ID code: '1K3W' 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' --------------------------------------------------------------------------------- 8 C1' G B 1 beta 4 9 7 30 C1' A B 2 beta 26 31 29 51 C1' C B 3 beta 47 52 50 70 C1' T B 4 beta 66 71 69 90 C1' T B 5 beta 86 91 89 110 C1' G B 6 beta 106 111 109 132 C1' T B 7 beta 128 133 131 152 C1' G B 8 beta 148 153 151 174 C1' T B 9 beta 170 175 173 194 C1' A B 10 beta 190 195 193 215 C1' T B 11 beta 211 216 214 235 C1' A B 12 beta 231 236 234 256 C1' A B 13 beta 252 257 255 277 C1' G B 14 beta 273 278 276 299 C1' A B 15 beta 295 300 298 320 C1' G B 16 beta 316 321 319 342 C1' T B 17 beta 338 343 341 362 C1' C B 18 beta 358 363 361 382 C1' G C 3 beta 378 383 381 404 C1' A C 4 beta 400 405 403 425 C1' C C 5 beta 421 426 424 444 C1' T C 6 beta 440 445 443 464 C1' C C 7 beta 460 465 463 483 C1' T C 8 beta 479 484 482 503 C1' T C 9 beta 499 504 502 523 C1' A C 10 beta 519 524 522 544 C1' T C 11 beta 540 545 543 564 C1' A C 12 beta 560 565 563 585 C1' C C 13 beta 581 586 584 604 C1' A C 14 beta 600 605 603 625 C1' C C 15 beta 621 626 624 644 C1' A C 16 beta 640 645 643 665 C1' A C 17 beta 661 666 664 686 C1' G C 18 beta 682 687 685 708 C1' T C 19 beta 704 709 707 728 C1' C C 20 beta 724 729 727 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 1 8 5 29 C2' A B 2 30 27 50 C2' C B 3 51 48 69 C2' T B 4 70 67 89 C2' T B 5 90 87 109 C2' G B 6 110 107 131 C2' T B 7 132 129 151 C2' G B 8 152 149 173 C2' T B 9 174 171 193 C2' A B 10 194 191 214 C2' T B 11 215 212 234 C2' A B 12 235 232 255 C2' A B 13 256 253 276 C2' G B 14 277 274 298 C2' A B 15 299 296 319 C2' G B 16 320 317 341 C2' T B 17 342 339 361 C2' C B 18 362 359 381 C2' G C 3 382 379 403 C2' A C 4 404 401 424 C2' C C 5 425 422 443 C2' T C 6 444 441 463 C2' C C 7 464 461 482 C2' T C 8 483 480 502 C2' T C 9 503 500 522 C2' A C 10 523 520 543 C2' T C 11 544 541 563 C2' A C 12 564 561 584 C2' C C 13 585 582 603 C2' A C 14 604 601 624 C2' C C 15 625 622 643 C2' A C 16 644 641 664 C2' A C 17 665 662 685 C2' G C 18 686 683 707 C2' T C 19 708 705 727 C2' C C 20 728 725 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 1 OK 3 6 7 27 C3' A B 2 OK 25 28 29 48 C3' C B 3 OK 46 49 50 67 C3' T B 4 OK 65 68 69 87 C3' T B 5 OK 85 88 89 107 C3' G B 6 OK 105 108 109 129 C3' T B 7 OK 127 130 131 149 C3' G B 8 OK 147 150 151 171 C3' T B 9 OK 169 172 173 191 C3' A B 10 OK 189 192 193 212 C3' T B 11 OK 210 213 214 232 C3' A B 12 OK 230 233 234 253 C3' A B 13 OK 251 254 255 274 C3' G B 14 OK 272 275 276 296 C3' A B 15 OK 294 297 298 317 C3' G B 16 OK 315 318 319 339 C3' T B 17 OK 337 340 341 359 C3' C B 18 OK 357 360 361 379 C3' G C 3 OK 377 380 381 401 C3' A C 4 OK 399 402 403 422 C3' C C 5 OK 420 423 424 441 C3' T C 6 OK 439 442 443 461 C3' C C 7 OK 459 462 463 480 C3' T C 8 OK 478 481 482 500 C3' T C 9 OK 498 501 502 520 C3' A C 10 OK 518 521 522 541 C3' T C 11 OK 539 542 543 561 C3' A C 12 OK 559 562 563 582 C3' C C 13 OK 580 583 584 601 C3' A C 14 OK 599 602 603 622 C3' C C 15 OK 620 623 624 641 C3' A C 16 OK 639 642 643 662 C3' A C 17 OK 660 663 664 683 C3' G C 18 OK 681 684 685 705 C3' T C 19 OK 703 706 707 725 C3' C C 20 OK 723 726 727 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 1 OK 5 2 4 25 C4' A B 2 OK 27 24 26 46 C4' C B 3 OK 48 45 47 65 C4' T B 4 OK 67 64 66 85 C4' T B 5 OK 87 84 86 105 C4' G B 6 OK 107 104 106 127 C4' T B 7 OK 129 126 128 147 C4' G B 8 OK 149 146 148 169 C4' T B 9 OK 