ID code: '1K5I' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 alpha beta 7 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' A A 3 alpha beta 75 97 81 78 113 C1' C A 4 alpha beta 108 128 114 111 144 C1' C A 5 alpha beta 139 159 145 142 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' G A 7 alpha beta 201 224 207 204 240 C1' G A 8 alpha beta 235 258 241 238 274 C1' G A 9 alpha beta 269 292 275 272 308 C1' C A 10 alpha beta 303 323 309 306 339 C1' U A 11 alpha beta 334 354 340 337 369 C1' C A 12 alpha beta 364 384 370 367 400 C1' A A 13 alpha beta 395 417 401 398 433 C1' A A 14 alpha beta 428 450 434 431 466 C1' C A 15 alpha beta 461 481 467 464 497 C1' C A 16 alpha beta 492 512 498 495 528 C1' U A 17 alpha beta 523 543 529 526 558 C1' G A 18 alpha beta 553 576 559 556 592 C1' G A 19 alpha beta 587 610 593 590 626 C1' G A 20 alpha beta 621 644 627 624 660 C1' U A 21 alpha beta 655 675 661 658 690 C1' C A 22 alpha beta 685 705 691 688 721 C1' C A 23 alpha beta 716 736 722 719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' G A 2 OK OK 46 42 62 45 78 C2' A A 3 OK OK 80 76 95 79 111 C2' C A 4 OK OK 113 109 126 112 142 C2' C A 5 OK OK 144 140 157 143 173 C2' C A 6 OK OK 175 171 188 174 204 C2' G A 7 OK OK 206 202 222 205 238 C2' G A 8 OK OK 240 236 256 239 272 C2' G A 9 OK OK 274 270 290 273 306 C2' C A 10 OK OK 308 304 321 307 337 C2' U A 11 OK OK 339 335 352 338 367 C2' C A 12 OK OK 369 365 382 368 398 C2' A A 13 OK OK 400 396 415 399 431 C2' A A 14 OK OK 433 429 448 432 464 C2' C A 15 OK OK 466 462 479 465 495 C2' C A 16 OK OK 497 493 510 496 526 C2' U A 17 OK OK 528 524 541 527 556 C2' G A 18 OK OK 558 554 574 557 590 C2' G A 19 OK OK 592 588 608 591 624 C2' G A 20 OK OK 626 622 642 625 658 C2' U A 21 OK OK 660 656 673 659 688 C2' C A 22 OK OK 690 686 703 689 719 C2' C A 23 OK OK 721 717 734 720 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' A A 3 OK OK 74 94 77 78 109 C3' C A 4 OK OK 107 125 110 111 140 C3' C A 5 OK OK 138 156 141 142 171 C3' C A 6 OK OK 169 187 172 173 202 C3' G A 7 OK OK 200 221 203 204 236 C3' G A 8 OK OK 234 255 237 238 270 C3' G A 9 OK OK 268 289 271 272 304 C3' C A 10 OK OK 302 320 305 306 335 C3' U A 11 OK OK 333 351 336 337 365 C3' C A 12 OK OK 363 381 366 367 396 C3' A A 13 OK OK 394 414 397 398 429 C3' A A 14 OK OK 427 447 430 431 462 C3' C A 15 OK OK 460 478 463 464 493 C3' C A 16 OK OK 491 509 494 495 524 C3' U A 17 OK OK 522 540 525 526 554 C3' G A 18 OK OK 552 573 555 556 588 C3' G A 19 OK OK 586 607 589 590 622 C3' G A 20 OK OK 620 641 623 624 656 C3' U A 21 OK OK 654 672 657 658 686 C3' C A 22 OK OK 684 702 687 688 717 C3' C A 23 OK OK 715 733 718 719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' A A 3 OK OK 76 93 73 75 107 C4' C A 4 OK OK 109 124 106 108 138 C4' C A 5 OK OK 140 155 137 139 169 C4' C A 6 OK OK 171 186 168 170 200 C4' G A 7 OK OK 202 220 199 201 234 C4' G A 8 OK OK 236 254 233 235 268 C4' G A 9 OK OK 270 288 267 269 302 C4' C A 10 OK OK 304 319 301 303 333 C4' U A 11 OK OK 335 350 332 334 363 C4' C A 12 OK OK 365 380 362 364 394 C4' A A 13 OK OK 396 413 393 395 427 C4' A A 14 OK OK 429 446 426 428 460 C4' C A 15 OK OK 462 477 459 461 491 C4' C A 16 OK OK 493 508 490 492 522 C4' U A 17 OK OK 524 539 521 523 552 C4' G A 18 OK OK 554 572 551 553 586 C4' G A 19 OK OK 588 606 585 587 620 C4' G A 20 OK OK 622 640 619 621 654 C4' U A 21 OK OK 656 671 653 655 684 C4' C A 22 OK OK 686 701 683 685 715 C4' C A 23 OK OK 717 732 714 716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' G A 2 OK OK 38 58 59 40 73 C5' A A 3 OK OK 72 91 92 74 106 C5' C A 4 OK OK 105 122 123 107 137 C5' C A 5 OK OK 136 153 154 138 168 C5' C A 6 OK OK 167 184 185 169 199 C5' G A 7 OK OK 198 218 219 200 233 C5' G A 8 OK OK 232 252 253 234 267 C5' G A 9 OK OK 266 286 287 268 301 C5' C A 10 OK OK 300 317 318 302 332 C5' U A 11 OK OK 331 348 349 333 362 C5' C A 12 OK OK 361 378 379 363 393 C5' A A 13 OK OK 392 411 412 394 426 C5' A A 14 OK OK 425 444 445 427 459 C5' C A 15 OK OK 458 475 476 460 490 C5' C A 16 OK OK 489 506 507 491 521 C5' U A 17 OK OK 520 537 538 522 551 C5' G A 18 OK OK 550 570 571 552 585 C5' G A 19 OK OK 584 604 605 586 619 C5' G A 20 OK OK 618 638 639 620 653 C5' U A 21 OK OK 652 669 670 654 683 C5' C A 22 OK OK 682 699 700 684 714 C5' C A 23 OK OK 713 730 731 715 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P A A 3 distorted distorted 43 70 71 72 102 P C A 4 distorted distorted 77 103 104 105 133 P C A 5 distorted distorted 110 134 135 136 164 P C A 6 distorted distorted 141 165 166 167 195 P G A 7 distorted distorted 172 196 197 198 229 P G A 8 distorted distorted 203 230 231 232 263 P G A 9 distorted distorted 237 264 265 266 297 P C A 10 distorted distorted 271 298 299 300 328 P U A 11 distorted distorted 305 329 330 331 358 P C A 12 distorted distorted 336 359 360 361 389 P A A 13 distorted distorted 366 390 391 392 422 P A A 14 distorted distorted 397 423 424 425 455 P C A 15 distorted distorted 430 456 457 458 486 P C A 16 distorted distorted 463 487 488 489 517 P U A 17 distorted distorted 494 518 519 520 547 P G A 18 distorted distorted 525 548 549 550 581 P G A 19 distorted distorted 555 582 583 584 615 P G A 20 distorted distorted 589 616 617 618 649 P U A 21 distorted distorted 623 650 651 652 679 P C A 22 distorted distorted 657 680 681 682 710 P C A 23 distorted distorted 687 711 712 713 ---------------------------------------------------------------------------------