ID code: '2G1W' 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' G A 3 alpha beta 73 96 79 76 112 C1' G A 4 alpha beta 107 130 113 110 146 C1' U A 5 alpha beta 141 161 147 144 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' G A 7 alpha beta 205 228 211 208 244 C1' C A 8 alpha beta 239 259 245 242 275 C1' U A 9 alpha beta 270 290 276 273 305 C1' C A 10 alpha beta 300 320 306 303 336 C1' C A 11 alpha beta 331 351 337 334 367 C1' C A 12 alpha beta 362 382 368 365 398 C1' C A 13 alpha beta 393 413 399 396 429 C1' U A 14 alpha beta 424 444 430 427 459 C1' A A 15 alpha beta 454 476 460 457 492 C1' A A 16 alpha beta 487 509 493 490 525 C1' C A 17 alpha beta 520 540 526 523 556 C1' A A 18 alpha beta 551 573 557 554 589 C1' G A 19 alpha beta 584 607 590 587 623 C1' C A 20 alpha beta 618 638 624 621 654 C1' C A 21 alpha beta 649 669 655 652 685 C1' G A 22 alpha beta 680 704 686 683 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' G A 4 OK OK 112 108 128 111 144 C2' U A 5 OK OK 146 142 159 145 174 C2' G A 6 OK OK 176 172 192 175 208 C2' G A 7 OK OK 210 206 226 209 242 C2' C A 8 OK OK 244 240 257 243 273 C2' U A 9 OK OK 275 271 288 274 303 C2' C A 10 OK OK 305 301 318 304 334 C2' C A 11 OK OK 336 332 349 335 365 C2' C A 12 OK OK 367 363 380 366 396 C2' C A 13 OK OK 398 394 411 397 427 C2' U A 14 OK OK 429 425 442 428 457 C2' A A 15 OK OK 459 455 474 458 490 C2' A A 16 OK OK 492 488 507 491 523 C2' C A 17 OK OK 525 521 538 524 554 C2' A A 18 OK OK 556 552 571 555 587 C2' G A 19 OK OK 589 585 605 588 621 C2' C A 20 OK OK 623 619 636 622 652 C2' C A 21 OK OK 654 650 667 653 683 C2' G A 22 OK OK 685 681 702 684 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' G A 4 OK OK 106 127 109 110 142 C3' U A 5 OK OK 140 158 143 144 172 C3' G A 6 OK OK 170 191 173 174 206 C3' G A 7 OK OK 204 225 207 208 240 C3' C A 8 OK OK 238 256 241 242 271 C3' U A 9 OK OK 269 287 272 273 301 C3' C A 10 OK OK 299 317 302 303 332 C3' C A 11 OK OK 330 348 333 334 363 C3' C A 12 OK OK 361 379 364 365 394 C3' C A 13 OK OK 392 410 395 396 425 C3' U A 14 OK OK 423 441 426 427 455 C3' A A 15 OK OK 453 473 456 457 488 C3' A A 16 OK OK 486 506 489 490 521 C3' C A 17 OK OK 519 537 522 523 552 C3' A A 18 OK OK 550 570 553 554 585 C3' G A 19 OK OK 583 604 586 587 619 C3' C A 20 OK OK 617 635 620 621 650 C3' C A 21 OK OK 648 666 651 652 681 C3' G A 22 OK OK 679 700 682 683 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' G A 4 OK OK 108 126 105 107 140 C4' U A 5 OK OK 142 157 139 141 170 C4' G A 6 OK OK 172 190 169 171 204 C4' G A 7 OK OK 206 224 203 205 238 C4' C A 8 OK OK 240 255 237 239 269 C4' U A 9 OK OK 271 286 268 270 299 C4' C A 10 OK OK 301 316 298 300 330 C4' C A 11 OK OK 332 347 329 331 361 C4' C A 12 OK OK 363 378 360 362 392 C4' C A 13 OK OK 394 409 391 393 423 C4' U A 14 OK OK 425 440 422 424 453 C4' A A 15 OK OK 455 472 452 454 486 C4' A A 16 OK OK 488 505 485 487 519 C4' C A 17 OK OK 521 536 518 520 550 C4' A A 18 OK OK 552 569 549 551 583 C4' G A 19 OK OK 585 603 582 584 617 C4' C A 20 OK OK 619 634 616 618 648 C4' C A 21 OK OK 650 665 647 649 679 C4' G A 22 OK OK 681 699 678 680 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' G A 4 OK OK 104 124 125 106 139 C5' U A 5 OK OK 138 155 156 140 169 C5' G A 6 OK OK 168 188 189 170 203 C5' G A 7 OK OK 202 222 223 204 237 C5' C A 8 OK OK 236 253 254 238 268 C5' U A 9 OK OK 267 284 285 269 298 C5' C A 10 OK OK 297 314 315 299 329 C5' C A 11 OK OK 328 345 346 330 360 C5' C A 12 OK OK 359 376 377 361 391 C5' C A 13 OK OK 390 407 408 392 422 C5' U A 14 OK OK 421 438 439 423 452 C5' A A 15 OK OK 451 470 471 453 485 C5' A A 16 OK OK 484 503 504 486 518 C5' C A 17 OK OK 517 534 535 519 549 C5' A A 18 OK OK 548 567 568 550 582 C5' G A 19 OK OK 581 601 602 583 616 C5' C A 20 OK OK 615 632 633 617 647 C5' C A 21 OK OK 646 663 664 648 678 C5' G A 22 OK OK 677 697 698 679 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P G A 4 distorted distorted 75 102 103 104 135 P U A 5 distorted distorted 109 136 137 138 165 P G A 6 distorted distorted 143 166 167 168 199 P G A 7 distorted distorted 173 200 201 202 233 P C A 8 distorted distorted 207 234 235 236 264 P U A 9 distorted distorted 241 265 266 267 294 P C A 10 distorted distorted 272 295 296 297 325 P C A 11 distorted distorted 302 326 327 328 356 P C A 12 distorted distorted 333 357 358 359 387 P C A 13 distorted distorted 364 388 389 390 418 P U A 14 distorted distorted 395 419 420 421 448 P A A 15 distorted distorted 426 449 450 451 481 P A A 16 distorted distorted 456 482 483 484 514 P C A 17 distorted distorted 489 515 516 517 545 P A A 18 distorted distorted 522 546 547 548 578 P G A 19 distorted distorted 553 579 580 581 612 P C A 20 distorted distorted 586 613 614 615 643 P C A 21 distorted distorted 620 644 645 646 674 P G A 22 distorted distorted 651 675 676 677 ---------------------------------------------------------------------------------