ID code: '1KBU' 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' A C 1 beta 4 9 7 29 C1' T C 2 beta 25 30 28 49 C1' A C 3 beta 45 50 48 70 C1' A C 4 beta 66 71 69 91 C1' G C 5 beta 87 92 90 113 C1' T C 6 beta 109 114 112 133 C1' T C 7 beta 129 134 132 153 C1' C C 8 beta 149 154 152 172 C1' G C 9 beta 168 173 171 194 C1' T C 10 beta 190 195 193 214 C1' A C 11 beta 210 215 213 235 C1' T C 12 beta 231 236 234 255 C1' A C 13 beta 251 256 254 276 C1' A C 14 beta 272 277 275 297 C1' T C 15 beta 293 298 296 359 C1' A D 20 beta 355 360 358 380 C1' T D 21 beta 376 381 379 400 C1' T D 22 beta 396 401 399 420 C1' A D 23 beta 416 421 419 441 C1' T D 24 beta 437 442 440 461 C1' A D 25 beta 457 462 460 482 C1' C D 26 beta 478 483 481 501 C1' G D 27 beta 497 502 500 523 C1' A D 28 beta 519 524 522 544 C1' A D 29 beta 540 545 543 565 C1' C D 30 beta 561 566 564 584 C1' T D 31 beta 580 585 583 604 C1' T D 32 beta 600 605 603 624 C1' A D 33 beta 620 625 623 645 C1' T D 34 beta 641 646 644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A C 1 8 5 28 C2' T C 2 29 26 48 C2' A C 3 49 46 69 C2' A C 4 70 67 90 C2' G C 5 91 88 112 C2' T C 6 113 110 132 C2' T C 7 133 130 152 C2' C C 8 153 150 171 C2' G C 9 172 169 193 C2' T C 10 194 191 213 C2' A C 11 214 211 234 C2' T C 12 235 232 254 C2' A C 13 255 252 275 C2' A C 14 276 273 296 C2' T C 15 297 294 358 C2' A D 20 359 356 379 C2' T D 21 380 377 399 C2' T D 22 400 397 419 C2' A D 23 420 417 440 C2' T D 24 441 438 460 C2' A D 25 461 458 481 C2' C D 26 482 479 500 C2' G D 27 501 498 522 C2' A D 28 523 520 543 C2' A D 29 544 541 564 C2' C D 30 565 562 583 C2' T D 31 584 581 603 C2' T D 32 604 601 623 C2' A D 33 624 621 644 C2' T D 34 645 642 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A C 1 OK 3 6 7 26 C3' T C 2 OK 24 27 28 46 C3' A C 3 OK 44 47 48 67 C3' A C 4 OK 65 68 69 88 C3' G C 5 OK 86 89 90 110 C3' T C 6 OK 108 111 112 130 C3' T C 7 OK 128 131 132 150 C3' C C 8 OK 148 151 152 169 C3' G C 9 OK 167 170 171 191 C3' T C 10 OK 189 192 193 211 C3' A C 11 OK 209 212 213 232 C3' T C 12 OK 230 233 234 252 C3' A C 13 OK 250 253 254 273 C3' A C 14 OK 271 274 275 294 C3' T C 15 OK 292 295 296 356 C3' A D 20 OK 354 357 358 377 C3' T D 21 OK 375 378 379 397 C3' T D 22 OK 395 398 399 417 C3' A D 23 OK 415 418 419 438 C3' T D 24 OK 436 439 440 458 C3' A D 25 OK 456 459 460 479 C3' C D 26 OK 477 480 481 498 C3' G D 27 OK 496 499 500 520 C3' A D 28 OK 518 521 522 541 C3' A D 29 OK 539 542 543 562 C3' C D 30 OK 560 563 564 581 C3' T D 31 OK 579 582 583 601 C3' T D 32 OK 599 602 603 621 C3' A D 33 OK 619 622 623 642 C3' T D 34 OK 640 643 644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A C 1 OK 5 2 4 24 C4' T C 2 OK 26 23 25 44 C4' A C 3 OK 46 43 45 65 C4' A C 4 OK 67 64 66 86 C4' G C 5 OK 88 85 87 108 C4' T C 6 OK 110 107 109 128 C4' T C 7 OK 130 127 129 148 C4' C C 8 OK 150 147 149 167 C4' G C 9 OK 169 166 