ID code: '1Z7V' 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' --------------------------------------------------------------------------------- 8 C1' C A 1 alpha beta 4 21 9 7 38 C1' G A 2 alpha beta 34 54 39 37 71 C1' G A 3 alpha beta 67 87 72 70 104 C1' A A 4 alpha beta 100 119 105 103 136 C1' C A 5 alpha beta 132 149 137 135 163 C1' 2BD A 6 alpha beta 162 185 169 179 208 C1' A A 7 alpha beta 204 223 209 207 240 C1' G A 8 alpha beta 236 256 241 239 273 C1' A A 9 alpha beta 269 288 274 272 305 C1' A A 10 alpha beta 301 320 306 304 337 C1' G A 11 alpha beta 333 354 338 336 369 C1' C B 12 alpha beta 365 382 370 368 400 C1' T B 13 alpha beta 396 416 401 399 432 C1' T B 14 alpha beta 428 448 433 431 464 C1' C B 15 alpha beta 460 477 465 463 494 C1' T B 16 alpha beta 490 510 495 493 526 C1' T B 17 alpha beta 522 542 527 525 558 C1' G B 18 alpha beta 554 574 559 557 591 C1' T B 19 alpha beta 587 607 592 590 623 C1' C B 20 alpha beta 619 636 624 622 653 C1' C B 21 alpha beta 649 666 654 652 683 C1' G B 22 alpha beta 679 700 684 682 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK OK 8 5 26 27 37 C2' G A 2 OK OK 38 35 59 60 70 C2' G A 3 OK OK 71 68 92 93 103 C2' A A 4 OK OK 104 101 124 125 135 C2' C A 5 OK OK 136 133 154 155 179 C2' 2BD A 6 OK OK 163 180 195 196 207 C2' A A 7 OK OK 208 205 228 229 239 C2' G A 8 OK OK 240 237 261 262 272 C2' A A 9 OK OK 273 270 293 294 304 C2' A A 10 OK OK 305 302 325 326 336 C2' G A 11 OK OK 337 334 359 360 368 C2' C B 12 OK OK 369 366 388 389 399 C2' T B 13 OK OK 400 397 414 415 431 C2' T B 14 OK OK 432 429 446 447 463 C2' C B 15 OK OK 464 461 482 483 493 C2' T B 16 OK OK 494 491 508 509 525 C2' T B 17 OK OK 526 523 540 541 557 C2' G B 18 OK OK 558 555 579 580 590 C2' T B 19 OK OK 591 588 605 606 622 C2' C B 20 OK OK 623 620 641 642 652 C2' C B 21 OK OK 653 650 671 672 682 C2' G B 22 OK OK 683 680 705 706 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 20 6 7 35 C3' G A 2 OK OK 33 53 36 37 68 C3' G A 3 OK OK 66 86 69 70 101 C3' A A 4 OK OK 99 118 102 103 133 C3' C A 5 OK OK 131 148 134 135 180 C3' 2BD A 6 OK OK 161 197 181 179 205 C3' A A 7 OK OK 203 222 206 207 237 C3' G A 8 OK OK 235 255 238 239 270 C3' A A 9 OK OK 268 287 271 272 302 C3' A A 10 OK OK 300 319 303 304 334 C3' G A 11 OK OK 332 352 335 336 366 C3' C B 12 OK OK 364 381 367 368 397 C3' T B 13 OK OK 395 413 398 399 429 C3' T B 14 OK OK 427 445 430 431 461 C3' C B 15 OK OK 459 476 462 463 491 C3' T B 16 OK OK 489 507 492 493 523 C3' T B 17 OK OK 521 539 524 525 555 C3' G B 18 OK OK 553 573 556 557 588 C3' T B 19 OK OK 586 604 589 590 620 C3' C B 20 OK OK 618 635 621 622 650 C3' C B 21 OK OK 648 665 651 652 680 C3' G B 22 OK OK 678 698 681 682 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 19 2 4 33 C4' G A 2 OK OK 35 52 32 34 66 C4' G A 3 OK OK 68 85 65 67 99 C4' A A 4 OK OK 101 117 98 100 131 C4' C A 5 OK OK 133 147 130 132 161 C4' 2BD A 6 OK OK 180 184 160 162 203 C4' A A 7 OK OK 205 221 202 204 235 C4' G A 8 OK OK 237 254 234 236 268 C4' A A 9 OK OK 270 286 267 269 300 C4' A A 10 OK OK 302 318 299 301 332 C4' G A 11 OK OK 334 351 331 333 364 C4' C B 12 OK OK 366 380 363 365 395 C4' T B 13 OK OK 397 412 394 396 427 C4' T B 14 OK OK 429 444 426 428 459 C4' C B 15 OK OK 461 475 458 460 489 C4' T B 16 OK OK 491 506 488 490 521 C4' T B 17 OK OK 523 538 520 522 553 C4' G B 18 OK OK 555 572 552 554 586 C4' T B 19 OK OK 588 603 585 587 618 C4' C B 20 OK OK 620 634 617 619 648 C4' C B 21 OK OK 650 664 647 649 678 C4' G B 22 OK OK 680 697 677 679 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 17 18 3 32 C5' G A 2 OK OK 31 50 51 33 65 C5' G A 3 OK OK 64 83 84 66 98 C5' A A 4 OK OK 97 115 116 99 130 C5' C A 5 OK OK 129 145 146 131 160 C5' 2BD A 6 OK OK 159 182 183 161 202 C5' A A 7 OK OK 201 219 220 203 234 C5' G A 8 OK OK 233 252 253 235 267 C5' A A 9 OK OK 266 284 285 268 299 C5' A A 10 OK OK 298 316 317 300 331 C5' G A 11 OK OK 330 349 350 332 363 C5' C B 12 OK OK 362 378 379 364 394 C5' T B 13 OK OK 393 410 411 395 426 C5' T B 14 OK OK 425 442 443 427 458 C5' C B 15 OK OK 457 473 474 459 488 C5' T B 16 OK OK 487 504 505 489 520 C5' T B 17 OK OK 519 536 537 521 552 C5' G B 18 OK OK 551 570 571 553 585 C5' T B 19 OK OK 584 601 602 586 617 C5' C B 20 OK OK 616 632 633 618 647 C5' C B 21 OK OK 646 662 663 648 677 C5' G B 22 OK OK 676 695 696 678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 28 P G A 2 distorted distorted 6 29 30 31 61 P G A 3 distorted distorted 36 62 63 64 94 P A A 4 distorted distorted 69 95 96 97 126 P C A 5 distorted distorted 102 127 128 129 156 P 2BD A 6 distorted distorted 134 157 158 159 198 P A A 7 distorted distorted 181 199 200 201 230 P G A 8 distorted distorted 206 231 232 233 263 P A A 9 distorted distorted 238 264 265 266 295 P A A 10 distorted distorted 271 296 297 298 327 P G A 11 distorted distorted 303 328 329 330 390 P T B 13 distorted distorted 367 391 392 393 422 P T B 14 distorted distorted 398 423 424 425 454 P C B 15 distorted distorted 430 455 456 457 484 P T B 16 distorted distorted 462 485 486 487 516 P T B 17 distorted distorted 492 517 518 519 548 P G B 18 distorted distorted 524 549 550 551 581 P T B 19 distorted distorted 556 582 583 584 613 P C B 20 distorted distorted 589 614 615 616 643 P C B 21 distorted distorted 621 644 645 646 673 P G B 22 distorted distorted 651 674 675 676 ---------------------------------------------------------------------------------