ID code: '1HW2' 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' --------------------------------------------------------------------------------- 11 C1' A D 3 beta 7 12 10 32 C1' T D 4 beta 28 33 31 52 C1' C D 5 beta 48 53 51 71 C1' T D 6 beta 67 72 70 91 C1' G D 7 beta 87 92 90 113 C1' G D 8 beta 109 114 112 135 C1' T D 9 beta 131 136 134 155 C1' C D 10 beta 151 156 154 174 C1' C D 11 beta 170 175 173 193 C1' G D 12 beta 189 194 192 215 C1' A D 13 beta 211 216 214 236 C1' C D 14 beta 232 237 235 255 C1' C D 15 beta 251 256 254 274 C1' A D 16 beta 270 275 273 295 C1' G D 17 beta 291 296 294 317 C1' A D 18 beta 313 318 316 338 C1' T D 19 beta 334 339 337 358 C1' G D 20 beta 354 359 357 378 C1' C E 2 beta 374 379 377 397 C1' A E 3 beta 393 398 396 418 C1' T E 4 beta 414 419 417 438 C1' C E 5 beta 434 439 437 457 C1' T E 6 beta 453 458 456 477 C1' G E 7 beta 473 478 476 499 C1' G E 8 beta 495 500 498 521 C1' T E 9 beta 517 522 520 541 C1' C E 10 beta 537 542 540 560 C1' G E 11 beta 556 561 559 582 C1' G E 12 beta 578 583 581 604 C1' A E 13 beta 600 605 603 625 C1' C E 14 beta 621 626 624 644 C1' C E 15 beta 640 645 643 663 C1' A E 16 beta 659 664 662 684 C1' G E 17 beta 680 685 683 706 C1' A E 18 beta 702 707 705 727 C1' T E 19 beta 723 728 726 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A D 3 11 8 31 C2' T D 4 32 29 51 C2' C D 5 52 49 70 C2' T D 6 71 68 90 C2' G D 7 91 88 112 C2' G D 8 113 110 134 C2' T D 9 135 132 154 C2' C D 10 155 152 173 C2' C D 11 174 171 192 C2' G D 12 193 190 214 C2' A D 13 215 212 235 C2' C D 14 236 233 254 C2' C D 15 255 252 273 C2' A D 16 274 271 294 C2' G D 17 295 292 316 C2' A D 18 317 314 337 C2' T D 19 338 335 357 C2' G D 20 358 355 377 C2' C E 2 378 375 396 C2' A E 3 397 394 417 C2' T E 4 418 415 437 C2' C E 5 438 435 456 C2' T E 6 457 454 476 C2' G E 7 477 474 498 C2' G E 8 499 496 520 C2' T E 9 521 518 540 C2' C E 10 541 538 559 C2' G E 11 560 557 581 C2' G E 12 582 579 603 C2' A E 13 604 601 624 C2' C E 14 625 622 643 C2' C E 15 644 641 662 C2' A E 16 663 660 683 C2' G E 17 684 681 705 C2' A E 18 706 703 726 C2' T E 19 727 724 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A D 3 OK 6 9 10 29 C3' T D 4 OK 27 30 31 49 C3' C D 5 OK 47 50 51 68 C3' T D 6 OK 66 69 70 88 C3' G D 7 OK 86 89 90 110 C3' G D 8 OK 108 111 112 132 C3' T D 9 OK 130 133 134 152 C3' C D 10 OK 150 153 154 171 C3' C D 11 OK 169 172 173 190 C3' G D 12 OK 188 191 192 212 C3' A D 13 OK 210 213 214 233 C3' C D 14 OK 231 234 235 252 C3' C D 15 OK 250 253 254 271 C3' A D 16 OK 269 272 273 292 C3' G D 17 OK 290 293 294 314 C3' A D 18 OK 312 315 316 335 C3' T D 19 OK 333 336 337 355 C3' G D 20 OK 353 356 357 375 C3' C E 2 OK 373 376 377 394 C3' A E 3 OK 392 395 396 415 C3' T E 4 OK 413 416 417 435 C3' C E 5 OK 433 436 437 454 C3' T E 6 OK 452 455 456 474 C3' G E 7 OK 472 475 476 496 C3' G E 8 OK 494 497 498 518 C3' T E 9 OK 516 519 520 538 C3' C E 10 OK 536 539 540 557 C3' G E 11 OK 555 558 559 579 C3' G E 12 OK 577 580 581 601 C3' A E 13 OK 599 602 603 622 C3' C E 14 OK 620 623 624 641 C3' C E 15 OK 639 642 643 660 C3' A E 16 OK 658 661 662 681 C3' G E 17 OK 679 682 683 703 C3' A E 18 OK 701 704 705 724 C3' T E 19 OK 722 725 726 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A D 3 OK 8 5 7 27 C4' T D 4 OK 29 26 28 47 C4' C D 5 OK 49 46 48 66 C4' T D 6 OK 68 65 67 86 C4' G D 7 OK 88 85 87 108 C4' G D 8 OK 110 107 109 130 C4' T D 9 OK 132 129 131 150 C4' C D 10 OK 152 149 151 169 