ID code: '2QH3' 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' A A 3 alpha beta 73 95 79 76 111 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' C A 7 alpha beta 204 224 210 207 240 C1' C A 8 alpha beta 235 255 241 238 271 C1' U A 9 alpha beta 266 286 272 269 301 C1' U A 10 alpha beta 296 316 302 299 331 C1' A A 11 alpha beta 326 348 332 329 364 C1' C A 12 alpha beta 359 379 365 362 395 C1' U A 13 alpha beta 390 410 396 393 425 C1' G A 14 alpha beta 420 443 426 423 459 C1' U A 15 alpha beta 454 474 460 457 489 C1' G A 16 alpha beta 484 507 490 487 523 C1' G A 17 alpha beta 518 541 524 521 557 C1' C A 18 alpha beta 552 572 558 555 588 C1' A A 19 alpha beta 583 605 589 586 621 C1' C A 20 alpha beta 616 636 622 619 652 C1' U A 21 alpha beta 647 667 653 650 682 C1' C A 22 alpha beta 677 697 683 680 713 C1' C A 23 alpha beta 708 729 714 711 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 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' C A 7 OK OK 209 205 222 208 238 C2' C A 8 OK OK 240 236 253 239 269 C2' U A 9 OK OK 271 267 284 270 299 C2' U A 10 OK OK 301 297 314 300 329 C2' A A 11 OK OK 331 327 346 330 362 C2' C A 12 OK OK 364 360 377 363 393 C2' U A 13 OK OK 395 391 408 394 423 C2' G A 14 OK OK 425 421 441 424 457 C2' U A 15 OK OK 459 455 472 458 487 C2' G A 16 OK OK 489 485 505 488 521 C2' G A 17 OK OK 523 519 539 522 555 C2' C A 18 OK OK 557 553 570 556 586 C2' A A 19 OK OK 588 584 603 587 619 C2' C A 20 OK OK 621 617 634 620 650 C2' U A 21 OK OK 652 648 665 651 680 C2' C A 22 OK OK 682 678 695 681 711 C2' C A 23 OK OK 713 709 727 712 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 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' C A 7 OK OK 203 221 206 207 236 C3' C A 8 OK OK 234 252 237 238 267 C3' U A 9 OK OK 265 283 268 269 297 C3' U A 10 OK OK 295 313 298 299 327 C3' A A 11 OK OK 325 345 328 329 360 C3' C A 12 OK OK 358 376 361 362 391 C3' U A 13 OK OK 389 407 392 393 421 C3' G A 14 OK OK 419 440 422 423 455 C3' U A 15 OK OK 453 471 456 457 485 C3' G A 16 OK OK 483 504 486 487 519 C3' G A 17 OK OK 517 538 520 521 553 C3' C A 18 OK OK 551 569 554 555 584 C3' A A 19 OK OK 582 602 585 586 617 C3' C A 20 OK OK 615 633 618 619 648 C3' U A 21 OK OK 646 664 649 650 678 C3' C A 22 OK OK 676 694 679 680 709 C3' C A 23 OK OK 707 725 710 711 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 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' C A 7 OK OK 205 220 202 204 234 C4' C A 8 OK OK 236 251 233 235 265 C4' U A 9 OK OK 267 282 264 266 295 C4' U A 10 OK OK 297 312 294 296 325 C4' A A 11 OK OK 327 344 324 326 358 C4' C A 12 OK OK 360 375 357 359 389 C4' U A 13 OK OK 391 406 388 390 419 C4' G A 14 OK OK 421 439 418 420 453 C4' U A 15 OK OK 455 470 452 454 483 C4' G A 16 OK OK 485 503 482 484 517 C4' G A 17 OK OK 519 537 516 518 551 C4' C A 18 OK OK 553 568 550 552 582 C4' A A 19 OK OK 584 601 581 583 615 C4' C A 20 OK OK 617 632 614 616 646 C4' U A 21 OK OK 648 663 645 647 676 C4' C A 22 OK OK 678 693 675 677 707 C4' C A 23 OK OK 709 724 706 708 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 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' C A 7 OK OK 201 218 219 203 233 C5' C A 8 OK OK 232 249 250 234 264 C5' U A 9 OK OK 263 280 281 265 294 C5' U A 10 OK OK 293 310 311 295 324 C5' A A 11 OK OK 323 342 343 325 357 C5' C A 12 OK OK 356 373 374 358 388 C5' U A 13 OK OK 387 404 405 389 418 C5' G A 14 OK OK 417 437 438 419 452 C5' U A 15 OK OK 451 468 469 453 482 C5' G A 16 OK OK 481 501 502 483 516 C5' G A 17 OK OK 515 535 536 517 550 C5' C A 18 OK OK 549 566 567 551 581 C5' A A 19 OK OK 580 599 600 582 614 C5' C A 20 OK OK 613 630 631 615 645 C5' U A 21 OK OK 644 661 662 646 675 C5' C A 22 OK OK 674 691 692 676 706 C5' C A 23 OK OK 705 722 723 707 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P U A 5 distorted distorted 108 135 136 137 164 P G A 6 distorted distorted 142 165 166 167 198 P C A 7 distorted distorted 172 199 200 201 229 P C A 8 distorted distorted 206 230 231 232 260 P U A 9 distorted distorted 237 261 262 263 290 P U A 10 distorted distorted 268 291 292 293 320 P A A 11 distorted distorted 298 321 322 323 353 P C A 12 distorted distorted 328 354 355 356 384 P U A 13 distorted distorted 361 385 386 387 414 P G A 14 distorted distorted 392 415 416 417 448 P U A 15 distorted distorted 422 449 450 451 478 P G A 16 distorted distorted 456 479 480 481 512 P G A 17 distorted distorted 486 513 514 515 546 P C A 18 distorted distorted 520 547 548 549 577 P A A 19 distorted distorted 554 578 579 580 610 P C A 20 distorted distorted 585 611 612 613 641 P U A 21 distorted distorted 618 642 643 644 671 P C A 22 distorted distorted 649 672 673 674 702 P C A 23 distorted distorted 679 703 704 705 ---------------------------------------------------------------------------------