ID code: '1HJC' 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 B 12 beta 7 12 10 32 C1' A B 13 beta 28 33 31 53 C1' C B 14 beta 49 54 52 72 C1' T B 15 beta 68 73 71 92 C1' C B 16 beta 88 93 91 111 C1' T B 17 beta 107 112 110 131 C1' G B 18 beta 127 132 130 153 C1' T B 19 beta 149 154 152 173 C1' G B 20 beta 169 174 172 195 C1' G B 21 beta 191 196 194 217 C1' T B 22 beta 213 218 216 237 C1' T B 23 beta 233 238 236 257 C1' G B 24 beta 253 258 256 279 C1' C B 25 beta 275 280 278 298 C1' G B 26 beta 294 299 297 321 C1' C C 2 beta 317 322 320 340 C1' G C 3 beta 336 341 339 362 C1' C C 4 beta 358 363 361 381 C1' A C 5 beta 377 382 380 402 C1' A C 6 beta 398 403 401 423 C1' C C 7 beta 419 424 422 442 C1' C C 8 beta 438 443 441 461 C1' A C 9 beta 457 462 460 482 C1' C C 10 beta 478 483 481 501 C1' A C 11 beta 497 502 500 522 C1' G C 12 beta 518 523 521 544 C1' A C 13 beta 540 545 543 565 C1' G C 14 beta 561 566 564 587 C1' T C 15 beta 583 588 586 607 C1' T C 16 beta 603 608 606 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A B 12 11 8 31 C2' A B 13 32 29 52 C2' C B 14 53 50 71 C2' T B 15 72 69 91 C2' C B 16 92 89 110 C2' T B 17 111 108 130 C2' G B 18 131 128 152 C2' T B 19 153 150 172 C2' G B 20 173 170 194 C2' G B 21 195 192 216 C2' T B 22 217 214 236 C2' T B 23 237 234 256 C2' G B 24 257 254 278 C2' C B 25 279 276 297 C2' G B 26 298 295 320 C2' C C 2 321 318 339 C2' G C 3 340 337 361 C2' C C 4 362 359 380 C2' A C 5 381 378 401 C2' A C 6 402 399 422 C2' C C 7 423 420 441 C2' C C 8 442 439 460 C2' A C 9 461 458 481 C2' C C 10 482 479 500 C2' A C 11 501 498 521 C2' G C 12 522 519 543 C2' A C 13 544 541 564 C2' G C 14 565 562 586 C2' T C 15 587 584 606 C2' T C 16 607 604 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A B 12 OK 6 9 10 29 C3' A B 13 OK 27 30 31 50 C3' C B 14 OK 48 51 52 69 C3' T B 15 OK 67 70 71 89 C3' C B 16 OK 87 90 91 108 C3' T B 17 OK 106 109 110 128 C3' G B 18 OK 126 129 130 150 C3' T B 19 OK 148 151 152 170 C3' G B 20 OK 168 171 172 192 C3' G B 21 OK 190 193 194 214 C3' T B 22 OK 212 215 216 234 C3' T B 23 OK 232 235 236 254 C3' G B 24 OK 252 255 256 276 C3' C B 25 OK 274 277 278 295 C3' G B 26 OK 293 296 297 318 C3' C C 2 OK 316 319 320 337 C3' G C 3 OK 335 338 339 359 C3' C C 4 OK 357 360 361 378 C3' A C 5 OK 376 379 380 399 C3' A C 6 OK 397 400 401 420 C3' C C 7 OK 418 421 422 439 C3' C C 8 OK 437 440 441 458 C3' A C 9 OK 456 459 460 479 C3' C C 10 OK 477 480 481 498 C3' A C 11 OK 496 499 500 519 C3' G C 12 OK 517 520 521 541 C3' A C 13 OK 539 542 543 562 C3' G C 14 OK 560 563 564 584 C3' T C 15 OK 582 585 586 604 C3' T C 16 OK 602 605 606 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A B 12 OK 8 5 7 27 C4' A B 13 OK 29 26 28 48 C4' C B 14 OK 50 47 49 67 C4' T B 15 OK 69 66 68 87 C4' C B 16 OK 89 86 88 106 C4' T B 17 OK 108 105 107 126 C4' G B 18 OK 128 125 127 148 C4' T B 19 OK 150 147 149 168 C4' G B 20 OK 