ID code: '1K6H' 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 A 1 alpha beta 7 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' C A 3 alpha beta 75 95 81 78 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' U A 7 alpha beta 204 224 210 207 239 C1' U A 8 alpha beta 234 254 240 237 269 C1' C A 9 alpha beta 264 284 270 267 300 C1' A A 10 alpha beta 295 317 301 298 333 C1' G A 11 alpha beta 328 351 334 331 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' A A 13 alpha beta 395 417 401 398 433 C1' G A 14 alpha beta 428 451 434 431 467 C1' A A 15 alpha beta 462 484 468 465 500 C1' A A 16 alpha beta 495 517 501 498 533 C1' C A 17 alpha beta 528 548 534 531 564 C1' G A 18 alpha beta 559 582 565 562 598 C1' C A 19 alpha beta 593 613 599 596 629 C1' G A 20 alpha beta 624 647 630 627 663 C1' C A 21 alpha beta 658 678 664 661 694 C1' C A 22 alpha beta 689 709 695 692 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' G A 2 OK OK 46 42 62 45 78 C2' C A 3 OK OK 80 76 93 79 109 C2' G A 4 OK OK 111 107 127 110 143 C2' U A 5 OK OK 145 141 158 144 173 C2' G A 6 OK OK 175 171 191 174 207 C2' U A 7 OK OK 209 205 222 208 237 C2' U A 8 OK OK 239 235 252 238 267 C2' C A 9 OK OK 269 265 282 268 298 C2' A A 10 OK OK 300 296 315 299 331 C2' G A 11 OK OK 333 329 349 332 365 C2' A A 12 OK OK 367 363 382 366 398 C2' A A 13 OK OK 400 396 415 399 431 C2' G A 14 OK OK 433 429 449 432 465 C2' A A 15 OK OK 467 463 482 466 498 C2' A A 16 OK OK 500 496 515 499 531 C2' C A 17 OK OK 533 529 546 532 562 C2' G A 18 OK OK 564 560 580 563 596 C2' C A 19 OK OK 598 594 611 597 627 C2' G A 20 OK OK 629 625 645 628 661 C2' C A 21 OK OK 663 659 676 662 692 C2' C A 22 OK OK 694 690 707 693 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' C A 3 OK OK 74 92 77 78 107 C3' G A 4 OK OK 105 126 108 109 141 C3' U A 5 OK OK 139 157 142 143 171 C3' G A 6 OK OK 169 190 172 173 205 C3' U A 7 OK OK 203 221 206 207 235 C3' U A 8 OK OK 233 251 236 237 265 C3' C A 9 OK OK 263 281 266 267 296 C3' A A 10 OK OK 294 314 297 298 329 C3' G A 11 OK OK 327 348 330 331 363 C3' A A 12 OK OK 361 381 364 365 396 C3' A A 13 OK OK 394 414 397 398 429 C3' G A 14 OK OK 427 448 430 431 463 C3' A A 15 OK OK 461 481 464 465 496 C3' A A 16 OK OK 494 514 497 498 529 C3' C A 17 OK OK 527 545 530 531 560 C3' G A 18 OK OK 558 579 561 562 594 C3' C A 19 OK OK 592 610 595 596 625 C3' G A 20 OK OK 623 644 626 627 659 C3' C A 21 OK OK 657 675 660 661 690 C3' C A 22 OK OK 688 706 691 692 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' C A 3 OK OK 76 91 73 75 105 C4' G A 4 OK OK 107 125 104 106 139 C4' U A 5 OK OK 141 156 138 140 169 C4' G A 6 OK OK 171 189 168 170 203 C4' U A 7 OK OK 205 220 202 204 233 C4' U A 8 OK OK 235 250 232 234 263 C4' C A 9 OK OK 265 280 262 264 294 C4' A A 10 OK OK 296 313 293 295 327 C4' G A 11 OK OK 329 347 326 328 361 C4' A A 12 OK OK 363 380 360 362 394 C4' A A 13 OK OK 396 413 393 395 427 C4' G A 14 OK OK 429 447 426 428 461 C4' A A 15 OK OK 463 480 460 462 494 C4' A A 16 OK OK 496 513 493 495 527 C4' C A 17 OK OK 529 544 526 528 558 C4' G A 18 OK OK 560 578 557 559 592 C4' C A 19 OK OK 594 609 591 593 623 C4' G A 20 OK OK 625 643 622 624 657 C4' C A 21 OK OK 659 674 656 658 688 C4' C A 22 OK OK 690 705 687 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' G A 2 OK OK 38 58 59 40 73 C5' C A 3 OK OK 72 89 90 74 104 C5' G A 4 OK OK 103 123 124 105 138 C5' U A 5 OK OK 137 154 155 139 168 C5' G A 6 OK OK 167 187 188 169 202 C5' U A 7 OK OK 201 218 219 203 232 C5' U A 8 OK OK 231 248 249 233 262 C5' C A 9 OK OK 261 278 279 263 293 C5' A A 10 OK OK 292 311 312 294 326 C5' G A 11 OK OK 325 345 346 327 360 C5' A A 12 OK OK 359 378 379 361 393 C5' A A 13 OK OK 392 411 412 394 426 C5' G A 14 OK OK 425 445 446 427 460 C5' A A 15 OK OK 459 478 479 461 493 C5' A A 16 OK OK 492 511 512 494 526 C5' C A 17 OK OK 525 542 543 527 557 C5' G A 18 OK OK 556 576 577 558 591 C5' C A 19 OK OK 590 607 608 592 622 C5' G A 20 OK OK 621 641 642 623 656 C5' C A 21 OK OK 655 672 673 657 687 C5' C A 22 OK OK 686 703 704 688 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 OK OK 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P C A 3 distorted distorted 43 70 71 72 100 P G A 4 distorted distorted 77 101 102 103 134 P U A 5 distorted distorted 108 135 136 137 164 P G A 6 distorted distorted 142 165 166 167 198 P U A 7 distorted distorted 172 199 200 201 228 P U A 8 distorted distorted 206 229 230 231 258 P C A 9 distorted distorted 236 259 260 261 289 P A A 10 distorted distorted 266 290 291 292 322 P G A 11 distorted distorted 297 323 324 325 356 P A A 12 distorted distorted 330 357 358 359 389 P A A 13 distorted distorted 364 390 391 392 422 P G A 14 distorted distorted 397 423 424 425 456 P A A 15 distorted distorted 430 457 458 459 489 P A A 16 distorted distorted 464 490 491 492 522 P C A 17 distorted distorted 497 523 524 525 553 P G A 18 distorted distorted 530 554 555 556 587 P C A 19 distorted distorted 561 588 589 590 618 P G A 20 distorted distorted 595 619 620 621 652 P C A 21 distorted distorted 626 653 654 655 683 P C A 22 distorted distorted 660 684 685 686 ---------------------------------------------------------------------------------