ID code: '2ZH8' 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' --------------------------------------------------------------------------------- 12 C1' G B 1 beta 7 13 10 35 C1' G B 2 beta 30 36 33 58 C1' C B 3 beta 53 59 56 78 C1' C B 4 beta 73 79 76 98 C1' C B 5 beta 93 99 96 118 C1' G B 6 beta 113 119 116 141 C1' G B 7 beta 136 142 139 164 C1' G B 8 beta 159 165 162 187 C1' G B 9 beta 182 188 185 210 C1' C B 10 beta 205 211 208 230 C1' G B 11 beta 225 231 228 253 C1' G B 12 beta 248 254 251 276 C1' U B 13 beta 271 277 274 296 C1' U B 14 beta 291 297 294 316 C1' C B 15 beta 311 317 314 336 C1' G B 16 beta 331 337 334 359 C1' A B 17 beta 354 360 357 381 C1' U B 18 beta 376 382 379 401 C1' U B 19 beta 396 402 399 421 C1' C B 20 beta 416 422 419 441 C1' C B 21 beta 436 442 439 461 C1' G B 22 beta 456 462 459 484 C1' C B 23 beta 479 485 482 504 C1' C B 24 beta 499 505 502 524 C1' C B 25 beta 519 525 522 544 C1' U B 26 beta 539 545 542 564 C1' G B 27 beta 559 565 562 587 C1' G B 28 beta 582 588 585 610 C1' G B 29 beta 605 611 608 633 C1' C B 30 beta 628 634 631 653 C1' C B 31 beta 648 654 651 673 C1' A B 32 beta 668 674 671 695 C1' G B 33 beta 690 696 693 718 C1' C B 34 beta 713 719 716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G B 1 OK 12 8 11 33 C2' G B 2 OK 35 31 34 56 C2' C B 3 OK 58 54 57 76 C2' C B 4 OK 78 74 77 96 C2' C B 5 OK 98 94 97 116 C2' G B 6 OK 118 114 117 139 C2' G B 7 OK 141 137 140 162 C2' G B 8 OK 164 160 163 185 C2' G B 9 OK 187 183 186 208 C2' C B 10 OK 210 206 209 228 C2' G B 11 OK 230 226 229 251 C2' G B 12 OK 253 249 252 274 C2' U B 13 OK 276 272 275 294 C2' U B 14 OK 296 292 295 314 C2' C B 15 OK 316 312 315 334 C2' G B 16 OK 336 332 335 357 C2' A B 17 OK 359 355 358 379 C2' U B 18 OK 381 377 380 399 C2' U B 19 OK 401 397 400 419 C2' C B 20 OK 421 417 420 439 C2' C B 21 OK 441 437 440 459 C2' G B 22 OK 461 457 460 482 C2' C B 23 OK 484 480 483 502 C2' C B 24 OK 504 500 503 522 C2' C B 25 OK 524 520 523 542 C2' U B 26 OK 544 540 543 562 C2' G B 27 OK 564 560 563 585 C2' G B 28 OK 587 583 586 608 C2' G B 29 OK 610 606 609 631 C2' C B 30 OK 633 629 632 651 C2' C B 31 OK 653 649 652 671 C2' A B 32 OK 673 669 672 693 C2' G B 33 OK 695 691 694 716 C2' C B 34 OK 718 714 717 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G B 1 OK 6 9 10 31 C3' G B 2 OK 29 32 33 54 C3' C B 3 OK 52 55 56 74 C3' C B 4 OK 72 75 76 94 C3' C B 5 OK 92 95 96 114 C3' G B 6 OK 112 115 116 137 C3' G B 7 OK 135 138 139 160 C3' G B 8 OK 158 161 162 183 C3' G B 9 OK 181 184 185 206 C3' C B 10 OK 204 207 208 226 C3' G B 11 OK 224 227 228 249 C3' G B 12 OK 247 250 251 272 C3' U B 13 OK 270 273 274 292 C3' U B 14 OK 290 293 294 312 C3' C B 15 OK 310 313 314 332 C3' G B 16 OK 330 333 334 355 C3' A B 17 OK 353 356 357 377 C3' U B 18 OK 375 378 379 397 C3' U B 19 OK 395 398 399 417 C3' C B 20 OK 415 418 419 437 C3' C B 21 OK 435 438 439 457 C3' G B 22 OK 455 458 459 480 C3' C B 23 OK 478 481 482 500 C3' C B 24 OK 498 501 502 520 C3' C B 25 OK 518 521 522 540 C3' U B 26 OK 538 541 542 560 C3' G B 27 OK 558 561 562 583 C3' G B 28 OK 581 584 585 606 C3' G B 29 OK 604 607 608 629 C3' C B 30 OK 627 630 631 649 C3' C B 31 OK 647 650 651 669 C3' A B 32 OK 667 670 671 691 C3' G B 33 OK 689 692 693 714 C3' C B 34 OK 712 715 716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G B 1 OK 8 5 7 29 C4' G B 2 OK 31 28 30 52 C4' C B 3 OK 54 51 53 72 C4' C B 4 OK 74 71 73 92 C4' C B 