170 167 169 190 C4' G B 21 OK 192 189 191 212 C4' T B 22 OK 214 211 213 232 C4' T B 23 OK 234 231 233 252 C4' G B 24 OK 254 251 253 274 C4' C B 25 OK 276 273 275 293 C4' G B 26 OK 295 292 294 316 C4' C C 2 OK 318 315 317 335 C4' G C 3 OK 337 334 336 357 C4' C C 4 OK 359 356 358 376 C4' A C 5 OK 378 375 377 397 C4' A C 6 OK 399 396 398 418 C4' C C 7 OK 420 417 419 437 C4' C C 8 OK 439 436 438 456 C4' A C 9 OK 458 455 457 477 C4' C C 10 OK 479 476 478 496 C4' A C 11 OK 498 495 497 517 C4' G C 12 OK 519 516 518 539 C4' A C 13 OK 541 538 540 560 C4' G C 14 OK 562 559 561 582 C4' T C 15 OK 584 581 583 602 C4' T C 16 OK 604 601 603 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A B 12 4 6 26 C5' A B 13 25 27 47 C5' C B 14 46 48 66 C5' T B 15 65 67 86 C5' C B 16 85 87 105 C5' T B 17 104 106 125 C5' G B 18 124 126 147 C5' T B 19 146 148 167 C5' G B 20 166 168 189 C5' G B 21 188 190 211 C5' T B 22 210 212 231 C5' T B 23 230 232 251 C5' G B 24 250 252 273 C5' C B 25 272 274 292 C5' G B 26 291 293 315 C5' C C 2 314 316 334 C5' G C 3 333 335 356 C5' C C 4 355 357 375 C5' A C 5 374 376 396 C5' A C 6 395 397 417 C5' C C 7 416 418 436 C5' C C 8 435 437 455 C5' A C 9 454 456 476 C5' C C 10 475 477 495 C5' A C 11 494 496 516 C5' G C 12 515 517 538 C5' A C 13 537 539 559 C5' G C 14 558 560 581 C5' T C 15 580 582 601 C5' T C 16 600 602 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A B 12 distorted distorted 2 3 4 22 P A B 13 distorted distorted 9 23 24 25 43 P C B 14 distorted distorted 30 44 45 46 62 P T B 15 distorted distorted 51 63 64 65 82 P C B 16 distorted distorted 70 83 84 85 101 P T B 17 distorted distorted 90 102 103 104 121 P G B 18 distorted distorted 109 122 123 124 143 P T B 19 distorted distorted 129 144 145 146 163 P G B 20 distorted distorted 151 164 165 166 185 P G B 21 distorted distorted 171 186 187 188 207 P T B 22 distorted distorted 193 208 209 210 227 P T B 23 distorted distorted 215 228 229 230 247 P G B 24 distorted distorted 235 248 249 250 269 P C B 25 distorted distorted 255 270 271 272 288 P G B 26 distorted distorted 277 289 290 291 311 P C C 2 distorted distorted 312 313 314 330 P G C 3 distorted distorted 319 331 332 333 352 P C C 4 distorted distorted 338 353 354 355 371 P A C 5 distorted distorted 360 372 373 374 392 P A C 6 distorted distorted 379 393 394 395 413 P C C 7 distorted distorted 400 414 415 416 432 P C C 8 distorted distorted 421 433 434 435 451 P A C 9 distorted distorted 440 452 453 454 472 P C C 10 distorted distorted 459 473 474 475 491 P A C 11 distorted distorted 480 492 493 494 512 P G C 12 distorted distorted 499 513 514 515 534 P A C 13 distorted distorted 520 535 536 537 555 P G C 14 distorted distorted 542 556 557 558 577 P T C 15 distorted distorted 563 578 579 580 597 P T C 16 distorted distorted 585 598 599 600 ---------------------------------------------------------------------------------