ID code: '1TC3' 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' G A 2 beta 25 30 28 51 C1' G A 3 beta 47 52 50 73 C1' G A 4 beta 69 74 72 95 C1' G A 5 beta 91 96 94 117 C1' G A 6 beta 113 118 116 139 C1' G A 7 beta 135 140 138 161 C1' G A 8 beta 157 162 160 183 C1' T A 9 beta 179 184 182 203 C1' C A 10 beta 199 204 202 222 C1' C A 11 beta 218 223 221 241 C1' T A 12 beta 237 242 240 261 C1' A A 13 beta 257 262 260 282 C1' T A 14 beta 278 283 281 302 C1' A A 15 beta 298 303 301 323 C1' G A 16 beta 319 324 322 345 C1' A A 17 beta 341 346 344 366 C1' A A 18 beta 362 367 365 387 C1' C A 19 beta 383 388 386 406 C1' T A 20 beta 402 407 405 444 C1' A B 101 beta 440 445 443 465 C1' G B 102 beta 461 466 464 487 C1' T B 103 beta 483 488 486 507 C1' T B 104 beta 503 508 506 527 C1' C B 105 beta 523 528 526 546 C1' T B 106 beta 542 547 545 566 C1' A B 107 beta 562 567 565 587 C1' T B 108 beta 583 588 586 607 C1' A B 109 beta 603 608 606 628 C1' G B 110 beta 624 629 627 650 C1' G B 111 beta 646 651 649 672 C1' A B 112 beta 668 673 671 693 C1' C B 113 beta 689 694 692 712 C1' C B 114 beta 708 713 711 731 C1' C B 115 beta 727 732 730 750 C1' C B 116 beta 746 751 749 769 C1' C B 117 beta 765 770 768 788 C1' C B 118 beta 784 789 787 807 C1' C B 119 beta 803 808 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 28 C2' G A 2 29 26 50 C2' G A 3 51 48 72 C2' G A 4 73 70 94 C2' G A 5 95 92 116 C2' G A 6 117 114 138 C2' G A 7 139 136 160 C2' G A 8 161 158 182 C2' T A 9 183 180 202 C2' C A 10 203 200 221 C2' C A 11 222 219 240 C2' T A 12 241 238 260 C2' A A 13 261 258 281 C2' T A 14 282 279 301 C2' A A 15 302 299 322 C2' G A 16 323 320 344 C2' A A 17 345 342 365 C2' A A 18 366 363 386 C2' C A 19 387 384 405 C2' T A 20 406 403 443 C2' A B 101 444 441 464 C2' G B 102 465 462 486 C2' T B 103 487 484 506 C2' T B 104 507 504 526 C2' C B 105 527 524 545 C2' T B 106 546 543 565 C2' A B 107 566 563 586 C2' T B 108 587 584 606 C2' A B 109 607 604 627 C2' G B 110 628 625 649 C2' G B 111 650 647 671 C2' A B 112 672 669 692 C2' C B 113 693 690 711 C2' C B 114 712 709 730 C2' C B 115 731 728 749 C2' C B 116 750 747 768 C2' C B 117 769 766 787 C2' C B 118 788 785 806 C2' C B 119 807 804 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 26 C3' G A 2 OK 24 27 28 48 C3' G A 3 OK 46 49 50 70 C3' G A 4 OK 68 71 72 92 C3' G A 5 OK 90 93 94 114 C3' G A 6 OK 112 115 116 136 C3' G A 7 OK 134 137 138 158 C3' G A 8 OK 156 159 160 180 C3' T A 9 OK 178 181 182 200 C3' C A 10 OK 198 201 202 219 C3' C A 11 OK 217 220 221 238 C3' T A 12 OK 236 239 240 258 C3' A A 13 OK 256 259 260 279 C3' T A 14 OK 277 280 281 299 C3' A A 15 OK 297 300 301 320 C3' G A 16 OK 318 321 322 342 C3' A A 17 OK 340 343 344 363 C3' A A 18 OK 361 364 365 384 C3' C A 19 OK 382 385 386 403 C3' T A 20 OK 401 404 405 441 C3' A B 101 OK 439 442 443 462 C3' G B 102 OK 460 463 464 484 C3' T B 103 OK 482 485 486 504 C3' T B 104 OK 502 505 506 524 C3' C B 105 OK 522 525 526 543 C3' T B 106 OK 541 544 545 563 C3' A B 107 OK 561 564 565 584 C3' T B 108 OK 582 585 586 604 C3' A B 109 OK 602 605 606 625 C3' G B 110 OK 623 626 627 647 C3' G B 111 OK 645 648 649 669 C3' A B 112 OK 667 670 671 690 C3' C B 113 OK 688 691 692 709 C3' C B 114 OK 707 710 711 728 C3' C B 115 OK 726 729 730 747 C3' C B 116 OK 745 748 749 766 C3' C B 117 OK 764 767 768 785 C3' C B 118 OK 783 786 787 804 C3' C B 119 OK 802 805 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 24 