ID code: '2JYM' 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' C A 3 alpha beta 73 93 79 76 109 C1' U A 4 alpha beta 104 124 110 107 139 C1' C A 5 alpha beta 134 154 140 137 170 C1' G A 6 alpha beta 165 188 171 168 204 C1' C A 7 alpha beta 199 219 205 202 235 C1' A A 8 alpha beta 230 252 236 233 268 C1' G A 9 alpha beta 263 286 269 266 302 C1' C A 10 alpha beta 297 317 303 300 333 C1' A A 11 alpha beta 328 350 334 331 366 C1' G A 12 alpha beta 361 384 367 364 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' U A 14 alpha beta 429 449 435 432 464 C1' C A 15 alpha beta 459 479 465 462 495 C1' U A 16 alpha beta 490 510 496 493 525 C1' G A 17 alpha beta 520 543 526 523 559 C1' G A 18 alpha beta 554 577 560 557 593 C1' A A 19 alpha beta 588 610 594 591 626 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 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' U A 4 OK OK 109 105 122 108 137 C2' C A 5 OK OK 139 135 152 138 168 C2' G A 6 OK OK 170 166 186 169 202 C2' C A 7 OK OK 204 200 217 203 233 C2' A A 8 OK OK 235 231 250 234 266 C2' G A 9 OK OK 268 264 284 267 300 C2' C A 10 OK OK 302 298 315 301 331 C2' A A 11 OK OK 333 329 348 332 364 C2' G A 12 OK OK 366 362 382 365 398 C2' G A 13 OK OK 400 396 416 399 432 C2' U A 14 OK OK 434 430 447 433 462 C2' C A 15 OK OK 464 460 477 463 493 C2' U A 16 OK OK 495 491 508 494 523 C2' G A 17 OK OK 525 521 541 524 557 C2' G A 18 OK OK 559 555 575 558 591 C2' A A 19 OK OK 593 589 608 592 624 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 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' U A 4 OK OK 103 121 106 107 135 C3' C A 5 OK OK 133 151 136 137 166 C3' G A 6 OK OK 164 185 167 168 200 C3' C A 7 OK OK 198 216 201 202 231 C3' A A 8 OK OK 229 249 232 233 264 C3' G A 9 OK OK 262 283 265 266 298 C3' C A 10 OK OK 296 314 299 300 329 C3' A A 11 OK OK 327 347 330 331 362 C3' G A 12 OK OK 360 381 363 364 396 C3' G A 13 OK OK 394 415 397 398 430 C3' U A 14 OK OK 428 446 431 432 460 C3' C A 15 OK OK 458 476 461 462 491 C3' U A 16 OK OK 489 507 492 493 521 C3' G A 17 OK OK 519 540 522 523 555 C3' G A 18 OK OK 553 574 556 557 589 C3' A A 19 OK OK 587 607 590 591 622 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 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' U A 4 OK OK 105 120 102 104 133 C4' C A 5 OK OK 135 150 132 134 164 C4' G A 6 OK OK 166 184 163 165 198 C4' C A 7 OK OK 200 215 197 199 229 C4' A A 8 OK OK 231 248 228 230 262 C4' G A 9 OK OK 264 282 261 263 296 C4' C A 10 OK OK 298 313 295 297 327 C4' A A 11 OK OK 329 346 326 328 360 C4' G A 12 OK OK 362 380 359 361 394 C4' G A 13 OK OK 396 414 393 395 428 C4' U A 14 OK OK 430 445 427 429 458 C4' C A 15 OK OK 460 475 457 459 489 C4' U A 16 OK OK 491 506 488 490 519 C4' G A 17 OK OK 521 539 518 520 553 C4' G A 18 OK OK 555 573 552 554 587 C4' A A 19 OK OK 589 606 586 588 620 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 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' U A 4 OK OK 101 118 119 103 132 C5' C A 5 OK OK 131 148 149 133 163 C5' G A 6 OK OK 162 182 183 164 197 C5' C A 7 OK OK 196 213 214 198 228 C5' A A 8 OK OK 227 246 247 229 261 C5' G A 9 OK OK 260 280 281 262 295 C5' C A 10 OK OK 294 311 312 296 326 C5' A A 11 OK OK 325 344 345 327 359 C5' G A 12 OK OK 358 378 379 360 393 C5' G A 13 OK OK 392 412 413 394 427 C5' U A 14 OK OK 426 443 444 428 457 C5' C A 15 OK OK 456 473 474 458 488 C5' U A 16 OK OK 487 504 505 489 518 C5' G A 17 OK OK 517 537 538 519 552 C5' G A 18 OK OK 551 571 572 553 586 C5' A A 19 OK OK 585 604 605 587 619 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 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P U A 4 distorted distorted 75 99 100 101 128 P C A 5 distorted distorted 106 129 130 131 159 P G A 6 distorted distorted 136 160 161 162 193 P C A 7 distorted distorted 167 194 195 196 224 P A A 8 distorted distorted 201 225 226 227 257 P G A 9 distorted distorted 232 258 259 260 291 P C A 10 distorted distorted 265 292 293 294 322 P A A 11 distorted distorted 299 323 324 325 355 P G A 12 distorted distorted 330 356 357 358 389 P G A 13 distorted distorted 363 390 391 392 423 P U A 14 distorted distorted 397 424 425 426 453 P C A 15 distorted distorted 431 454 455 456 484 P U A 16 distorted distorted 461 485 486 487 514 P G A 17 distorted distorted 492 515 516 517 548 P G A 18 distorted distorted 522 549 550 551 582 P A A 19 distorted distorted 556 583 584 585 615 P G A 20 distorted distorted 590 616 617 618 649 P U A 21 distorted distorted 623 650 651 652 679 P C A 22 distorted distorted 657 680 681 682 ---------------------------------------------------------------------------------