ID code: '3CRO' 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' --------------------------------------------------------------------------------- 33 C1' A A 2 beta 29 34 32 54 C1' G A 3 beta 50 55 53 76 C1' T A 4 beta 72 77 75 96 C1' A A 5 beta 92 97 95 117 C1' C A 6 beta 113 118 116 136 C1' A A 7 beta 132 137 135 157 C1' A A 8 beta 153 158 156 178 C1' A A 9 beta 174 179 177 199 C1' C A 10 beta 195 200 198 218 C1' T A 11 beta 214 219 217 238 C1' T A 12 beta 234 239 237 258 C1' T A 13 beta 254 259 257 278 C1' C A 14 beta 274 279 277 297 C1' T A 15 beta 293 298 296 317 C1' T A 16 beta 313 318 316 337 C1' G A 17 beta 333 338 336 359 C1' T A 18 beta 355 360 358 379 C1' A A 19 beta 375 380 378 400 C1' T A 20 beta 396 401 399 442 C1' A B 2 beta 438 443 441 463 C1' T B 3 beta 459 464 462 483 C1' A B 4 beta 479 484 482 504 C1' C B 5 beta 500 505 503 523 C1' A B 6 beta 519 524 522 544 C1' A B 7 beta 540 545 543 565 C1' G B 8 beta 561 566 564 587 C1' A B 9 beta 583 588 586 608 C1' A B 10 beta 604 609 607 629 C1' A B 11 beta 625 630 628 650 C1' G B 12 beta 646 651 649 672 C1' T B 13 beta 668 673 671 692 C1' T B 14 beta 688 693 691 712 C1' T B 15 beta 708 713 711 732 C1' G B 16 beta 728 733 731 754 C1' T B 17 beta 750 755 753 774 C1' A B 18 beta 770 775 773 795 C1' C B 19 beta 791 796 794 814 C1' T B 20 beta 810 815 813 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 32 C2' A A 2 33 30 53 C2' G A 3 54 51 75 C2' T A 4 76 73 95 C2' A A 5 96 93 116 C2' C A 6 117 114 135 C2' A A 7 136 133 156 C2' A A 8 157 154 177 C2' A A 9 178 175 198 C2' C A 10 199 196 217 C2' T A 11 218 215 237 C2' T A 12 238 235 257 C2' T A 13 258 255 277 C2' C A 14 278 275 296 C2' T A 15 297 294 316 C2' T A 16 317 314 336 C2' G A 17 337 334 358 C2' T A 18 359 356 378 C2' A A 19 379 376 399 C2' T A 20 400 397 441 C2' A B 2 442 439 462 C2' T B 3 463 460 482 C2' A B 4 483 480 503 C2' C B 5 504 501 522 C2' A B 6 523 520 543 C2' A B 7 544 541 564 C2' G B 8 565 562 586 C2' A B 9 587 584 607 C2' A B 10 608 605 628 C2' A B 11 629 626 649 C2' G B 12 650 647 671 C2' T B 13 672 669 691 C2' T B 14 692 689 711 C2' T B 15 712 709 731 C2' G B 16 732 729 753 C2' T B 17 754 751 773 C2' A B 18 774 771 794 C2' C B 19 795 792 813 C2' T B 20 814 811 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 30 C3' A A 2 OK 28 31 32 51 C3' G A 3 OK 49 52 53 73 C3' T A 4 OK 71 74 75 93 C3' A A 5 OK 91 94 95 114 C3' C A 6 OK 112 115 116 133 C3' A A 7 OK 131 134 135 154 C3' A A 8 OK 152 155 156 175 C3' A A 9 OK 173 176 177 196 C3' C A 10 OK 194 197 198 215 C3' T A 11 OK 213 216 217 235 C3' T A 12 OK 233 236 237 255 C3' T A 13 OK 253 256 257 275 C3' C A 14 OK 273 276 277 294 C3' T A 15 OK 292 295 296 314 C3' T A 16 OK 312 315 316 334 C3' G A 17 OK 332 335 336 356 C3' T A 18 OK 354 357 358 376 C3' A A 19 OK 374 377 378 397 C3' T A 20 OK 395 398 399 439 C3' A B 2 OK 437 440 441 460 C3' T B 3 OK 458 461 462 480 C3' A B 4 OK 478 481 482 501 C3' C B 5 OK 499 502 503 520 C3' A B 6 OK 518 521 522 541 C3' A B 7 OK 539 542 543 562 C3' G B 8 OK 560 563 564 584 C3' A B 9 OK 582 585 586 605 C3' A B 10 OK 603 606 607 626 C3' A B 11 OK 624 627 628 647 C3' G B 12 OK 645 648 649 669 C3' T B 13 OK 667 670 671 689 C3' T B 14 OK 687 690 691 709 C3' T B 15 OK 707 710 711 729 C3' G B 16 OK 727 730 731 751 C3' T B 17 OK 749 752 753 771 C3' A B 18 OK 769 772 773 792 C3' C B 19 OK 790 793 794 811 C3' T B 20 OK 809 812 813 