C4' G A 2 OK 26 23 25 46 C4' G A 3 OK 48 45 47 68 C4' G A 4 OK 70 67 69 90 C4' G A 5 OK 92 89 91 112 C4' G A 6 OK 114 111 113 134 C4' G A 7 OK 136 133 135 156 C4' G A 8 OK 158 155 157 178 C4' T A 9 OK 180 177 179 198 C4' C A 10 OK 200 197 199 217 C4' C A 11 OK 219 216 218 236 C4' T A 12 OK 238 235 237 256 C4' A A 13 OK 258 255 257 277 C4' T A 14 OK 279 276 278 297 C4' A A 15 OK 299 296 298 318 C4' G A 16 OK 320 317 319 340 C4' A A 17 OK 342 339 341 361 C4' A A 18 OK 363 360 362 382 C4' C A 19 OK 384 381 383 401 C4' T A 20 OK 403 400 402 439 C4' A B 101 OK 441 438 440 460 C4' G B 102 OK 462 459 461 482 C4' T B 103 OK 484 481 483 502 C4' T B 104 OK 504 501 503 522 C4' C B 105 OK 524 521 523 541 C4' T B 106 OK 543 540 542 561 C4' A B 107 OK 563 560 562 582 C4' T B 108 OK 584 581 583 602 C4' A B 109 OK 604 601 603 623 C4' G B 110 OK 625 622 624 645 C4' G B 111 OK 647 644 646 667 C4' A B 112 OK 669 666 668 688 C4' C B 113 OK 690 687 689 707 C4' C B 114 OK 709 706 708 726 C4' C B 115 OK 728 725 727 745 C4' C B 116 OK 747 744 746 764 C4' C B 117 OK 766 763 765 783 C4' C B 118 OK 785 782 784 802 C4' C B 119 OK 804 801 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 23 C5' G A 2 22 24 45 C5' G A 3 44 46 67 C5' G A 4 66 68 89 C5' G A 5 88 90 111 C5' G A 6 110 112 133 C5' G A 7 132 134 155 C5' G A 8 154 156 177 C5' T A 9 176 178 197 C5' C A 10 196 198 216 C5' C A 11 215 217 235 C5' T A 12 234 236 255 C5' A A 13 254 256 276 C5' T A 14 275 277 296 C5' A A 15 295 297 317 C5' G A 16 316 318 339 C5' A A 17 338 340 360 C5' A A 18 359 361 381 C5' C A 19 380 382 400 C5' T A 20 399 401 438 C5' A B 101 437 439 459 C5' G B 102 458 460 481 C5' T B 103 480 482 501 C5' T B 104 500 502 521 C5' C B 105 520 522 540 C5' T B 106 539 541 560 C5' A B 107 559 561 581 C5' T B 108 580 582 601 C5' A B 109 600 602 622 C5' G B 110 621 623 644 C5' G B 111 643 645 666 C5' A B 112 665 667 687 C5' C B 113 686 688 706 C5' C B 114 705 707 725 C5' C B 115 724 726 744 C5' C B 116 743 745 763 C5' C B 117 762 764 782 C5' C B 118 781 783 801 C5' C B 119 800 802 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 41 P G A 3 OK OK 27 42 43 44 63 P G A 4 OK OK 49 64 65 66 85 P G A 5 OK OK 71 86 87 88 107 P G A 6 OK OK 93 108 109 110 129 P G A 7 OK OK 115 130 131 132 151 P G A 8 OK OK 137 152 153 154 173 P T A 9 OK OK 159 174 175 176 193 P C A 10 OK OK 181 194 195 196 212 P C A 11 OK OK 201 213 214 215 231 P T A 12 OK OK 220 232 233 234 251 P A A 13 OK OK 239 252 253 254 272 P T A 14 OK OK 259 273 274 275 292 P A A 15 OK OK 280 293 294 295 313 P G A 16 OK OK 300 314 315 316 335 P A A 17 OK OK 321 336 337 338 356 P A A 18 OK OK 343 357 358 359 377 P C A 19 OK OK 364 378 379 380 396 P T A 20 OK OK 385 397 398 399 455 P G B 102 OK OK 442 456 457 458 477 P T B 103 OK OK 463 478 479 480 497 P T B 104 OK OK 485 498 499 500 517 P C B 105 OK OK 505 518 519 520 536 P T B 106 OK OK 525 537 538 539 556 P A B 107 OK OK 544 557 558 559 577 P T B 108 OK OK 564 578 579 580 597 P A B 109 OK OK 585 598 599 600 618 P G B 110 OK OK 605 619 620 621 640 P G B 111 OK OK 626 641 642 643 662 P A B 112 OK OK 648 663 664 665 683 P C B 113 OK OK 670 684 685 686 702 P C B 114 OK OK 691 703 704 705 721 P C B 115 OK OK 710 722 723 724 740 P C B 116 OK OK 729 741 742 743 759 P C B 117 OK OK 748 760 761 762 778 P C B 118 OK OK 767 779 780 781 797 P C B 119 OK OK 786 798 799 800 ---------------------------------------------------------------------------------