C4' C D 11 OK 171 168 170 188 C4' G D 12 OK 190 187 189 210 C4' A D 13 OK 212 209 211 231 C4' C D 14 OK 233 230 232 250 C4' C D 15 OK 252 249 251 269 C4' A D 16 OK 271 268 270 290 C4' G D 17 OK 292 289 291 312 C4' A D 18 OK 314 311 313 333 C4' T D 19 OK 335 332 334 353 C4' G D 20 OK 355 352 354 373 C4' C E 2 OK 375 372 374 392 C4' A E 3 OK 394 391 393 413 C4' T E 4 OK 415 412 414 433 C4' C E 5 OK 435 432 434 452 C4' T E 6 OK 454 451 453 472 C4' G E 7 OK 474 471 473 494 C4' G E 8 OK 496 493 495 516 C4' T E 9 OK 518 515 517 536 C4' C E 10 OK 538 535 537 555 C4' G E 11 OK 557 554 556 577 C4' G E 12 OK 579 576 578 599 C4' A E 13 OK 601 598 600 620 C4' C E 14 OK 622 619 621 639 C4' C E 15 OK 641 638 640 658 C4' A E 16 OK 660 657 659 679 C4' G E 17 OK 681 678 680 701 C4' A E 18 OK 703 700 702 722 C4' T E 19 OK 724 721 723 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A D 3 4 6 26 C5' T D 4 25 27 46 C5' C D 5 45 47 65 C5' T D 6 64 66 85 C5' G D 7 84 86 107 C5' G D 8 106 108 129 C5' T D 9 128 130 149 C5' C D 10 148 150 168 C5' C D 11 167 169 187 C5' G D 12 186 188 209 C5' A D 13 208 210 230 C5' C D 14 229 231 249 C5' C D 15 248 250 268 C5' A D 16 267 269 289 C5' G D 17 288 290 311 C5' A D 18 310 312 332 C5' T D 19 331 333 352 C5' G D 20 351 353 372 C5' C E 2 371 373 391 C5' A E 3 390 392 412 C5' T E 4 411 413 432 C5' C E 5 431 433 451 C5' T E 6 450 452 471 C5' G E 7 470 472 493 C5' G E 8 492 494 515 C5' T E 9 514 516 535 C5' C E 10 534 536 554 C5' G E 11 553 555 576 C5' G E 12 575 577 598 C5' A E 13 597 599 619 C5' C E 14 618 620 638 C5' C E 15 637 639 657 C5' A E 16 656 658 678 C5' G E 17 677 679 700 C5' A E 18 699 701 721 C5' T E 19 720 722 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A D 3 distorted distorted 2 3 4 22 P T D 4 distorted distorted 9 23 24 25 42 P C D 5 distorted distorted 30 43 44 45 61 P T D 6 distorted distorted 50 62 63 64 81 P G D 7 distorted distorted 69 82 83 84 103 P G D 8 distorted distorted 89 104 105 106 125 P T D 9 distorted distorted 111 126 127 128 145 P C D 10 distorted distorted 133 146 147 148 164 P C D 11 distorted distorted 153 165 166 167 183 P G D 12 distorted distorted 172 184 185 186 205 P A D 13 distorted distorted 191 206 207 208 226 P C D 14 distorted distorted 213 227 228 229 245 P C D 15 distorted distorted 234 246 247 248 264 P A D 16 distorted distorted 253 265 266 267 285 P G D 17 distorted distorted 272 286 287 288 307 P A D 18 distorted distorted 293 308 309 310 328 P T D 19 distorted distorted 315 329 330 331 348 P G D 20 distorted distorted 336 349 350 351 387 P A E 3 distorted distorted 376 388 389 390 408 P T E 4 distorted distorted 395 409 410 411 428 P C E 5 distorted distorted 416 429 430 431 447 P T E 6 distorted distorted 436 448 449 450 467 P G E 7 distorted distorted 455 468 469 470 489 P G E 8 distorted distorted 475 490 491 492 511 P T E 9 distorted distorted 497 512 513 514 531 P C E 10 distorted distorted 519 532 533 534 550 P G E 11 distorted distorted 539 551 552 553 572 P G E 12 distorted distorted 558 573 574 575 594 P A E 13 distorted distorted 580 595 596 597 615 P C E 14 distorted distorted 602 616 617 618 634 P C E 15 distorted distorted 623 635 636 637 653 P A E 16 distorted distorted 642 654 655 656 674 P G E 17 distorted distorted 661 675 676 677 696 P A E 18 distorted distorted 682 697 698 699 717 P T E 19 distorted distorted 704 718 719 720 ---------------------------------------------------------------------------------