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 28 C4' A A 2 OK 30 27 29 49 C4' G A 3 OK 51 48 50 71 C4' T A 4 OK 73 70 72 91 C4' A A 5 OK 93 90 92 112 C4' C A 6 OK 114 111 113 131 C4' A A 7 OK 133 130 132 152 C4' A A 8 OK 154 151 153 173 C4' A A 9 OK 175 172 174 194 C4' C A 10 OK 196 193 195 213 C4' T A 11 OK 215 212 214 233 C4' T A 12 OK 235 232 234 253 C4' T A 13 OK 255 252 254 273 C4' C A 14 OK 275 272 274 292 C4' T A 15 OK 294 291 293 312 C4' T A 16 OK 314 311 313 332 C4' G A 17 OK 334 331 333 354 C4' T A 18 OK 356 353 355 374 C4' A A 19 OK 376 373 375 395 C4' T A 20 OK 397 394 396 437 C4' A B 2 OK 439 436 438 458 C4' T B 3 OK 460 457 459 478 C4' A B 4 OK 480 477 479 499 C4' C B 5 OK 501 498 500 518 C4' A B 6 OK 520 517 519 539 C4' A B 7 OK 541 538 540 560 C4' G B 8 OK 562 559 561 582 C4' A B 9 OK 584 581 583 603 C4' A B 10 OK 605 602 604 624 C4' A B 11 OK 626 623 625 645 C4' G B 12 OK 647 644 646 667 C4' T B 13 OK 669 666 668 687 C4' T B 14 OK 689 686 688 707 C4' T B 15 OK 709 706 708 727 C4' G B 16 OK 729 726 728 749 C4' T B 17 OK 751 748 750 769 C4' A B 18 OK 771 768 770 790 C4' C B 19 OK 792 789 791 809 C4' T B 20 OK 811 808 810 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 27 C5' A A 2 26 28 48 C5' G A 3 47 49 70 C5' T A 4 69 71 90 C5' A A 5 89 91 111 C5' C A 6 110 112 130 C5' A A 7 129 131 151 C5' A A 8 150 152 172 C5' A A 9 171 173 193 C5' C A 10 192 194 212 C5' T A 11 211 213 232 C5' T A 12 231 233 252 C5' T A 13 251 253 272 C5' C A 14 271 273 291 C5' T A 15 290 292 311 C5' T A 16 310 312 331 C5' G A 17 330 332 353 C5' T A 18 352 354 373 C5' A A 19 372 374 394 C5' T A 20 393 395 436 C5' A B 2 435 437 457 C5' T B 3 456 458 477 C5' A B 4 476 478 498 C5' C B 5 497 499 517 C5' A B 6 516 518 538 C5' A B 7 537 539 559 C5' G B 8 558 560 581 C5' A B 9 580 582 602 C5' A B 10 601 603 623 C5' A B 11 622 624 644 C5' G B 12 643 645 666 C5' T B 13 665 667 686 C5' T B 14 685 687 706 C5' T B 15 705 707 726 C5' G B 16 725 727 748 C5' T B 17 747 749 768 C5' A B 18 767 769 789 C5' C B 19 788 790 808 C5' T B 20 807 809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 44 P G A 3 OK OK 31 45 46 47 66 P T A 4 OK OK 52 67 68 69 86 P A A 5 OK OK 74 87 88 89 107 P C A 6 OK OK 94 108 109 110 126 P A A 7 OK OK 115 127 128 129 147 P A A 8 OK OK 134 148 149 150 168 P A A 9 OK OK 155 169 170 171 189 P C A 10 OK OK 176 190 191 192 208 P T A 11 OK OK 197 209 210 211 228 P T A 12 OK OK 216 229 230 231 248 P T A 13 OK OK 236 249 250 251 268 P C A 14 OK OK 256 269 270 271 287 P T A 15 OK OK 276 288 289 290 307 P T A 16 distorted distorted 295 308 309 310 327 P G A 17 OK OK 315 328 329 330 349 P T A 18 OK OK 335 350 351 352 369 P A A 19 OK OK 357 370 371 372 390 P T A 20 OK OK 377 391 392 393 453 P T B 3 OK OK 440 454 455 456 473 P A B 4 OK OK 461 474 475 476 494 P C B 5 OK OK 481 495 496 497 513 P A B 6 OK OK 502 514 515 516 534 P A B 7 OK OK 521 535 536 537 555 P G B 8 OK OK 542 556 557 558 577 P A B 9 OK OK 563 578 579 580 598 P A B 10 OK OK 585 599 600 601 619 P A B 11 OK OK 606 620 621 622 640 P G B 12 OK OK 627 641 642 643 662 P T B 13 OK OK 648 663 664 665 682 P T B 14 OK OK 670 683 684 685 702 P T B 15 OK OK 690 703 704 705 722 P G B 16 OK OK 710 723 724 725 744 P T B 17 OK OK 730 745 746 747 764 P A B 18 OK OK 752 765 766 767 785 P C B 19 OK OK 772 786 787 788 804 P T B 20 OK OK 793 805 806 807 ---------------------------------------------------------------------------------