ID code: '1BG1' 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' --------------------------------------------------------------------------------- 28 C1' G B 2 beta 24 29 27 50 C1' C B 3 beta 46 51 49 69 C1' A B 4 beta 65 70 68 90 C1' T B 5 beta 86 91 89 110 C1' T B 6 beta 106 111 109 130 C1' T B 7 beta 126 131 129 150 C1' C B 8 beta 146 151 149 169 C1' C B 9 beta 165 170 168 188 C1' C B 10 beta 184 189 187 207 C1' G B 11 beta 203 208 206 229 C1' T B 12 beta 225 230 228 249 C1' A B 13 beta 245 250 248 270 C1' A B 14 beta 266 271 269 291 C1' A B 15 beta 287 292 290 312 C1' T B 16 beta 308 313 311 332 C1' C B 17 beta 328 333 331 351 C1' T B 18 beta 347 352 350 388 C1' A C 2 beta 384 397 387 413 C1' G C 3 beta 409 423 412 439 C1' A C 4 beta 435 440 438 460 C1' T C 5 beta 456 461 459 480 C1' T C 6 beta 476 481 479 500 C1' T C 7 beta 496 501 499 520 C1' A C 8 beta 516 529 519 545 C1' C C 9 beta 541 546 544 564 C1' G C 10 beta 560 574 563 590 C1' G C 11 beta 586 591 589 612 C1' G C 12 beta 608 622 611 638 C1' A C 13 beta 634 639 637 659 C1' A C 14 beta 655 660 658 680 C1' A C 15 beta 676 681 679 701 C1' T C 16 beta 697 702 700 721 C1' G C 17 beta 717 731 720 747 C1' C C 18 beta 743 755 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 27 C2' G B 2 28 25 49 C2' C B 3 50 47 68 C2' A B 4 69 66 89 C2' T B 5 90 87 109 C2' T B 6 110 107 129 C2' T B 7 130 127 149 C2' C B 8 150 147 168 C2' C B 9 169 166 187 C2' C B 10 188 185 206 C2' G B 11 207 204 228 C2' T B 12 229 226 248 C2' A B 13 249 246 269 C2' A B 14 270 267 290 C2' A B 15 291 288 311 C2' T B 16 312 309 331 C2' C B 17 332 329 350 C2' T B 18 351 348 387 C2' A C 2 388 385 412 C2' G C 3 413 410 438 C2' A C 4 439 436 459 C2' T C 5 460 457 479 C2' T C 6 480 477 499 C2' T C 7 500 497 519 C2' A C 8 520 517 544 C2' C C 9 545 542 563 C2' G C 10 564 561 589 C2' G C 11 590 587 611 C2' G C 12 612 609 637 C2' A C 13 638 635 658 C2' A C 14 659 656 679 C2' A C 15 680 677 700 C2' T C 16 701 698 720 C2' G C 17 721 718 746 C2' C C 18 747 744 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 25 C3' G B 2 OK 23 26 27 47 C3' C B 3 OK 45 48 49 66 C3' A B 4 OK 64 67 68 87 C3' T B 5 OK 85 88 89 107 C3' T B 6 OK 105 108 109 127 C3' T B 7 OK 125 128 129 147 C3' C B 8 OK 145 148 149 166 C3' C B 9 OK 164 167 168 185 C3' C B 10 OK 183 186 187 204 C3' G B 11 OK 202 205 206 226 C3' T B 12 OK 224 227 228 246 C3' A B 13 OK 244 247 248 267 C3' A B 14 OK 265 268 269 288 C3' A B 15 OK 286 289 290 309 C3' T B 16 OK 307 310 311 329 C3' C B 17 OK 327 330 331 348 C3' T B 18 OK 346 349 350 385 C3' A C 2 OK 383 386 387 410 C3' G C 3 OK 408 411 412 436 C3' A C 4 OK 434 437 438 457 C3' T C 5 OK 455 458 459 477 C3' T C 6 OK 475 478 479 497 C3' T C 7 OK 495 498 499 517 C3' A C 8 OK 515 518 519 542 C3' C C 9 OK 540 543 544 561 C3' G C 10 OK 559 562 563 587 C3' G C 11 OK 585 588 589 609 C3' G C 12 OK 607 610 611 635 C3' A C 13 OK 633 636 637 656 C3' A C 14 OK 654 657 658 677 C3' A C 15 OK 675 678 679 698 C3' T C 16 OK 696 699 700 718 C3' G C 17 OK 716 719 720 744 C3' C C 18 OK 742 745 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 23 C4' G B 2 OK 25 22 24 45 C4' C B 3 OK 47 44 46 64 C4' A B 4 OK 66 63 65 85 C4' T B 5 OK 87 84 86 105 C4' T B 6 OK 107 104 106 125 C4' T B 7 OK 127 124 126 145 C4' C B 8 OK 147 144 