ID code: '2LX1' 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' C A 3 alpha beta 72 92 78 75 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' U A 7 alpha beta 204 224 210 207 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' U A 9 alpha beta 268 288 274 271 303 C1' C A 10 alpha beta 298 318 304 301 334 C1' A A 11 alpha beta 329 352 335 332 366 C1' G B 12 alpha beta 361 384 367 364 401 C1' A B 13 alpha beta 396 418 402 399 434 C1' C B 14 alpha beta 429 449 435 432 465 C1' G B 15 alpha beta 460 483 466 463 499 C1' A B 16 alpha beta 494 516 500 497 532 C1' G B 17 alpha beta 527 550 533 530 566 C1' U B 18 alpha beta 561 581 567 564 596 C1' G B 19 alpha beta 591 614 597 594 630 C1' U B 20 alpha beta 625 645 631 628 660 C1' C B 21 alpha beta 655 675 661 658 691 C1' A B 22 alpha beta 686 709 692 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 77 73 90 76 106 C2' G A 4 OK OK 108 104 124 107 140 C2' A A 5 OK OK 142 138 157 141 173 C2' G A 6 OK OK 175 171 191 174 207 C2' U A 7 OK OK 209 205 222 208 237 C2' G A 8 OK OK 239 235 255 238 271 C2' U A 9 OK OK 273 269 286 272 301 C2' C A 10 OK OK 303 299 316 302 332 C2' A A 11 OK OK 334 330 350 333 364 C2' G B 12 OK OK 366 362 382 365 399 C2' A B 13 OK OK 401 397 416 400 432 C2' C B 14 OK OK 434 430 447 433 463 C2' G B 15 OK OK 465 461 481 464 497 C2' A B 16 OK OK 499 495 514 498 530 C2' G B 17 OK OK 532 528 548 531 564 C2' U B 18 OK OK 566 562 579 565 594 C2' G B 19 OK OK 596 592 612 595 628 C2' U B 20 OK OK 630 626 643 629 658 C2' C B 21 OK OK 660 656 673 659 689 C2' A B 22 OK OK 691 687 707 690 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 71 89 74 75 104 C3' G A 4 OK OK 102 123 105 106 138 C3' A A 5 OK OK 136 156 139 140 171 C3' G A 6 OK OK 169 190 172 173 205 C3' U A 7 OK OK 203 221 206 207 235 C3' G A 8 OK OK 233 254 236 237 269 C3' U A 9 OK OK 267 285 270 271 299 C3' C A 10 OK OK 297 315 300 301 330 C3' A A 11 OK OK 328 348 331 332 362 C3' G B 12 OK OK 360 381 363 364 397 C3' A B 13 OK OK 395 415 398 399 430 C3' C B 14 OK OK 428 446 431 432 461 C3' G B 15 OK OK 459 480 462 463 495 C3' A B 16 OK OK 493 513 496 497 528 C3' G B 17 OK OK 526 547 529 530 562 C3' U B 18 OK OK 560 578 563 564 592 C3' G B 19 OK OK 590 611 593 594 626 C3' U B 20 OK OK 624 642 627 628 656 C3' C B 21 OK OK 654 672 657 658 687 C3' A B 22 OK OK 685 705 688 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 73 88 70 72 102 C4' G A 4 OK OK 104 122 101 103 136 C4' A A 5 OK OK 138 155 135 137 169 C4' G A 6 OK OK 171 189 168 170 203 C4' U A 7 OK OK 205 220 202 204 233 C4' G A 8 OK OK 235 253 232 234 267 C4' U A 9 OK OK 269 284 266 268 297 C4' C A 10 OK OK 299 314 296 298 328 C4' A A 11 OK OK 330 347 327 329 360 C4' G B 12 OK OK 362 380 359 361 395 C4' A B 13 OK OK 397 414 394 396 428 C4' C B 14 OK OK 430 445 427 429 459 C4' G B 15 OK OK 461 479 458 460 493 C4' A B 16 OK OK 495 512 492 494 526 C4' G B 17 OK OK 528 546 525 527 560 C4' U B 18 OK OK 562 577 559 561 590 C4' G B 19 OK OK 592 610 589 591 624 C4' U B 20 OK OK 626 641 623 625 654 C4' C B 21 OK OK 656 671 653 655 685 C4' A B 22 OK OK 687 704 684 686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 69 86 87 71 101 C5' G A 4 OK OK 100 120 121 102 135 C5' A A 5 OK OK 134 153 154 136 168 C5' G A 6 OK OK 167 187 188 169 202 C5' U A 7 OK OK 201 218 219 203 232 C5' G A 8 OK OK 231 251 252 233 266 C5' U A 9 OK OK 265 282 283 267 296 C5' C A 10 OK OK 295 312 313 297 327 C5' A A 11 OK OK 326 345 346 328 359 C5' G B 12 OK OK 358 378 379 360 394 C5' A B 13 OK OK 393 412 413 395 427 C5' C B 14 OK OK 426 443 444 428 458 C5' G B 15 OK OK 457 477 478 459 492 C5' A B 16 OK OK 491 510 511 493 525 C5' G B 17 OK OK 524 544 545 526 559 C5' U B 18 OK OK 558 575 576 560 589 C5' G B 19 OK OK 588 608 609 590 623 C5' U B 20 OK OK 622 639 640 624 653 C5' C B 21 OK OK 652 669 670 654 684 C5' A B 22 OK OK 683 702 703 685 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P C A 3 distorted distorted 41 67 68 69 97 P G A 4 distorted distorted 74 98 99 100 131 P A A 5 distorted distorted 105 132 133 134 164 P G A 6 distorted distorted 139 165 166 167 198 P U A 7 distorted distorted 172 199 200 201 228 P G A 8 distorted distorted 206 229 230 231 262 P U A 9 distorted distorted 236 263 264 265 292 P C A 10 distorted distorted 270 293 294 295 323 P A A 11 distorted distorted 300 324 325 326 390 P A B 13 distorted distorted 363 391 392 393 423 P C B 14 distorted distorted 398 424 425 426 454 P G B 15 distorted distorted 431 455 456 457 488 P A B 16 distorted distorted 462 489 490 491 521 P G B 17 distorted distorted 496 522 523 524 555 P U B 18 distorted distorted 529 556 557 558 585 P G B 19 distorted distorted 563 586 587 588 619 P U B 20 distorted distorted 593 620 621 622 649 P C B 21 distorted distorted 627 650 651 652 680 P A B 22 distorted distorted 657 681 682 683 ---------------------------------------------------------------------------------