ID code: '2HNS' 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' G A 4 alpha beta 104 127 110 107 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' A A 7 alpha beta 202 224 208 205 240 C1' U A 8 alpha beta 235 255 241 238 270 C1' C A 9 alpha beta 265 285 271 268 301 C1' A A 10 alpha beta 296 318 302 299 334 C1' A A 11 alpha beta 329 351 335 332 367 C1' G A 12 alpha beta 362 385 368 365 401 C1' U A 13 alpha beta 396 416 402 399 431 C1' G A 14 alpha beta 426 449 432 429 465 C1' A A 15 alpha beta 460 482 466 463 498 C1' U A 16 alpha beta 493 513 499 496 528 C1' C A 17 alpha beta 523 543 529 526 559 C1' G A 18 alpha beta 554 577 560 557 593 C1' C A 19 alpha beta 588 608 594 591 624 C1' G A 20 alpha beta 619 642 625 622 658 C1' C A 21 alpha beta 653 673 659 656 689 C1' C A 22 alpha beta 684 705 690 687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 4 OK OK 109 105 125 108 141 C2' U A 5 OK OK 143 139 156 142 171 C2' G A 6 OK OK 173 169 189 172 205 C2' A A 7 OK OK 207 203 222 206 238 C2' U A 8 OK OK 240 236 253 239 268 C2' C A 9 OK OK 270 266 283 269 299 C2' A A 10 OK OK 301 297 316 300 332 C2' A A 11 OK OK 334 330 349 333 365 C2' G A 12 OK OK 367 363 383 366 399 C2' U A 13 OK OK 401 397 414 400 429 C2' G A 14 OK OK 431 427 447 430 463 C2' A A 15 OK OK 465 461 480 464 496 C2' U A 16 OK OK 498 494 511 497 526 C2' C A 17 OK OK 528 524 541 527 557 C2' G A 18 OK OK 559 555 575 558 591 C2' C A 19 OK OK 593 589 606 592 622 C2' G A 20 OK OK 624 620 640 623 656 C2' C A 21 OK OK 658 654 671 657 687 C2' C A 22 OK OK 689 685 703 688 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 103 124 106 107 139 C3' U A 5 OK OK 137 155 140 141 169 C3' G A 6 OK OK 167 188 170 171 203 C3' A A 7 OK OK 201 221 204 205 236 C3' U A 8 OK OK 234 252 237 238 266 C3' C A 9 OK OK 264 282 267 268 297 C3' A A 10 OK OK 295 315 298 299 330 C3' A A 11 OK OK 328 348 331 332 363 C3' G A 12 OK OK 361 382 364 365 397 C3' U A 13 OK OK 395 413 398 399 427 C3' G A 14 OK OK 425 446 428 429 461 C3' A A 15 OK OK 459 479 462 463 494 C3' U A 16 OK OK 492 510 495 496 524 C3' C A 17 OK OK 522 540 525 526 555 C3' G A 18 OK OK 553 574 556 557 589 C3' C A 19 OK OK 587 605 590 591 620 C3' G A 20 OK OK 618 639 621 622 654 C3' C A 21 OK OK 652 670 655 656 685 C3' C A 22 OK OK 683 701 686 687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 105 123 102 104 137 C4' U A 5 OK OK 139 154 136 138 167 C4' G A 6 OK OK 169 187 166 168 201 C4' A A 7 OK OK 203 220 200 202 234 C4' U A 8 OK OK 236 251 233 235 264 C4' C A 9 OK OK 266 281 263 265 295 C4' A A 10 OK OK 297 314 294 296 328 C4' A A 11 OK OK 330 347 327 329 361 C4' G A 12 OK OK 363 381 360 362 395 C4' U A 13 OK OK 397 412 394 396 425 C4' G A 14 OK OK 427 445 424 426 459 C4' A A 15 OK OK 461 478 458 460 492 C4' U A 16 OK OK 494 509 491 493 522 C4' C A 17 OK OK 524 539 521 523 553 C4' G A 18 OK OK 555 573 552 554 587 C4' C A 19 OK OK 589 604 586 588 618 C4' G A 20 OK OK 620 638 617 619 652 C4' C A 21 OK OK 654 669 651 653 683 C4' C A 22 OK OK 685 700 682 684 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 101 121 122 103 136 C5' U A 5 OK OK 135 152 153 137 166 C5' G A 6 OK OK 165 185 186 167 200 C5' A A 7 OK OK 199 218 219 201 233 C5' U A 8 OK OK 232 249 250 234 263 C5' C A 9 OK OK 262 279 280 264 294 C5' A A 10 OK OK 293 312 313 295 327 C5' A A 11 OK OK 326 345 346 328 360 C5' G A 12 OK OK 359 379 380 361 394 C5' U A 13 OK OK 393 410 411 395 424 C5' G A 14 OK OK 423 443 444 425 458 C5' A A 15 OK OK 457 476 477 459 491 C5' U A 16 OK OK 490 507 508 492 521 C5' C A 17 OK OK 520 537 538 522 552 C5' G A 18 OK OK 551 571 572 553 586 C5' C A 19 OK OK 585 602 603 587 617 C5' G A 20 OK OK 616 636 637 618 651 C5' C A 21 OK OK 650 667 668 652 682 C5' C A 22 OK OK 681 698 699 683 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 4 distorted distorted 75 99 100 101 132 P U A 5 distorted distorted 106 133 134 135 162 P G A 6 distorted distorted 140 163 164 165 196 P A A 7 distorted distorted 170 197 198 199 229 P U A 8 distorted distorted 204 230 231 232 259 P C A 9 distorted distorted 237 260 261 262 290 P A A 10 distorted distorted 267 291 292 293 323 P A A 11 distorted distorted 298 324 325 326 356 P G A 12 distorted distorted 331 357 358 359 390 P U A 13 distorted distorted 364 391 392 393 420 P G A 14 distorted distorted 398 421 422 423 454 P A A 15 distorted distorted 428 455 456 457 487 P U A 16 distorted distorted 462 488 489 490 517 P C A 17 distorted distorted 495 518 519 520 548 P G A 18 distorted distorted 525 549 550 551 582 P C A 19 distorted distorted 556 583 584 585 613 P G A 20 distorted distorted 590 614 615 616 647 P C A 21 distorted distorted 621 648 649 650 678 P C A 22 distorted distorted 655 679 680 681 ---------------------------------------------------------------------------------