beta 412 417 415 435 C1' G H 22 beta 431 436 434 457 C1' T H 23 beta 453 458 456 477 C1' A H 24 beta 473 478 476 498 C1' C H 25 beta 494 499 497 517 C1' C H 26 beta 513 518 516 536 C1' C H 27 beta 532 537 535 555 C1' A H 28 beta 551 556 554 576 C1' T H 29 beta 572 577 575 596 C1' T H 30 beta 592 597 595 616 C1' A H 31 beta 612 617 615 637 C1' A H 32 beta 633 638 636 658 C1' T H 33 beta 654 659 657 678 C1' G H 34 beta 674 679 677 700 C1' G H 35 beta 696 701 699 722 C1' G H 36 beta 718 723 721 744 C1' T H 37 beta 740 745 743 764 C1' A H 38 beta 760 765 763 785 C1' C H 39 beta 781 786 784 804 C1' G H 40 beta 800 805 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C G 1 8 5 26 C2' G G 2 27 24 48 C2' T G 3 49 46 68 C2' A G 4 69 66 89 C2' C G 5 90 87 108 C2' C G 6 109 106 127 C2' C G 7 128 125 146 C2' A G 8 147 144 167 C2' T G 9 168 165 187 C2' T G 10 188 185 207 C2' A G 11 208 205 228 C2' A G 12 229 226 249 C2' T G 13 250 247 269 C2' G G 14 270 267 291 C2' G G 15 292 289 313 C2' G G 16 314 311 335 C2' T G 17 336 333 355 C2' A G 18 356 353 376 C2' C G 19 377 374 395 C2' G G 20 396 393 415 C2' C H 21 416 413 434 C2' G H 22 435 432 456 C2' T H 23 457 454 476 C2' A H 24 477 474 497 C2' C H 25 498 495 516 C2' C H 26 517 514 535 C2' C H 27 536 533 554 C2' A H 28 555 552 575 C2' T H 29 576 573 595 C2' T H 30 596 593 615 C2' A H 31 616 613 636 C2' A H 32 637 634 657 C2' T H 33 658 655 677 C2' G H 34 678 675 699 C2' G H 35 700 697 721 C2' G H 36 722 719 743 C2' T H 37 744 741 763 C2' A H 38 764 761 784 C2' C H 39 785 782 803 C2' G H 40 804 801 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C G 1 OK 3 6 7 24 C3' G G 2 OK 22 25 26 46 C3' T G 3 OK 44 47 48 66 C3' A G 4 OK 64 67 68 87 C3' C G 5 OK 85 88 89 106 C3' C G 6 OK 104 107 108 125 C3' C G 7 OK 123 126 127 144 C3' A G 8 OK 142 145 146 165 C3' T G 9 OK 163 166 167 185 C3' T G 10 OK 183 186 187 205 C3' A G 11 OK 203 206 207 226 C3' A G 12 OK 224 227 228 247 C3' T G 13 OK 245 248 249 267 C3' G G 14 OK 265 268 269 289 C3' G G 15 OK 287 290 291 311 C3' G G 16 OK 309 312 313 333 C3' T G 17 OK 331 334 335 353 C3' A G 18 OK 351 354 355 374 C3' C G 19 OK 372 375 376 393 C3' G G 20 OK 391 394 395 413 C3' C H 21 OK 411 414 415 432 C3' G H 22 OK 430 433 434 454 C3' T H 23 OK 452 455 456 474 C3' A H 24 OK 472 475 476 495 C3' C H 25 OK 493 496 497 514 C3' C H 26 OK 512 515 516 533 C3' C H 27 OK 531 534 535 552 C3' A H 28 OK 550 553 554 573 C3' T H 29 OK 571 574 575 593 C3' T H 30 OK 591 594 595 613 C3' A H 31 OK 611 614 615 634 C3' A H 32 OK 632 635 636 655 C3' T H 33 OK 653 656 657 675 C3' G H 34 OK 673 676 677 697 C3' G H 35 OK 695 698 699 719 C3' G H 36 OK 717 720 721 741 C3' T H 37 OK 739 742 743 761 C3' A H 38 OK 759 762 763 782 C3' C H 39 OK 780 783 784 801 C3' G H 40 OK 799 802 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C G 1 OK 5 2 4 22 C4' G G 2 OK 24 21 23 44 C4' T G 3 OK 46 43 45 64 C4' A G 4 OK 66 63 65 85 C4' C G 5 OK 87 84 86 104 C4' C G 6 OK 106 103 105 123 C4' C G 7 OK 125 122 124 142 C4' A G 8 OK 144 141 143 163 C4' T G 9 OK 165 162 164 183 C4' T G 10 OK 185 182 184 203 C4' A G 11 OK 205 202 204 224 C4' A G 12 OK 226 223 225 245 C4' T G 13 OK 247 244 246 265 C4' G G 14 OK 267 264 266 287 C4' G G 15 OK 289 286 288 309 C4' G G 16 OK 311 308 310 331 C4' T G 17 OK 333 330 332 351 C4' A G 18 OK 353 350 352 372 C4' C G 19 OK 374 371 373 391 C4' G G 20 OK 393 390 392 411 C4' C H 21 OK 413 410 412 430 C4' G H 22 OK 432 429 