ID code: '1IG7' 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' C B 4 beta 4 9 7 27 C1' A B 5 beta 23 28 26 48 C1' C B 6 beta 44 49 47 67 C1' T B 7 beta 63 68 66 87 C1' A B 8 beta 83 88 86 108 C1' A B 9 beta 104 109 107 129 C1' T B 10 beta 125 130 128 149 C1' T B 11 beta 145 150 148 169 C1' G B 12 beta 165 170 168 191 C1' A B 13 beta 187 192 190 212 C1' A B 14 beta 208 213 211 233 C1' G B 15 beta 229 234 232 255 C1' G B 16 beta 251 256 254 278 C1' C C 18 beta 274 279 277 297 C1' C C 19 beta 293 298 296 316 C1' T C 20 beta 312 317 315 336 C1' T C 21 beta 332 337 335 356 C1' C C 22 beta 352 357 355 375 C1' A C 23 beta 371 376 374 396 C1' A C 24 beta 392 397 395 417 C1' T C 25 beta 413 418 416 437 C1' T C 26 beta 433 438 436 457 C1' A C 27 beta 453 458 456 478 C1' G C 28 beta 474 479 477 500 C1' T C 29 beta 496 501 499 520 C1' G C 30 beta 516 521 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C B 4 8 5 26 C2' A B 5 27 24 47 C2' C B 6 48 45 66 C2' T B 7 67 64 86 C2' A B 8 87 84 107 C2' A B 9 108 105 128 C2' T B 10 129 126 148 C2' T B 11 149 146 168 C2' G B 12 169 166 190 C2' A B 13 191 188 211 C2' A B 14 212 209 232 C2' G B 15 233 230 254 C2' G B 16 255 252 277 C2' C C 18 278 275 296 C2' C C 19 297 294 315 C2' T C 20 316 313 335 C2' T C 21 336 333 355 C2' C C 22 356 353 374 C2' A C 23 375 372 395 C2' A C 24 396 393 416 C2' T C 25 417 414 436 C2' T C 26 437 434 456 C2' A C 27 457 454 477 C2' G C 28 478 475 499 C2' T C 29 500 497 519 C2' G C 30 520 517 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C B 4 OK 3 6 7 24 C3' A B 5 OK 22 25 26 45 C3' C B 6 OK 43 46 47 64 C3' T B 7 OK 62 65 66 84 C3' A B 8 OK 82 85 86 105 C3' A B 9 OK 103 106 107 126 C3' T B 10 OK 124 127 128 146 C3' T B 11 OK 144 147 148 166 C3' G B 12 OK 164 167 168 188 C3' A B 13 OK 186 189 190 209 C3' A B 14 OK 207 210 211 230 C3' G B 15 OK 228 231 232 252 C3' G B 16 OK 250 253 254 275 C3' C C 18 OK 273 276 277 294 C3' C C 19 OK 292 295 296 313 C3' T C 20 OK 311 314 315 333 C3' T C 21 OK 331 334 335 353 C3' C C 22 OK 351 354 355 372 C3' A C 23 OK 370 373 374 393 C3' A C 24 OK 391 394 395 414 C3' T C 25 OK 412 415 416 434 C3' T C 26 OK 432 435 436 454 C3' A C 27 OK 452 455 456 475 C3' G C 28 OK 473 476 477 497 C3' T C 29 OK 495 498 499 517 C3' G C 30 OK 515 518 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C B 4 OK 5 2 4 22 C4' A B 5 OK 24 21 23 43 C4' C B 6 OK 45 42 44 62 C4' T B 7 OK 64 61 63 82 C4' A B 8 OK 84 81 83 103 C4' A B 9 OK 105 102 104 124 C4' T B 10 OK 126 123 125 144 C4' T B 11 OK 146 143 145 164 C4' G B 12 OK 166 163 165 186 C4' A B 13 OK 188 185 187 207 C4' A B 14 OK 209 206 208 228 C4' G B 15 OK 230 227 229 250 C4' G B 16 OK 252 249 251 273 C4' C C 18 OK 275 272 274 292 C4' C C 19 OK 294 291 293 311 C4' T C 20 OK 313 310 312 331 C4' T C 21 OK 333 330 332 351 C4' C C 22 OK 353 350 352 370 C4' A C 23 OK 372 369 371 391 C4' A C 24 OK 393 390 392 412 C4' T C 25 OK 414 411 413 432 C4' T C 26 OK 434 431 433 452 C4' A C 27 OK 454 451 453 473 C4' G C 28 OK 475 472 474 495 C4' T C 29 OK 497 494 496 515 C4' G C 30 OK 517 514 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C B 4 1 3 21 C5' A B 5 20 22 42 C5' C B 6 41 43 61 C5' T B 7 60 62 81 C5' A B 8 80 82 102 C5' A B 9 101 103 123 C5' T B 10 122 124 143 C5' T B 11 142 144 163 C5' G B 12 162 164 185 C5' A B 13 184 186 206 C5' A B 14 205 207 227 C5' G B 15 226 228 249 C5' G B 16 248 250 272 C5' C C 18 271 273 291 C5' C C 19 290 292 310 C5' T C 20 309 311 330 C5' T C 21 329 331 350 C5' C C 22 349 351 369 C5' A C 23 368 370 390 C5' A C 24 389 391 411 C5' T C 25 410 412 431 C5' T C 26 430 432 451 C5' A C 27 450 452 472 C5' G C 28 471 473 494 C5' T C 29 493 495 514 C5' G C 30 513 515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A B 5 distorted distorted 6 18 19 20 38 P C B 6 distorted distorted 25 39 40 41 57 P T B 7 distorted distorted 46 58 59 60 77 P A B 8 distorted distorted 65 78 79 80 98 P A B 9 distorted distorted 85 99 100 101 119 P T B 10 distorted distorted 106 120 121 122 139 P T B 11 distorted distorted 127 140 141 142 159 P G B 12 distorted distorted 147 160 161 162 181 P A B 13 distorted distorted 167 182 183 184 202 P A B 14 distorted distorted 189 203 204 205 223 P G B 15 distorted distorted 210 224 225 226 245 P G B 16 distorted distorted 231 246 247 248 268 P C C 18 distorted distorted 269 270 271 287 P C C 19 distorted distorted 276 288 289 290 306 P T C 20 distorted distorted 295 307 308 309 326 P T C 21 distorted distorted 314 327 328 329 346 P C C 22 distorted distorted 334 347 348 349 365 P A C 23 distorted distorted 354 366 367 368 386 P A C 24 distorted distorted 373 387 388 389 407 P T C 25 distorted distorted 394 408 409 410 427 P T C 26 distorted distorted 415 428 429 430 447 P A C 27 distorted distorted 435 448 449 450 468 P G C 28 distorted distorted 455 469 470 471 490 P T C 29 distorted distorted 476 491 492 493 510 P G C 30 distorted distorted 498 511 512 513 ---------------------------------------------------------------------------------