ID code: '1NKC' 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 2 beta 4 9 7 30 C1' C B 3 beta 26 31 29 49 C1' G B 4 beta 45 50 48 71 C1' A B 5 beta 67 72 70 92 C1' T B 6 beta 88 93 91 112 C1' C B 7 beta 108 113 111 131 C1' A B 8 beta 127 132 130 152 C1' G B 9 beta 148 153 151 174 C1' C B 10 beta 170 175 173 193 C1' G B 11 beta 189 194 192 215 C1' C B 12 beta 211 216 214 234 C1' G B 13 beta 230 235 233 256 C1' T B 14 beta 252 257 255 276 C1' A B 15 beta 272 277 275 297 C1' C B 16 beta 293 298 296 314 C1' G C 27 beta 310 315 313 336 C1' T C 28 beta 332 337 335 356 C1' A C 29 beta 352 357 355 377 C1' C C 30 beta 373 378 376 396 C1' G C 31 beta 392 397 395 418 C1' T C 32 beta 414 419 417 438 C1' G C 33 beta 434 439 437 460 C1' C C 34 beta 456 461 459 479 C1' T C 35 beta 475 480 478 499 C1' G C 36 beta 495 500 498 521 C1' A C 37 beta 517 522 520 542 C1' T C 38 beta 538 543 541 562 C1' C C 39 beta 558 563 561 581 C1' G C 40 beta 577 582 580 603 C1' C C 41 beta 599 604 602 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 2 8 5 29 C2' C B 3 30 27 48 C2' G B 4 49 46 70 C2' A B 5 71 68 91 C2' T B 6 92 89 111 C2' C B 7 112 109 130 C2' A B 8 131 128 151 C2' G B 9 152 149 173 C2' C B 10 174 171 192 C2' G B 11 193 190 214 C2' C B 12 215 212 233 C2' G B 13 234 231 255 C2' T B 14 256 253 275 C2' A B 15 276 273 296 C2' C B 16 297 294 313 C2' G C 27 314 311 335 C2' T C 28 336 333 355 C2' A C 29 356 353 376 C2' C C 30 377 374 395 C2' G C 31 396 393 417 C2' T C 32 418 415 437 C2' G C 33 438 435 459 C2' C C 34 460 457 478 C2' T C 35 479 476 498 C2' G C 36 499 496 520 C2' A C 37 521 518 541 C2' T C 38 542 539 561 C2' C C 39 562 559 580 C2' G C 40 581 578 602 C2' C C 41 603 600 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 2 OK 3 6 7 27 C3' C B 3 OK 25 28 29 46 C3' G B 4 OK 44 47 48 68 C3' A B 5 OK 66 69 70 89 C3' T B 6 OK 87 90 91 109 C3' C B 7 OK 107 110 111 128 C3' A B 8 OK 126 129 130 149 C3' G B 9 OK 147 150 151 171 C3' C B 10 OK 169 172 173 190 C3' G B 11 OK 188 191 192 212 C3' C B 12 OK 210 213 214 231 C3' G B 13 OK 229 232 233 253 C3' T B 14 OK 251 254 255 273 C3' A B 15 OK 271 274 275 294 C3' C B 16 OK 292 295 296 311 C3' G C 27 OK 309 312 313 333 C3' T C 28 OK 331 334 335 353 C3' A C 29 OK 351 354 355 374 C3' C C 30 OK 372 375 376 393 C3' G C 31 OK 391 394 395 415 C3' T C 32 OK 413 416 417 435 C3' G C 33 OK 433 436 437 457 C3' C C 34 OK 455 458 459 476 C3' T C 35 OK 474 477 478 496 C3' G C 36 OK 494 497 498 518 C3' A C 37 OK 516 519 520 539 C3' T C 38 OK 537 540 541 559 C3' C C 39 OK 557 560 561 578 C3' G C 40 OK 576 579 580 600 C3' C C 41 OK 598 601 602 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 2 OK 5 2 4 25 C4' C B 3 OK 27 24 26 44 C4' G B 4 OK 46 43 45 66 C4' A B 5 OK 68 65 67 87 C4' T B 6 OK 89 86 88 107 C4' C B 7 OK 109 106 108 126 C4' A B 8 OK 128 125 127 147 C4' G B 9 OK 