431 452 C4' T H 23 OK 454 451 453 472 C4' A H 24 OK 474 471 473 493 C4' C H 25 OK 495 492 494 512 C4' C H 26 OK 514 511 513 531 C4' C H 27 OK 533 530 532 550 C4' A H 28 OK 552 549 551 571 C4' T H 29 OK 573 570 572 591 C4' T H 30 OK 593 590 592 611 C4' A H 31 OK 613 610 612 632 C4' A H 32 OK 634 631 633 653 C4' T H 33 OK 655 652 654 673 C4' G H 34 OK 675 672 674 695 C4' G H 35 OK 697 694 696 717 C4' G H 36 OK 719 716 718 739 C4' T H 37 OK 741 738 740 759 C4' A H 38 OK 761 758 760 780 C4' C H 39 OK 782 779 781 799 C4' G H 40 OK 801 798 800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C G 1 1 3 21 C5' G G 2 20 22 43 C5' T G 3 42 44 63 C5' A G 4 62 64 84 C5' C G 5 83 85 103 C5' C G 6 102 104 122 C5' C G 7 121 123 141 C5' A G 8 140 142 162 C5' T G 9 161 163 182 C5' T G 10 181 183 202 C5' A G 11 201 203 223 C5' A G 12 222 224 244 C5' T G 13 243 245 264 C5' G G 14 263 265 286 C5' G G 15 285 287 308 C5' G G 16 307 309 330 C5' T G 17 329 331 350 C5' A G 18 349 351 371 C5' C G 19 370 372 390 C5' G G 20 389 391 410 C5' C H 21 409 411 429 C5' G H 22 428 430 451 C5' T H 23 450 452 471 C5' A H 24 470 472 492 C5' C H 25 491 493 511 C5' C H 26 510 512 530 C5' C H 27 529 531 549 C5' A H 28 548 550 570 C5' T H 29 569 571 590 C5' T H 30 589 591 610 C5' A H 31 609 611 631 C5' A H 32 630 632 652 C5' T H 33 651 653 672 C5' G H 34 671 673 694 C5' G H 35 693 695 716 C5' G H 36 715 717 738 C5' T H 37 737 739 758 C5' A H 38 757 759 779 C5' C H 39 778 780 798 C5' G H 40 797 799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P G G 2 distorted distorted 6 18 19 20 39 P T G 3 distorted distorted 25 40 41 42 59 P A G 4 distorted distorted 47 60 61 62 80 P C G 5 distorted distorted 67 81 82 83 99 P C G 6 distorted distorted 88 100 101 102 118 P C G 7 distorted distorted 107 119 120 121 137 P A G 8 distorted distorted 126 138 139 140 158 P T G 9 distorted distorted 145 159 160 161 178 P T G 10 distorted distorted 166 179 180 181 198 P A G 11 distorted distorted 186 199 200 201 219 P A G 12 distorted distorted 206 220 221 222 240 P T G 13 distorted distorted 227 241 242 243 260 P G G 14 distorted distorted 248 261 262 263 282 P G G 15 distorted distorted 268 283 284 285 304 P G G 16 distorted distorted 290 305 306 307 326 P T G 17 distorted distorted 312 327 328 329 346 P A G 18 distorted distorted 334 347 348 349 367 P C G 19 distorted distorted 354 368 369 370 386 P G G 20 distorted distorted 375 387 388 389 425 P G H 22 distorted distorted 414 426 427 428 447 P T H 23 distorted distorted 433 448 449 450 467 P A H 24 distorted distorted 455 468 469 470 488 P C H 25 distorted distorted 475 489 490 491 507 P C H 26 distorted distorted 496 508 509 510 526 P C H 27 distorted distorted 515 527 528 529 545 P A H 28 distorted distorted 534 546 547 548 566 P T H 29 distorted distorted 553 567 568 569 586 P T H 30 distorted distorted 574 587 588 589 606 P A H 31 distorted distorted 594 607 608 609 627 P A H 32 distorted distorted 614 628 629 630 648 P T H 33 distorted distorted 635 649 650 651 668 P G H 34 distorted distorted 656 669 670 671 690 P G H 35 distorted distorted 676 691 692 693 712 P G H 36 distorted distorted 698 713 714 715 734 P T H 37 distorted distorted 720 735 736 737 754 P A H 38 distorted distorted 742 755 756 757 775 P C H 39 distorted distorted 762 776 777 778 794 P G H 40 distorted distorted 783 795 796 797 ---------------------------------------------------------------------------------