171 168 170 189 C4' A B 10 OK 191 188 190 210 C4' T B 11 OK 212 209 211 230 C4' A B 12 OK 232 229 231 251 C4' A B 13 OK 253 250 252 272 C4' G B 14 OK 274 271 273 294 C4' A B 15 OK 296 293 295 315 C4' G B 16 OK 317 314 316 337 C4' T B 17 OK 339 336 338 357 C4' C B 18 OK 359 356 358 377 C4' G C 3 OK 379 376 378 399 C4' A C 4 OK 401 398 400 420 C4' C C 5 OK 422 419 421 439 C4' T C 6 OK 441 438 440 459 C4' C C 7 OK 461 458 460 478 C4' T C 8 OK 480 477 479 498 C4' T C 9 OK 500 497 499 518 C4' A C 10 OK 520 517 519 539 C4' T C 11 OK 541 538 540 559 C4' A C 12 OK 561 558 560 580 C4' C C 13 OK 582 579 581 599 C4' A C 14 OK 601 598 600 620 C4' C C 15 OK 622 619 621 639 C4' A C 16 OK 641 638 640 660 C4' A C 17 OK 662 659 661 681 C4' G C 18 OK 683 680 682 703 C4' T C 19 OK 705 702 704 723 C4' C C 20 OK 725 722 724 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 1 1 3 24 C5' A B 2 23 25 45 C5' C B 3 44 46 64 C5' T B 4 63 65 84 C5' T B 5 83 85 104 C5' G B 6 103 105 126 C5' T B 7 125 127 146 C5' G B 8 145 147 168 C5' T B 9 167 169 188 C5' A B 10 187 189 209 C5' T B 11 208 210 229 C5' A B 12 228 230 250 C5' A B 13 249 251 271 C5' G B 14 270 272 293 C5' A B 15 292 294 314 C5' G B 16 313 315 336 C5' T B 17 335 337 356 C5' C B 18 355 357 376 C5' G C 3 375 377 398 C5' A C 4 397 399 419 C5' C C 5 418 420 438 C5' T C 6 437 439 458 C5' C C 7 457 459 477 C5' T C 8 476 478 497 C5' T C 9 496 498 517 C5' A C 10 516 518 538 C5' T C 11 537 539 558 C5' A C 12 557 559 579 C5' C C 13 578 580 598 C5' A C 14 597 599 619 C5' C C 15 618 620 638 C5' A C 16 637 639 659 C5' A C 17 658 660 680 C5' G C 18 679 681 702 C5' T C 19 701 703 722 C5' C C 20 721 723 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A B 2 distorted distorted 6 21 22 23 41 P C B 3 distorted distorted 28 42 43 44 60 P T B 4 distorted distorted 49 61 62 63 80 P T B 5 distorted distorted 68 81 82 83 100 P G B 6 distorted distorted 88 101 102 103 122 P T B 7 distorted distorted 108 123 124 125 142 P G B 8 distorted distorted 130 143 144 145 164 P T B 9 distorted distorted 150 165 166 167 184 P A B 10 distorted distorted 172 185 186 187 205 P T B 11 distorted distorted 192 206 207 208 225 P A B 12 distorted distorted 213 226 227 228 246 P A B 13 distorted distorted 233 247 248 249 267 P G B 14 distorted distorted 254 268 269 270 289 P A B 15 distorted distorted 275 290 291 292 310 P G B 16 distorted distorted 297 311 312 313 332 P T B 17 distorted distorted 318 333 334 335 352 P C B 18 distorted distorted 340 353 354 355 372 P G C 3 distorted distorted 373 374 375 394 P A C 4 distorted distorted 380 395 396 397 415 P C C 5 distorted distorted 402 416 417 418 434 P T C 6 distorted distorted 423 435 436 437 454 P C C 7 distorted distorted 442 455 456 457 473 P T C 8 distorted distorted 462 474 475 476 493 P T C 9 distorted distorted 481 494 495 496 513 P A C 10 distorted distorted 501 514 515 516 534 P T C 11 distorted distorted 521 535 536 537 554 P A C 12 distorted distorted 542 555 556 557 575 P C C 13 distorted distorted 562 576 577 578 594 P A C 14 distorted distorted 583 595 596 597 615 P C C 15 distorted distorted 602 616 617 618 634 P A C 16 distorted distorted 623 635 636 637 655 P A C 17 distorted distorted 642 656 657 658 676 P G C 18 distorted distorted 663 677 678 679 698 P T C 19 distorted distorted 684 699 700 701 718 P C C 20 distorted distorted 706 719 720 721 ---------------------------------------------------------------------------------