149 146 148 169 C4' C B 10 OK 171 168 170 188 C4' G B 11 OK 190 187 189 210 C4' C B 12 OK 212 209 211 229 C4' G B 13 OK 231 228 230 251 C4' T B 14 OK 253 250 252 271 C4' A B 15 OK 273 270 272 292 C4' C B 16 OK 294 291 293 309 C4' G C 27 OK 311 308 310 331 C4' T C 28 OK 333 330 332 351 C4' A C 29 OK 353 350 352 372 C4' C C 30 OK 374 371 373 391 C4' G C 31 OK 393 390 392 413 C4' T C 32 OK 415 412 414 433 C4' G C 33 OK 435 432 434 455 C4' C C 34 OK 457 454 456 474 C4' T C 35 OK 476 473 475 494 C4' G C 36 OK 496 493 495 516 C4' A C 37 OK 518 515 517 537 C4' T C 38 OK 539 536 538 557 C4' C C 39 OK 559 556 558 576 C4' G C 40 OK 578 575 577 598 C4' C C 41 OK 600 597 599 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 2 1 3 24 C5' C B 3 23 25 43 C5' G B 4 42 44 65 C5' A B 5 64 66 86 C5' T B 6 85 87 106 C5' C B 7 105 107 125 C5' A B 8 124 126 146 C5' G B 9 145 147 168 C5' C B 10 167 169 187 C5' G B 11 186 188 209 C5' C B 12 208 210 228 C5' G B 13 227 229 250 C5' T B 14 249 251 270 C5' A B 15 269 271 291 C5' C B 16 290 292 308 C5' G C 27 307 309 330 C5' T C 28 329 331 350 C5' A C 29 349 351 371 C5' C C 30 370 372 390 C5' G C 31 389 391 412 C5' T C 32 411 413 432 C5' G C 33 431 433 454 C5' C C 34 453 455 473 C5' T C 35 472 474 493 C5' G C 36 492 494 515 C5' A C 37 514 516 536 C5' T C 38 535 537 556 C5' C C 39 555 557 575 C5' G C 40 574 576 597 C5' C C 41 596 598 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 3 distorted distorted 6 21 22 23 39 P G B 4 distorted distorted 28 40 41 42 61 P A B 5 distorted distorted 47 62 63 64 82 P T B 6 distorted distorted 69 83 84 85 102 P C B 7 distorted distorted 90 103 104 105 121 P A B 8 distorted distorted 110 122 123 124 142 P G B 9 distorted distorted 129 143 144 145 164 P C B 10 distorted distorted 150 165 166 167 183 P G B 11 distorted distorted 172 184 185 186 205 P C B 12 distorted distorted 191 206 207 208 224 P G B 13 distorted distorted 213 225 226 227 246 P T B 14 distorted distorted 232 247 248 249 266 P A B 15 distorted distorted 254 267 268 269 287 P C B 16 distorted distorted 274 288 289 290 326 P T C 28 distorted distorted 312 327 328 329 346 P A C 29 distorted distorted 334 347 348 349 367 P C C 30 distorted distorted 354 368 369 370 386 P G C 31 distorted distorted 375 387 388 389 408 P T C 32 distorted distorted 394 409 410 411 428 P G C 33 distorted distorted 416 429 430 431 450 P C C 34 distorted distorted 436 451 452 453 469 P T C 35 distorted distorted 458 470 471 472 489 P G C 36 distorted distorted 477 490 491 492 511 P A C 37 distorted distorted 497 512 513 514 532 P T C 38 distorted distorted 519 533 534 535 552 P C C 39 distorted distorted 540 553 554 555 571 P G C 40 distorted distorted 560 572 573 574 593 P C C 41 distorted distorted 579 594 595 596 ---------------------------------------------------------------------------------