ID code: '1PJY' 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' C A 4 alpha beta 104 124 110 107 140 C1' U A 5 alpha beta 135 155 141 138 170 C1' U A 6 alpha beta 165 185 171 168 200 C1' C A 7 alpha beta 195 215 201 198 231 C1' C A 8 alpha beta 226 246 232 229 262 C1' C A 9 alpha beta 257 277 263 260 293 C1' A A 10 alpha beta 288 310 294 291 326 C1' C A 11 alpha beta 321 341 327 324 357 C1' A A 12 alpha beta 352 374 358 355 390 C1' A A 13 alpha beta 385 407 391 388 423 C1' G A 14 alpha beta 418 441 424 421 457 C1' G A 15 alpha beta 452 475 458 455 491 C1' G A 16 alpha beta 486 509 492 489 525 C1' A A 17 alpha beta 520 542 526 523 558 C1' A A 18 alpha beta 553 575 559 556 591 C1' G A 19 alpha beta 586 609 592 589 625 C1' G A 20 alpha beta 620 643 626 623 659 C1' C A 21 alpha beta 654 674 660 657 690 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' C A 4 OK OK 109 105 122 108 138 C2' U A 5 OK OK 140 136 153 139 168 C2' U A 6 OK OK 170 166 183 169 198 C2' C A 7 OK OK 200 196 213 199 229 C2' C A 8 OK OK 231 227 244 230 260 C2' C A 9 OK OK 262 258 275 261 291 C2' A A 10 OK OK 293 289 308 292 324 C2' C A 11 OK OK 326 322 339 325 355 C2' A A 12 OK OK 357 353 372 356 388 C2' A A 13 OK OK 390 386 405 389 421 C2' G A 14 OK OK 423 419 439 422 455 C2' G A 15 OK OK 457 453 473 456 489 C2' G A 16 OK OK 491 487 507 490 523 C2' A A 17 OK OK 525 521 540 524 556 C2' A A 18 OK OK 558 554 573 557 589 C2' G A 19 OK OK 591 587 607 590 623 C2' G A 20 OK OK 625 621 641 624 657 C2' C A 21 OK OK 659 655 672 658 688 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' C A 4 OK OK 103 121 106 107 136 C3' U A 5 OK OK 134 152 137 138 166 C3' U A 6 OK OK 164 182 167 168 196 C3' C A 7 OK OK 194 212 197 198 227 C3' C A 8 OK OK 225 243 228 229 258 C3' C A 9 OK OK 256 274 259 260 289 C3' A A 10 OK OK 287 307 290 291 322 C3' C A 11 OK OK 320 338 323 324 353 C3' A A 12 OK OK 351 371 354 355 386 C3' A A 13 OK OK 384 404 387 388 419 C3' G A 14 OK OK 417 438 420 421 453 C3' G A 15 OK OK 451 472 454 455 487 C3' G A 16 OK OK 485 506 488 489 521 C3' A A 17 OK OK 519 539 522 523 554 C3' A A 18 OK OK 552 572 555 556 587 C3' G A 19 OK OK 585 606 588 589 621 C3' G A 20 OK OK 619 640 622 623 655 C3' C A 21 OK OK 653 671 656 657 686 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' C A 4 OK OK 105 120 102 104 134 C4' U A 5 OK OK 136 151 133 135 164 C4' U A 6 OK OK 166 181 163 165 194 C4' C A 7 OK OK 196 211 193 195 225 C4' C A 8 OK OK 227 242 224 226 256 C4' C A 9 OK OK 258 273 255 257 287 C4' A A 10 OK OK 289 306 286 288 320 C4' C A 11 OK OK 322 337 319 321 351 C4' A A 12 OK OK 353 370 350 352 384 C4' A A 13 OK OK 386 403 383 385 417 C4' G A 14 OK OK 419 437 416 418 451 C4' G A 15 OK OK 453 471 450 452 485 C4' G A 16 OK OK 487 505 484 486 519 C4' A A 17 OK OK 521 538 518 520 552 C4' A A 18 OK OK 554 571 551 553 585 C4' G A 19 OK OK 587 605 584 586 619 C4' G A 20 OK OK 621 639 618 620 653 C4' C A 21 OK OK 655 670 652 654 684 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' C A 4 OK OK 101 118 119 103 133 C5' U A 5 OK OK 132 149 150 134 163 C5' U A 6 OK OK 162 179 180 164 193 C5' C A 7 OK OK 192 209 210 194 224 C5' C A 8 OK OK 223 240 241 225 255 C5' C A 9 OK OK 254 271 272 256 286 C5' A A 10 OK OK 285 304 305 287 319 C5' C A 11 OK OK 318 335 336 320 350 C5' A A 12 OK OK 349 368 369 351 383 C5' A A 13 OK OK 382 401 402 384 416 C5' G A 14 OK OK 415 435 436 417 450 C5' G A 15 OK OK 449 469 470 451 484 C5' G A 16 OK OK 483 503 504 485 518 C5' A A 17 OK OK 517 536 537 519 551 C5' A A 18 OK OK 550 569 570 552 584 C5' G A 19 OK OK 583 603 604 585 618 C5' G A 20 OK OK 617 637 638 619 652 C5' C A 21 OK OK 651 668 669 653 683 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 C A 4 distorted distorted 75 99 100 101 129 P U A 5 distorted distorted 106 130 131 132 159 P U A 6 distorted distorted 137 160 161 162 189 P C A 7 distorted distorted 167 190 191 192 220 P C A 8 distorted distorted 197 221 222 223 251 P C A 9 distorted distorted 228 252 253 254 282 P A A 10 distorted distorted 259 283 284 285 315 P C A 11 distorted distorted 290 316 317 318 346 P A A 12 distorted distorted 323 347 348 349 379 P A A 13 distorted distorted 354 380 381 382 412 P G A 14 distorted distorted 387 413 414 415 446 P G A 15 distorted distorted 420 447 448 449 480 P G A 16 distorted distorted 454 481 482 483 514 P A A 17 distorted distorted 488 515 516 517 547 P A A 18 distorted distorted 522 548 549 550 580 P G A 19 distorted distorted 555 581 582 583 614 P G A 20 distorted distorted 588 615 616 617 648 P C A 21 distorted distorted 622 649 650 651 679 P C A 22 distorted distorted 656 680 681 682 ---------------------------------------------------------------------------------