ID code: '6CRO' 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' --------------------------------------------------------------------------------- 29 C1' C R 2 beta 25 30 28 48 C1' T R 3 beta 44 49 47 68 C1' A R 4 beta 64 69 67 89 C1' T R 5 beta 85 90 88 109 C1' C R 6 beta 105 110 108 128 C1' A R 7 beta 124 129 127 149 C1' C R 8 beta 145 150 148 168 C1' C R 9 beta 164 169 167 187 C1' G R 10 beta 183 188 186 209 C1' C T 11 beta 205 210 208 228 C1' G T 12 beta 224 229 227 250 C1' G T 13 beta 246 251 249 272 C1' G T 14 beta 268 273 271 294 C1' T T 15 beta 290 295 293 314 C1' G T 16 beta 310 315 313 336 C1' A T 17 beta 332 337 335 357 C1' T T 18 beta 353 358 356 377 C1' A T 19 beta 373 378 376 398 C1' C T 20 beta 394 399 397 435 C1' G U 2 beta 431 436 434 457 C1' T U 3 beta 453 458 456 477 C1' A U 4 beta 473 478 476 498 C1' T U 5 beta 494 499 497 518 C1' C U 6 beta 514 519 517 537 C1' A U 7 beta 533 538 536 558 C1' C U 8 beta 554 559 557 577 C1' C U 9 beta 573 578 576 596 C1' C U 10 beta 592 597 595 615 C1' G S 11 beta 611 616 614 637 C1' C S 12 beta 633 638 636 656 C1' G S 13 beta 652 657 655 678 C1' G S 14 beta 674 679 677 700 C1' T S 15 beta 696 701 699 720 C1' G S 16 beta 716 721 719 742 C1' A S 17 beta 738 743 741 763 C1' T S 18 beta 759 764 762 783 C1' A S 19 beta 779 784 782 804 C1' G S 20 beta 800 805 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 28 C2' C R 2 29 26 47 C2' T R 3 48 45 67 C2' A R 4 68 65 88 C2' T R 5 89 86 108 C2' C R 6 109 106 127 C2' A R 7 128 125 148 C2' C R 8 149 146 167 C2' C R 9 168 165 186 C2' G R 10 187 184 208 C2' C T 11 209 206 227 C2' G T 12 228 225 249 C2' G T 13 250 247 271 C2' G T 14 272 269 293 C2' T T 15 294 291 313 C2' G T 16 314 311 335 C2' A T 17 336 333 356 C2' T T 18 357 354 376 C2' A T 19 377 374 397 C2' C T 20 398 395 434 C2' G U 2 435 432 456 C2' T U 3 457 454 476 C2' A U 4 477 474 497 C2' T U 5 498 495 517 C2' C U 6 518 515 536 C2' A U 7 537 534 557 C2' C U 8 558 555 576 C2' C U 9 577 574 595 C2' C U 10 596 593 614 C2' G S 11 615 612 636 C2' C S 12 637 634 655 C2' G S 13 656 653 677 C2' G S 14 678 675 699 C2' T S 15 700 697 719 C2' G S 16 720 717 741 C2' A S 17 742 739 762 C2' T S 18 763 760 782 C2' A S 19 783 780 803 C2' G S 20 804 801 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 26 C3' C R 2 OK 24 27 28 45 C3' T R 3 OK 43 46 47 65 C3' A R 4 OK 63 66 67 86 C3' T R 5 OK 84 87 88 106 C3' C R 6 OK 104 107 108 125 C3' A R 7 OK 123 126 127 146 C3' C R 8 OK 144 147 148 165 C3' C R 9 OK 163 166 167 184 C3' G R 10 OK 182 185 186 206 C3' C T 11 OK 204 207 208 225 C3' G T 12 OK 223 226 227 247 C3' G T 13 OK 245 248 249 269 C3' G T 14 OK 267 270 271 291 C3' T T 15 OK 289 292 293 311 C3' G T 16 OK 309 312 313 333 C3' A T 17 OK 331 334 335 354 C3' T T 18 OK 352 355 356 374 C3' A T 19 OK 372 375 376 395 C3' C T 20 OK 393 396 397 432 C3' G U 2 OK 430 433 434 454 C3' T U 3 OK 452 455 456 474 C3' A U 4 OK 472 475 476 495 C3' T U 5 OK 493 496 497 515 C3' C U 6 OK 513 516 517 534 C3' A U 7 OK 532 535 536 555 C3' C U 8 OK 553 556 557 574 C3' C U 9 OK 572 575 576 593 C3' C U 10 OK 591 594 595 612 C3' G S 11 OK 610 613 614 634 C3' C S 12 OK 632 635 636 653 C3' G S 13 OK 651 654 655 675 C3' G S 14 OK 673 676 677 697 C3' T S 15 OK 695 698 699 717 C3' G S 16 OK 715 718 719 739 C3' A S 17 OK 737 740 741 760 C3' T S 18 OK 758 761 762 780 C3' A S 19 OK 778 781 782 801 C3' G S 20 OK 799 802 