ID code: '3PHP' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' U A 4 alpha beta 103 123 109 106 138 C1' C A 5 alpha beta 133 153 139 136 169 C1' C A 6 alpha beta 164 184 170 167 200 C1' G A 7 alpha beta 195 218 201 198 234 C1' A A 8 alpha beta 229 251 235 232 267 C1' G A 9 alpha beta 262 285 268 265 301 C1' G A 10 alpha beta 296 319 302 299 335 C1' G A 11 alpha beta 330 353 336 333 369 C1' U A 12 alpha beta 364 384 370 367 399 C1' C A 13 alpha beta 394 414 400 397 430 C1' A A 14 alpha beta 425 447 431 428 463 C1' U A 15 alpha beta 458 478 464 461 493 C1' C A 16 alpha beta 488 508 494 491 524 C1' G A 17 alpha beta 519 542 525 522 558 C1' G A 18 alpha beta 553 576 559 556 592 C1' A A 19 alpha beta 587 609 593 590 625 C1' A A 20 alpha beta 620 642 626 623 658 C1' C A 21 alpha beta 653 673 659 656 689 C1' C A 22 alpha beta 684 704 690 687 720 C1' A A 23 alpha beta 715 738 721 718 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' U A 4 OK OK 108 104 121 107 136 C2' C A 5 OK OK 138 134 151 137 167 C2' C A 6 OK OK 169 165 182 168 198 C2' G A 7 OK OK 200 196 216 199 232 C2' A A 8 OK OK 234 230 249 233 265 C2' G A 9 OK OK 267 263 283 266 299 C2' G A 10 OK OK 301 297 317 300 333 C2' G A 11 OK OK 335 331 351 334 367 C2' U A 12 OK OK 369 365 382 368 397 C2' C A 13 OK OK 399 395 412 398 428 C2' A A 14 OK OK 430 426 445 429 461 C2' U A 15 OK OK 463 459 476 462 491 C2' C A 16 OK OK 493 489 506 492 522 C2' G A 17 OK OK 524 520 540 523 556 C2' G A 18 OK OK 558 554 574 557 590 C2' A A 19 OK OK 592 588 607 591 623 C2' A A 20 OK OK 625 621 640 624 656 C2' C A 21 OK OK 658 654 671 657 687 C2' C A 22 OK OK 689 685 702 688 718 C2' A A 23 OK OK 720 716 736 719 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' U A 4 OK OK 102 120 105 106 134 C3' C A 5 OK OK 132 150 135 136 165 C3' C A 6 OK OK 163 181 166 167 196 C3' G A 7 OK OK 194 215 197 198 230 C3' A A 8 OK OK 228 248 231 232 263 C3' G A 9 OK OK 261 282 264 265 297 C3' G A 10 OK OK 295 316 298 299 331 C3' G A 11 OK OK 329 350 332 333 365 C3' U A 12 OK OK 363 381 366 367 395 C3' C A 13 OK OK 393 411 396 397 426 C3' A A 14 OK OK 424 444 427 428 459 C3' U A 15 OK OK 457 475 460 461 489 C3' C A 16 OK OK 487 505 490 491 520 C3' G A 17 OK OK 518 539 521 522 554 C3' G A 18 OK OK 552 573 555 556 588 C3' A A 19 OK OK 586 606 589 590 621 C3' A A 20 OK OK 619 639 622 623 654 C3' C A 21 OK OK 652 670 655 656 685 C3' C A 22 OK OK 683 701 686 687 716 C3' A A 23 OK OK 714 734 717 718 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' U A 4 OK OK 104 119 101 103 132 C4' C A 5 OK OK 134 149 131 133 163 C4' C A 6 OK OK 165 180 162 164 194 C4' G A 7 OK OK 196 214 193 195 228 C4' A A 8 OK OK 230 247 227 229 261 C4' G A 9 OK OK 263 281 260 262 295 C4' G A 10 OK OK 297 315 294 296 329 C4' G A 11 OK OK 331 349 328 330 363 C4' U A 12 OK OK 365 380 362 364 393 C4' C A 13 OK OK 395 410 392 394 424 C4' A A 14 OK OK 426 443 423 425 457 C4' U A 15 OK OK 459 474 456 458 487 C4' C A 16 OK OK 489 504 486 488 518 C4' G A 17 OK OK 520 538 517 519 552 C4' G A 18 OK OK 554 572 551 553 586 C4' A A 19 OK OK 588 605 585 587 619 C4' A A 20 OK OK 621 638 618 620 652 C4' C A 21 OK OK 654 669 651 653 683 C4' C A 22 OK OK 685 700 682 684 714 C4' A A 23 OK OK 716 733 713 715 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' U A 4 OK OK 100 117 118 102 131 C5' C A 5 OK OK 130 147 148 132 162 C5' C A 6 OK OK 161 178 179 163 193 C5' G A 7 OK OK 192 212 213 194 227 C5' A A 8 OK OK 226 245 246 228 260 C5' G A 9 OK OK 259 279 280 261 294 C5' G A 10 OK OK 293 313 314 295 328 C5' G A 11 OK OK 327 347 348 329 362 C5' U A 12 OK OK 361 378 379 363 392 C5' C A 13 OK OK 391 408 409 393 423 C5' A A 14 OK OK 422 441 442 424 456 C5' U A 15 OK OK 455 472 473 457 486 C5' C A 16 OK OK 485 502 503 487 517 C5' G A 17 OK OK 516 536 537 518 551 C5' G A 18 OK OK 550 570 571 552 585 C5' A A 19 OK OK 584 603 604 586 618 C5' A A 20 OK OK 617 636 637 619 651 C5' C A 21 OK OK 650 667 668 652 682 C5' C A 22 OK OK 681 698 699 683 713 C5' A A 23 OK OK 712 731 732 714 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P U A 4 distorted distorted 75 98 99 100 127 P C A 5 distorted distorted 105 128 129 130 158 P C A 6 distorted distorted 135 159 160 161 189 P G A 7 distorted distorted 166 190 191 192 223 P A A 8 distorted distorted 197 224 225 226 256 P G A 9 distorted distorted 231 257 258 259 290 P G A 10 distorted distorted 264 291 292 293 324 P G A 11 distorted distorted 298 325 326 327 358 P U A 12 distorted distorted 332 359 360 361 388 P C A 13 distorted distorted 366 389 390 391 419 P A A 14 distorted distorted 396 420 421 422 452 P U A 15 distorted distorted 427 453 454 455 482 P C A 16 distorted distorted 460 483 484 485 513 P G A 17 distorted distorted 490 514 515 516 547 P G A 18 distorted distorted 521 548 549 550 581 P A A 19 distorted distorted 555 582 583 584 614 P A A 20 distorted distorted 589 615 616 617 647 P C A 21 distorted distorted 622 648 649 650 678 P C A 22 distorted distorted 655 679 680 681 709 P A A 23 distorted distorted 686 710 711 712 ---------------------------------------------------------------------------------