ID code: '2M5U' 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' A A 4 alpha beta 104 126 110 107 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' A A 6 alpha beta 171 193 177 174 209 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' U A 10 alpha beta 295 315 301 298 330 C1' G A 11 alpha beta 325 348 331 328 364 C1' G A 12 alpha beta 359 382 365 362 398 C1' U A 13 alpha beta 393 413 399 396 428 C1' G A 14 alpha beta 423 446 429 426 462 C1' A A 15 alpha beta 457 479 463 460 495 C1' A A 16 alpha beta 490 512 496 493 528 C1' U A 17 alpha beta 523 543 529 526 558 C1' C A 18 alpha beta 553 573 559 556 589 C1' U A 19 alpha beta 584 604 590 587 619 C1' G A 20 alpha beta 614 637 620 617 653 C1' C A 21 alpha beta 648 668 654 651 684 C1' C A 22 alpha beta 679 699 685 682 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 4 OK OK 109 105 124 108 140 C2' G A 5 OK OK 142 138 158 141 174 C2' A A 6 OK OK 176 172 191 175 207 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' U A 10 OK OK 300 296 313 299 328 C2' G A 11 OK OK 330 326 346 329 362 C2' G A 12 OK OK 364 360 380 363 396 C2' U A 13 OK OK 398 394 411 397 426 C2' G A 14 OK OK 428 424 444 427 460 C2' A A 15 OK OK 462 458 477 461 493 C2' A A 16 OK OK 495 491 510 494 526 C2' U A 17 OK OK 528 524 541 527 556 C2' C A 18 OK OK 558 554 571 557 587 C2' U A 19 OK OK 589 585 602 588 617 C2' G A 20 OK OK 619 615 635 618 651 C2' C A 21 OK OK 653 649 666 652 682 C2' C A 22 OK OK 684 680 697 683 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 103 123 106 107 138 C3' G A 5 OK OK 136 157 139 140 172 C3' A A 6 OK OK 170 190 173 174 205 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' U A 10 OK OK 294 312 297 298 326 C3' G A 11 OK OK 324 345 327 328 360 C3' G A 12 OK OK 358 379 361 362 394 C3' U A 13 OK OK 392 410 395 396 424 C3' G A 14 OK OK 422 443 425 426 458 C3' A A 15 OK OK 456 476 459 460 491 C3' A A 16 OK OK 489 509 492 493 524 C3' U A 17 OK OK 522 540 525 526 554 C3' C A 18 OK OK 552 570 555 556 585 C3' U A 19 OK OK 583 601 586 587 615 C3' G A 20 OK OK 613 634 616 617 649 C3' C A 21 OK OK 647 665 650 651 680 C3' C A 22 OK OK 678 696 681 682 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 105 122 102 104 136 C4' G A 5 OK OK 138 156 135 137 170 C4' A A 6 OK OK 172 189 169 171 203 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' U A 10 OK OK 296 311 293 295 324 C4' G A 11 OK OK 326 344 323 325 358 C4' G A 12 OK OK 360 378 357 359 392 C4' U A 13 OK OK 394 409 391 393 422 C4' G A 14 OK OK 424 442 421 423 456 C4' A A 15 OK OK 458 475 455 457 489 C4' A A 16 OK OK 491 508 488 490 522 C4' U A 17 OK OK 524 539 521 523 552 C4' C A 18 OK OK 554 569 551 553 583 C4' U A 19 OK OK 585 600 582 584 613 C4' G A 20 OK OK 615 633 612 614 647 C4' C A 21 OK OK 649 664 646 648 678 C4' C A 22 OK OK 680 695 677 679 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 101 120 121 103 135 C5' G A 5 OK OK 134 154 155 136 169 C5' A A 6 OK OK 168 187 188 170 202 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' U A 10 OK OK 292 309 310 294 323 C5' G A 11 OK OK 322 342 343 324 357 C5' G A 12 OK OK 356 376 377 358 391 C5' U A 13 OK OK 390 407 408 392 421 C5' G A 14 OK OK 420 440 441 422 455 C5' A A 15 OK OK 454 473 474 456 488 C5' A A 16 OK OK 487 506 507 489 521 C5' U A 17 OK OK 520 537 538 522 551 C5' C A 18 OK OK 550 567 568 552 582 C5' U A 19 OK OK 581 598 599 583 612 C5' G A 20 OK OK 611 631 632 613 646 C5' C A 21 OK OK 645 662 663 647 677 C5' C A 22 OK OK 676 693 694 678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 4 distorted distorted 75 99 100 101 131 P G A 5 distorted distorted 106 132 133 134 165 P A A 6 distorted distorted 139 166 167 168 198 P U A 7 distorted distorted 173 199 200 201 228 P U A 8 distorted distorted 206 229 230 231 258 P C A 9 distorted distorted 236 259 260 261 289 P U A 10 distorted distorted 266 290 291 292 319 P G A 11 distorted distorted 297 320 321 322 353 P G A 12 distorted distorted 327 354 355 356 387 P U A 13 distorted distorted 361 388 389 390 417 P G A 14 distorted distorted 395 418 419 420 451 P A A 15 distorted distorted 425 452 453 454 484 P A A 16 distorted distorted 459 485 486 487 517 P U A 17 distorted distorted 492 518 519 520 547 P C A 18 distorted distorted 525 548 549 550 578 P U A 19 distorted distorted 555 579 580 581 608 P G A 20 distorted distorted 586 609 610 611 642 P C A 21 distorted distorted 616 643 644 645 673 P C A 22 distorted distorted 650 674 675 676 ---------------------------------------------------------------------------------