5 OK 94 91 93 112 C4' G B 6 OK 114 111 113 135 C4' G B 7 OK 137 134 136 158 C4' G B 8 OK 160 157 159 181 C4' G B 9 OK 183 180 182 204 C4' C B 10 OK 206 203 205 224 C4' G B 11 OK 226 223 225 247 C4' G B 12 OK 249 246 248 270 C4' U B 13 OK 272 269 271 290 C4' U B 14 OK 292 289 291 310 C4' C B 15 OK 312 309 311 330 C4' G B 16 OK 332 329 331 353 C4' A B 17 OK 355 352 354 375 C4' U B 18 OK 377 374 376 395 C4' U B 19 OK 397 394 396 415 C4' C B 20 OK 417 414 416 435 C4' C B 21 OK 437 434 436 455 C4' G B 22 OK 457 454 456 478 C4' C B 23 OK 480 477 479 498 C4' C B 24 OK 500 497 499 518 C4' C B 25 OK 520 517 519 538 C4' U B 26 OK 540 537 539 558 C4' G B 27 OK 560 557 559 581 C4' G B 28 OK 583 580 582 604 C4' G B 29 OK 606 603 605 627 C4' C B 30 OK 629 626 628 647 C4' C B 31 OK 649 646 648 667 C4' A B 32 OK 669 666 668 689 C4' G B 33 OK 691 688 690 712 C4' C B 34 OK 714 711 713 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G B 1 4 6 28 C5' G B 2 27 29 51 C5' C B 3 50 52 71 C5' C B 4 70 72 91 C5' C B 5 90 92 111 C5' G B 6 110 112 134 C5' G B 7 133 135 157 C5' G B 8 156 158 180 C5' G B 9 179 181 203 C5' C B 10 202 204 223 C5' G B 11 222 224 246 C5' G B 12 245 247 269 C5' U B 13 268 270 289 C5' U B 14 288 290 309 C5' C B 15 308 310 329 C5' G B 16 328 330 352 C5' A B 17 351 353 374 C5' U B 18 373 375 394 C5' U B 19 393 395 414 C5' C B 20 413 415 434 C5' C B 21 433 435 454 C5' G B 22 453 455 477 C5' C B 23 476 478 497 C5' C B 24 496 498 517 C5' C B 25 516 518 537 C5' U B 26 536 538 557 C5' G B 27 556 558 580 C5' G B 28 579 581 603 C5' G B 29 602 604 626 C5' C B 30 625 627 646 C5' C B 31 645 647 666 C5' A B 32 665 667 688 C5' G B 33 687 689 711 C5' C B 34 710 712 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G B 1 distorted distorted 2 3 4 24 P G B 2 distorted distorted 9 25 26 27 47 P C B 3 distorted distorted 32 48 49 50 67 P C B 4 distorted distorted 55 68 69 70 87 P C B 5 distorted distorted 75 88 89 90 107 P G B 6 distorted distorted 95 108 109 110 130 P G B 7 distorted distorted 115 131 132 133 153 P G B 8 distorted distorted 138 154 155 156 176 P G B 9 distorted distorted 161 177 178 179 199 P C B 10 distorted distorted 184 200 201 202 219 P G B 11 distorted distorted 207 220 221 222 242 P G B 12 distorted distorted 227 243 244 245 265 P U B 13 distorted distorted 250 266 267 268 285 P U B 14 distorted distorted 273 286 287 288 305 P C B 15 distorted distorted 293 306 307 308 325 P G B 16 distorted distorted 313 326 327 328 348 P A B 17 distorted distorted 333 349 350 351 370 P U B 18 distorted distorted 356 371 372 373 390 P U B 19 distorted distorted 378 391 392 393 410 P C B 20 distorted distorted 398 411 412 413 430 P C B 21 distorted distorted 418 431 432 433 450 P G B 22 distorted distorted 438 451 452 453 473 P C B 23 distorted distorted 458 474 475 476 493 P C B 24 distorted distorted 481 494 495 496 513 P C B 25 distorted distorted 501 514 515 516 533 P U B 26 distorted distorted 521 534 535 536 553 P G B 27 distorted distorted 541 554 555 556 576 P G B 28 distorted distorted 561 577 578 579 599 P G B 29 distorted distorted 584 600 601 602 622 P C B 30 distorted distorted 607 623 624 625 642 P C B 31 distorted distorted 630 643 644 645 662 P A B 32 distorted distorted 650 663 664 665 684 P G B 33 distorted distorted 670 685 686 687 707 P C B 34 distorted distorted 692 708 709 710 ---------------------------------------------------------------------------------