ID code: '1IE1' 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' C A 3 alpha beta 73 93 79 76 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' G A 5 alpha beta 135 158 141 138 174 C1' A A 6 alpha beta 169 191 175 172 207 C1' A A 7 alpha beta 202 224 208 205 240 C1' A A 8 alpha beta 235 257 241 238 273 C1' U A 9 alpha beta 268 288 274 271 303 C1' C A 10 alpha beta 298 318 304 301 334 C1' C A 11 alpha beta 329 349 335 332 365 C1' C A 12 alpha beta 360 380 366 363 396 C1' G A 13 alpha beta 391 414 397 394 430 C1' A A 14 alpha beta 425 447 431 428 463 C1' A A 15 alpha beta 458 480 464 461 496 C1' G A 16 alpha beta 491 514 497 494 530 C1' U A 17 alpha beta 525 545 531 528 560 C1' A A 18 alpha beta 555 577 561 558 593 C1' G A 19 alpha beta 588 611 594 591 627 C1' G A 20 alpha beta 622 645 628 625 661 C1' C A 21 alpha beta 656 676 662 659 692 C1' C A 22 alpha beta 687 708 693 690 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' C A 4 OK OK 109 105 122 108 138 C2' G A 5 OK OK 140 136 156 139 172 C2' A A 6 OK OK 174 170 189 173 205 C2' A A 7 OK OK 207 203 222 206 238 C2' A A 8 OK OK 240 236 255 239 271 C2' U A 9 OK OK 273 269 286 272 301 C2' C A 10 OK OK 303 299 316 302 332 C2' C A 11 OK OK 334 330 347 333 363 C2' C A 12 OK OK 365 361 378 364 394 C2' G A 13 OK OK 396 392 412 395 428 C2' A A 14 OK OK 430 426 445 429 461 C2' A A 15 OK OK 463 459 478 462 494 C2' G A 16 OK OK 496 492 512 495 528 C2' U A 17 OK OK 530 526 543 529 558 C2' A A 18 OK OK 560 556 575 559 591 C2' G A 19 OK OK 593 589 609 592 625 C2' G A 20 OK OK 627 623 643 626 659 C2' C A 21 OK OK 661 657 674 660 690 C2' C A 22 OK OK 692 688 706 691 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' C A 4 OK OK 103 121 106 107 136 C3' G A 5 OK OK 134 155 137 138 170 C3' A A 6 OK OK 168 188 171 172 203 C3' A A 7 OK OK 201 221 204 205 236 C3' A A 8 OK OK 234 254 237 238 269 C3' U A 9 OK OK 267 285 270 271 299 C3' C A 10 OK OK 297 315 300 301 330 C3' C A 11 OK OK 328 346 331 332 361 C3' C A 12 OK OK 359 377 362 363 392 C3' G A 13 OK OK 390 411 393 394 426 C3' A A 14 OK OK 424 444 427 428 459 C3' A A 15 OK OK 457 477 460 461 492 C3' G A 16 OK OK 490 511 493 494 526 C3' U A 17 OK OK 524 542 527 528 556 C3' A A 18 OK OK 554 574 557 558 589 C3' G A 19 OK OK 587 608 590 591 623 C3' G A 20 OK OK 621 642 624 625 657 C3' C A 21 OK OK 655 673 658 659 688 C3' C A 22 OK OK 686 704 689 690 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' C A 4 OK OK 105 120 102 104 134 C4' G A 5 OK OK 136 154 133 135 168 C4' A A 6 OK OK 170 187 167 169 201 C4' A A 7 OK OK 203 220 200 202 234 C4' A A 8 OK OK 236 253 233 235 267 C4' U A 9 OK OK 269 284 266 268 297 C4' C A 10 OK OK 299 314 296 298 328 C4' C A 11 OK OK 330 345 327 329 359 C4' C A 12 OK OK 361 376 358 360 390 C4' G A 13 OK OK 392 410 389 391 424 C4' A A 14 OK OK 426 443 423 425 457 C4' A A 15 OK OK 459 476 456 458 490 C4' G A 16 OK OK 492 510 489 491 524 C4' U A 17 OK OK 526 541 523 525 554 C4' A A 18 OK OK 556 573 553 555 587 C4' G A 19 OK OK 589 607 586 588 621 C4' G A 20 OK OK 623 641 620 622 655 C4' C A 21 OK OK 657 672 654 656 686 C4' C A 22 OK OK 688 703 685 687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' C A 4 OK OK 101 118 119 103 133 C5' G A 5 OK OK 132 152 153 134 167 C5' A A 6 OK OK 166 185 186 168 200 C5' A A 7 OK OK 199 218 219 201 233 C5' A A 8 OK OK 232 251 252 234 266 C5' U A 9 OK OK 265 282 283 267 296 C5' C A 10 OK OK 295 312 313 297 327 C5' C A 11 OK OK 326 343 344 328 358 C5' C A 12 OK OK 357 374 375 359 389 C5' G A 13 OK OK 388 408 409 390 423 C5' A A 14 OK OK 422 441 442 424 456 C5' A A 15 OK OK 455 474 475 457 489 C5' G A 16 OK OK 488 508 509 490 523 C5' U A 17 OK OK 522 539 540 524 553 C5' A A 18 OK OK 552 571 572 554 586 C5' G A 19 OK OK 585 605 606 587 620 C5' G A 20 OK OK 619 639 640 621 654 C5' C A 21 OK OK 653 670 671 655 685 C5' C A 22 OK OK 684 701 702 686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P C A 4 distorted distorted 75 99 100 101 129 P G A 5 distorted distorted 106 130 131 132 163 P A A 6 distorted distorted 137 164 165 166 196 P A A 7 distorted distorted 171 197 198 199 229 P A A 8 distorted distorted 204 230 231 232 262 P U A 9 distorted distorted 237 263 264 265 292 P C A 10 distorted distorted 270 293 294 295 323 P C A 11 distorted distorted 300 324 325 326 354 P C A 12 distorted distorted 331 355 356 357 385 P G A 13 distorted distorted 362 386 387 388 419 P A A 14 distorted distorted 393 420 421 422 452 P A A 15 distorted distorted 427 453 454 455 485 P G A 16 distorted distorted 460 486 487 488 519 P U A 17 distorted distorted 493 520 521 522 549 P A A 18 distorted distorted 527 550 551 552 582 P G A 19 distorted distorted 557 583 584 585 616 P G A 20 distorted distorted 590 617 618 619 650 P C A 21 distorted distorted 624 651 652 653 681 P C A 22 distorted distorted 658 682 683 684 ---------------------------------------------------------------------------------