146 164 C4' C B 9 OK 166 163 165 183 C4' C B 10 OK 185 182 184 202 C4' G B 11 OK 204 201 203 224 C4' T B 12 OK 226 223 225 244 C4' A B 13 OK 246 243 245 265 C4' A B 14 OK 267 264 266 286 C4' A B 15 OK 288 285 287 307 C4' T B 16 OK 309 306 308 327 C4' C B 17 OK 329 326 328 346 C4' T B 18 OK 348 345 347 383 C4' A C 2 OK 385 382 384 408 C4' G C 3 OK 410 407 409 434 C4' A C 4 OK 436 433 435 455 C4' T C 5 OK 457 454 456 475 C4' T C 6 OK 477 474 476 495 C4' T C 7 OK 497 494 496 515 C4' A C 8 OK 517 514 516 540 C4' C C 9 OK 542 539 541 559 C4' G C 10 OK 561 558 560 585 C4' G C 11 OK 587 584 586 607 C4' G C 12 OK 609 606 608 633 C4' A C 13 OK 635 632 634 654 C4' A C 14 OK 656 653 655 675 C4' A C 15 OK 677 674 676 696 C4' T C 16 OK 698 695 697 716 C4' G C 17 OK 718 715 717 742 C4' C C 18 OK 744 741 743 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 22 C5' G B 2 21 23 44 C5' C B 3 43 45 63 C5' A B 4 62 64 84 C5' T B 5 83 85 104 C5' T B 6 103 105 124 C5' T B 7 123 125 144 C5' C B 8 143 145 163 C5' C B 9 162 164 182 C5' C B 10 181 183 201 C5' G B 11 200 202 223 C5' T B 12 222 224 243 C5' A B 13 242 244 264 C5' A B 14 263 265 285 C5' A B 15 284 286 306 C5' T B 16 305 307 326 C5' C B 17 325 327 345 C5' T B 18 344 346 382 C5' A C 2 381 383 407 C5' G C 3 406 408 433 C5' A C 4 432 434 454 C5' T C 5 453 455 474 C5' T C 6 473 475 494 C5' T C 7 493 495 514 C5' A C 8 513 515 539 C5' C C 9 538 540 558 C5' G C 10 557 559 584 C5' G C 11 583 585 606 C5' G C 12 605 607 632 C5' A C 13 631 633 653 C5' A C 14 652 654 674 C5' A C 15 673 675 695 C5' T C 16 694 696 715 C5' G C 17 714 716 741 C5' C C 18 740 742 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 40 P C B 3 distorted distorted 26 41 42 43 59 P A B 4 distorted distorted 48 60 61 62 80 P T B 5 distorted distorted 67 81 82 83 100 P T B 6 distorted distorted 88 101 102 103 120 P T B 7 distorted distorted 108 121 122 123 140 P C B 8 distorted distorted 128 141 142 143 159 P C B 9 distorted distorted 148 160 161 162 178 P C B 10 distorted distorted 167 179 180 181 197 P G B 11 distorted distorted 186 198 199 200 219 P T B 12 distorted distorted 205 220 221 222 239 P A B 13 distorted distorted 227 240 241 242 260 P A B 14 distorted distorted 247 261 262 263 281 P A B 15 distorted distorted 268 282 283 284 302 P T B 16 distorted distorted 289 303 304 305 322 P C B 17 distorted distorted 310 323 324 325 341 P T B 18 distorted distorted 330 342 343 344 403 P G C 3 distorted distorted 386 404 405 406 429 P A C 4 distorted distorted 411 430 431 432 450 P T C 5 distorted distorted 437 451 452 453 470 P T C 6 distorted distorted 458 471 472 473 490 P T C 7 distorted distorted 478 491 492 493 510 P A C 8 distorted distorted 498 511 512 513 535 P C C 9 distorted distorted 518 536 537 538 554 P G C 10 distorted distorted 543 555 556 557 580 P G C 11 distorted distorted 562 581 582 583 602 P G C 12 distorted distorted 588 603 604 605 628 P A C 13 distorted distorted 610 629 630 631 649 P A C 14 distorted distorted 636 650 651 652 670 P A C 15 distorted distorted 657 671 672 673 691 P T C 16 distorted distorted 678 692 693 694 711 P G C 17 distorted distorted 699 712 713 714 737 P C C 18 distorted distorted 719 738 739 740 ---------------------------------------------------------------------------------