168 189 C4' T C 10 OK 191 188 190 209 C4' A C 11 OK 211 208 210 230 C4' T C 12 OK 232 229 231 250 C4' A C 13 OK 252 249 251 271 C4' A C 14 OK 273 270 272 292 C4' T C 15 OK 294 291 293 354 C4' A D 20 OK 356 353 355 375 C4' T D 21 OK 377 374 376 395 C4' T D 22 OK 397 394 396 415 C4' A D 23 OK 417 414 416 436 C4' T D 24 OK 438 435 437 456 C4' A D 25 OK 458 455 457 477 C4' C D 26 OK 479 476 478 496 C4' G D 27 OK 498 495 497 518 C4' A D 28 OK 520 517 519 539 C4' A D 29 OK 541 538 540 560 C4' C D 30 OK 562 559 561 579 C4' T D 31 OK 581 578 580 599 C4' T D 32 OK 601 598 600 619 C4' A D 33 OK 621 618 620 640 C4' T D 34 OK 642 639 641 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A C 1 1 3 23 C5' T C 2 22 24 43 C5' A C 3 42 44 64 C5' A C 4 63 65 85 C5' G C 5 84 86 107 C5' T C 6 106 108 127 C5' T C 7 126 128 147 C5' C C 8 146 148 166 C5' G C 9 165 167 188 C5' T C 10 187 189 208 C5' A C 11 207 209 229 C5' T C 12 228 230 249 C5' A C 13 248 250 270 C5' A C 14 269 271 291 C5' T C 15 290 292 353 C5' A D 20 352 354 374 C5' T D 21 373 375 394 C5' T D 22 393 395 414 C5' A D 23 413 415 435 C5' T D 24 434 436 455 C5' A D 25 454 456 476 C5' C D 26 475 477 495 C5' G D 27 494 496 517 C5' A D 28 516 518 538 C5' A D 29 537 539 559 C5' C D 30 558 560 578 C5' T D 31 577 579 598 C5' T D 32 597 599 618 C5' A D 33 617 619 639 C5' T D 34 638 640 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P T C 2 distorted distorted 6 20 21 22 39 P A C 3 distorted distorted 27 40 41 42 60 P A C 4 distorted distorted 47 61 62 63 81 P G C 5 distorted distorted 68 82 83 84 103 P T C 6 distorted distorted 89 104 105 106 123 P T C 7 distorted distorted 111 124 125 126 143 P C C 8 distorted distorted 131 144 145 146 162 P G C 9 distorted distorted 151 163 164 165 184 P T C 10 distorted distorted 170 185 186 187 204 P A C 11 distorted distorted 192 205 206 207 225 P T C 12 distorted distorted 212 226 227 228 245 P A C 13 distorted distorted 233 246 247 248 266 P A C 14 distorted distorted 253 267 268 269 287 P T C 15 distorted distorted 274 288 289 290 307 P G C 16 295 330 P C D 19 349 P A D 20 distorted distorted 350 351 352 370 P T D 21 distorted distorted 357 371 372 373 390 P T D 22 distorted distorted 378 391 392 393 410 P A D 23 distorted distorted 398 411 412 413 431 P T D 24 distorted distorted 418 432 433 434 451 P A D 25 distorted distorted 439 452 453 454 472 P C D 26 distorted distorted 459 473 474 475 491 P G D 27 distorted distorted 480 492 493 494 513 P A D 28 distorted distorted 499 514 515 516 534 P A D 29 distorted distorted 521 535 536 537 555 P C D 30 distorted distorted 542 556 557 558 574 P T D 31 distorted distorted 563 575 576 577 594 P T D 32 distorted distorted 582 595 596 597 614 P A D 33 distorted distorted 602 615 616 617 635 P T D 34 distorted distorted 622 636 637 638 ---------------------------------------------------------------------------------