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 24 C4' C R 2 OK 26 23 25 43 C4' T R 3 OK 45 42 44 63 C4' A R 4 OK 65 62 64 84 C4' T R 5 OK 86 83 85 104 C4' C R 6 OK 106 103 105 123 C4' A R 7 OK 125 122 124 144 C4' C R 8 OK 146 143 145 163 C4' C R 9 OK 165 162 164 182 C4' G R 10 OK 184 181 183 204 C4' C T 11 OK 206 203 205 223 C4' G T 12 OK 225 222 224 245 C4' G T 13 OK 247 244 246 267 C4' G T 14 OK 269 266 268 289 C4' T T 15 OK 291 288 290 309 C4' G T 16 OK 311 308 310 331 C4' A T 17 OK 333 330 332 352 C4' T T 18 OK 354 351 353 372 C4' A T 19 OK 374 371 373 393 C4' C T 20 OK 395 392 394 430 C4' G U 2 OK 432 429 431 452 C4' T U 3 OK 454 451 453 472 C4' A U 4 OK 474 471 473 493 C4' T U 5 OK 495 492 494 513 C4' C U 6 OK 515 512 514 532 C4' A U 7 OK 534 531 533 553 C4' C U 8 OK 555 552 554 572 C4' C U 9 OK 574 571 573 591 C4' C U 10 OK 593 590 592 610 C4' G S 11 OK 612 609 611 632 C4' C S 12 OK 634 631 633 651 C4' G S 13 OK 653 650 652 673 C4' G S 14 OK 675 672 674 695 C4' T S 15 OK 697 694 696 715 C4' G S 16 OK 717 714 716 737 C4' A S 17 OK 739 736 738 758 C4' T S 18 OK 760 757 759 778 C4' A S 19 OK 780 777 779 799 C4' G S 20 OK 801 798 800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 23 C5' C R 2 22 24 42 C5' T R 3 41 43 62 C5' A R 4 61 63 83 C5' T R 5 82 84 103 C5' C R 6 102 104 122 C5' A R 7 121 123 143 C5' C R 8 142 144 162 C5' C R 9 161 163 181 C5' G R 10 180 182 203 C5' C T 11 202 204 222 C5' G T 12 221 223 244 C5' G T 13 243 245 266 C5' G T 14 265 267 288 C5' T T 15 287 289 308 C5' G T 16 307 309 330 C5' A T 17 329 331 351 C5' T T 18 350 352 371 C5' A T 19 370 372 392 C5' C T 20 391 393 429 C5' G U 2 428 430 451 C5' T U 3 450 452 471 C5' A U 4 470 472 492 C5' T U 5 491 493 512 C5' C U 6 511 513 531 C5' A U 7 530 532 552 C5' C U 8 551 553 571 C5' C U 9 570 572 590 C5' C U 10 589 591 609 C5' G S 11 608 610 631 C5' C S 12 630 632 650 C5' G S 13 649 651 672 C5' G S 14 671 673 694 C5' T S 15 693 695 714 C5' G S 16 713 715 736 C5' A S 17 735 737 757 C5' T S 18 756 758 777 C5' A S 19 776 778 798 C5' G S 20 797 799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 38 P T R 3 OK OK 27 39 40 41 58 P A R 4 OK OK 46 59 60 61 79 P T R 5 OK OK 66 80 81 82 99 P C R 6 OK OK 87 100 101 102 118 P A R 7 OK OK 107 119 120 121 139 P C R 8 OK OK 126 140 141 142 158 P C R 9 OK OK 147 159 160 161 177 P G R 10 OK OK 166 178 179 180 199 P C T 11 OK OK 185 200 201 202 218 P G T 12 OK OK 207 219 220 221 240 P G T 13 OK OK 226 241 242 243 262 P G T 14 OK OK 248 263 264 265 284 P T T 15 OK OK 270 285 286 287 304 P G T 16 OK OK 292 305 306 307 326 P A T 17 OK OK 312 327 328 329 347 P T T 18 OK OK 334 348 349 350 367 P A T 19 OK OK 355 368 369 370 388 P C T 20 OK OK 375 389 390 391 447 P T U 3 OK OK 433 448 449 450 467 P A U 4 OK OK 455 468 469 470 488 P T U 5 OK OK 475 489 490 491 508 P C U 6 OK OK 496 509 510 511 527 P A U 7 OK OK 516 528 529 530 548 P C U 8 OK OK 535 549 550 551 567 P C U 9 OK OK 556 568 569 570 586 P C U 10 OK OK 575 587 588 589 605 P G S 11 OK OK 594 606 607 608 627 P C S 12 OK OK 613 628 629 630 646 P G S 13 OK OK 635 647 648 649 668 P G S 14 OK OK 654 669 670 671 690 P T S 15 OK OK 676 691 692 693 710 P G S 16 OK OK 698 711 712 713 732 P A S 17 OK OK 718 733 734 735 753 P T S 18 OK OK 740 754 755 756 773 P A S 19 OK OK 761 774 775 776 794 P G S 20 OK OK 781 795 796 797 ---------------------------------------------------------------------------------