ID code: '1TUT' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' A A 5 alpha beta 140 162 146 143 178 C1' A A 6 alpha beta 173 195 179 176 211 C1' G A 7 alpha beta 206 229 212 209 245 C1' G A 8 alpha beta 240 263 246 243 279 C1' C A 9 alpha beta 274 294 280 277 310 C1' G A 10 alpha beta 305 328 311 308 344 C1' A A 11 alpha beta 339 362 345 342 376 C1' U B 11 alpha beta 371 391 377 374 407 C1' C B 12 alpha beta 402 422 408 405 438 C1' G B 13 alpha beta 433 456 439 436 472 C1' U B 14 alpha beta 467 487 473 470 502 C1' U B 15 alpha beta 497 517 503 500 532 C1' A B 16 alpha beta 527 549 533 530 565 C1' A B 17 alpha beta 560 582 566 563 598 C1' U B 18 alpha beta 593 613 599 596 628 C1' C B 19 alpha beta 623 643 629 626 659 C1' U B 20 alpha beta 654 674 660 657 689 C1' C B 21 alpha beta 684 704 690 687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' G A 4 OK OK 111 107 127 110 143 C2' A A 5 OK OK 145 141 160 144 176 C2' A A 6 OK OK 178 174 193 177 209 C2' G A 7 OK OK 211 207 227 210 243 C2' G A 8 OK OK 245 241 261 244 277 C2' C A 9 OK OK 279 275 292 278 308 C2' G A 10 OK OK 310 306 326 309 342 C2' A A 11 OK OK 344 340 360 343 374 C2' U B 11 OK OK 376 372 389 375 405 C2' C B 12 OK OK 407 403 420 406 436 C2' G B 13 OK OK 438 434 454 437 470 C2' U B 14 OK OK 472 468 485 471 500 C2' U B 15 OK OK 502 498 515 501 530 C2' A B 16 OK OK 532 528 547 531 563 C2' A B 17 OK OK 565 561 580 564 596 C2' U B 18 OK OK 598 594 611 597 626 C2' C B 19 OK OK 628 624 641 627 657 C2' U B 20 OK OK 659 655 672 658 687 C2' C B 21 OK OK 689 685 702 688 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' G A 4 OK OK 105 126 108 109 141 C3' A A 5 OK OK 139 159 142 143 174 C3' A A 6 OK OK 172 192 175 176 207 C3' G A 7 OK OK 205 226 208 209 241 C3' G A 8 OK OK 239 260 242 243 275 C3' C A 9 OK OK 273 291 276 277 306 C3' G A 10 OK OK 304 325 307 308 340 C3' A A 11 OK OK 338 358 341 342 372 C3' U B 11 OK OK 370 388 373 374 403 C3' C B 12 OK OK 401 419 404 405 434 C3' G B 13 OK OK 432 453 435 436 468 C3' U B 14 OK OK 466 484 469 470 498 C3' U B 15 OK OK 496 514 499 500 528 C3' A B 16 OK OK 526 546 529 530 561 C3' A B 17 OK OK 559 579 562 563 594 C3' U B 18 OK OK 592 610 595 596 624 C3' C B 19 OK OK 622 640 625 626 655 C3' U B 20 OK OK 653 671 656 657 685 C3' C B 21 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' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' G A 4 OK OK 107 125 104 106 139 C4' A A 5 OK OK 141 158 138 140 172 C4' A A 6 OK OK 174 191 171 173 205 C4' G A 7 OK OK 207 225 204 206 239 C4' G A 8 OK OK 241 259 238 240 273 C4' C A 9 OK OK 275 290 272 274 304 C4' G A 10 OK OK 306 324 303 305 338 C4' A A 11 OK OK 340 357 337 339 370 C4' U B 11 OK OK 372 387 369 371 401 C4' C B 12 OK OK 403 418 400 402 432 C4' G B 13 OK OK 434 452 431 433 466 C4' U B 14 OK OK 468 483 465 467 496 C4' U B 15 OK OK 498 513 495 497 526 C4' A B 16 OK OK 528 545 525 527 559 C4' A B 17 OK OK 561 578 558 560 592 C4' U B 18 OK OK 594 609 591 593 622 C4' C B 19 OK OK 624 639 621 623 653 C4' U B 20 OK OK 655 670 652 654 683 C4' C B 21 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' G A 4 OK OK 103 123 124 105 138 C5' A A 5 OK OK 137 156 157 139 171 C5' A A 6 OK OK 170 189 190 172 204 C5' G A 7 OK OK 203 223 224 205 238 C5' G A 8 OK OK 237 257 258 239 272 C5' C A 9 OK OK 271 288 289 273 303 C5' G A 10 OK OK 302 322 323 304 337 C5' A A 11 OK OK 336 355 356 338 369 C5' U B 11 OK OK 368 385 386 370 400 C5' C B 12 OK OK 399 416 417 401 431 C5' G B 13 OK OK 430 450 451 432 465 C5' U B 14 OK OK 464 481 482 466 495 C5' U B 15 OK OK 494 511 512 496 525 C5' A B 16 OK OK 524 543 544 526 558 C5' A B 17 OK OK 557 576 577 559 591 C5' U B 18 OK OK 590 607 608 592 621 C5' C B 19 OK OK 620 637 638 622 652 C5' U B 20 OK OK 651 668 669 653 682 C5' C B 21 OK OK 681 698 699 683 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P G A 4 distorted distorted 74 101 102 103 134 P A A 5 distorted distorted 108 135 136 137 167 P A A 6 distorted distorted 142 168 169 170 200 P G A 7 distorted distorted 175 201 202 203 234 P G A 8 distorted distorted 208 235 236 237 268 P C A 9 distorted distorted 242 269 270 271 299 P G A 10 distorted distorted 276 300 301 302 333 P A A 11 distorted distorted 307 334 335 336 396 P C B 12 distorted distorted 373 397 398 399 427 P G B 13 distorted distorted 404 428 429 430 461 P U B 14 distorted distorted 435 462 463 464 491 P U B 15 distorted distorted 469 492 493 494 521 P A B 16 distorted distorted 499 522 523 524 554 P A B 17 distorted distorted 529 555 556 557 587 P U B 18 distorted distorted 562 588 589 590 617 P C B 19 distorted distorted 595 618 619 620 648 P U B 20 distorted distorted 625 649 650 651 678 P C B 21 distorted distorted 656 679 680 681 ---------------------------------------------------------------------------------