ID code: '1LO1' 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' C B 2 beta 26 31 29 49 C1' T B 3 beta 45 50 48 69 C1' C B 4 beta 65 70 68 88 C1' A B 5 beta 84 89 87 109 C1' A B 6 beta 105 110 108 130 C1' G B 7 beta 126 131 129 152 C1' G B 8 beta 148 153 151 174 C1' T B 9 beta 170 175 173 194 C1' C B 10 beta 190 195 193 213 C1' A B 11 beta 209 214 212 234 C1' C B 12 beta 230 235 233 253 C1' G B 13 beta 249 254 252 273 C1' C C 14 beta 269 274 272 292 C1' G C 15 beta 288 293 291 314 C1' T C 16 beta 310 315 313 334 C1' G C 17 beta 330 335 333 356 C1' A C 18 beta 352 357 355 377 C1' C C 19 beta 373 378 376 396 C1' C C 20 beta 392 397 395 415 C1' T C 21 beta 411 416 414 435 C1' T C 22 beta 431 436 434 455 C1' G C 23 beta 451 456 454 477 C1' A C 24 beta 473 478 476 498 C1' G C 25 beta 494 499 497 520 C1' C C 26 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' G B 1 8 5 29 C2' C B 2 30 27 48 C2' T B 3 49 46 68 C2' C B 4 69 66 87 C2' A B 5 88 85 108 C2' A B 6 109 106 129 C2' G B 7 130 127 151 C2' G B 8 152 149 173 C2' T B 9 174 171 193 C2' C B 10 194 191 212 C2' A B 11 213 210 233 C2' C B 12 234 231 252 C2' G B 13 253 250 272 C2' C C 14 273 270 291 C2' G C 15 292 289 313 C2' T C 16 314 311 333 C2' G C 17 334 331 355 C2' A C 18 356 353 376 C2' C C 19 377 374 395 C2' C C 20 396 393 414 C2' T C 21 415 412 434 C2' T C 22 435 432 454 C2' G C 23 455 452 476 C2' A C 24 477 474 497 C2' G C 25 498 495 519 C2' C C 26 520 517 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 1 OK 3 6 7 27 C3' C B 2 OK 25 28 29 46 C3' T B 3 OK 44 47 48 66 C3' C B 4 OK 64 67 68 85 C3' A B 5 OK 83 86 87 106 C3' A B 6 OK 104 107 108 127 C3' G B 7 OK 125 128 129 149 C3' G B 8 OK 147 150 151 171 C3' T B 9 OK 169 172 173 191 C3' C B 10 OK 189 192 193 210 C3' A B 11 OK 208 211 212 231 C3' C B 12 OK 229 232 233 250 C3' G B 13 OK 248 251 252 270 C3' C C 14 OK 268 271 272 289 C3' G C 15 OK 287 290 291 311 C3' T C 16 OK 309 312 313 331 C3' G C 17 OK 329 332 333 353 C3' A C 18 OK 351 354 355 374 C3' C C 19 OK 372 375 376 393 C3' C C 20 OK 391 394 395 412 C3' T C 21 OK 410 413 414 432 C3' T C 22 OK 430 433 434 452 C3' G C 23 OK 450 453 454 474 C3' A C 24 OK 472 475 476 495 C3' G C 25 OK 493 496 497 517 C3' C C 26 OK 515 518 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 1 OK 5 2 4 25 C4' C B 2 OK 27 24 26 44 C4' T B 3 OK 46 43 45 64 C4' C B 4 OK 66 63 65 83 C4' A B 5 OK 85 82 84 104 C4' A B 6 OK 106 103 105 125 C4' G B 7 OK 127 124 126 147 C4' G B 8 OK 149 146 148 169 C4' T B 9 OK 171 168 170 189 C4' C B 10 OK 191 188 190 208 C4' A B 11 OK 210 207 209 229 C4' C B 12 OK 231 228 230 248 C4' G B 13 OK 250 247 249 268 C4' C C 14 OK 270 267 269 287 C4' G C 15 OK 289 286 288 309 C4' T C 16 OK 311 308 310 329 C4' G C 17 OK 331 328 330 351 C4' A C 18 OK 353 350 352 372 C4' C C 19 OK 374 371 373 391 C4' C C 20 OK 393 390 392 410 C4' T C 21 OK 412 409 411 430 C4' T C 22 OK 432 429 431 450 C4' G C 23 OK 452 449 451 472 C4' A C 24 OK 474 471 473 493 C4' G C 25 OK 495 492 494 515 C4' C C 26 OK 517 514 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 1 1 3 24 C5' C B 2 23 25 43 C5' T B 3 42 44 63 C5' C B 4 62 64 82 C5' A B 5 81 83 103 C5' A B 6 102 104 124 C5' G B 7 123 125 146 C5' G B 8 145 147 168 C5' T B 9 167 169 188 C5' C B 10 187 189 207 C5' A B 11 206 208 228 C5' C B 12 227 229 247 C5' G B 13 246 248 267 C5' C C 14 266 268 286 C5' G C 15 285 287 308 C5' T C 16 307 309 328 C5' G C 17 327 329 350 C5' A C 18 349 351 371 C5' C C 19 370 372 390 C5' C C 20 389 391 409 C5' T C 21 408 410 429 C5' T C 22 428 430 449 C5' G C 23 448 450 471 C5' A C 24 470 472 492 C5' G C 25 491 493 514 C5' C C 26 513 515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 2 distorted distorted 6 21 22 23 39 P T B 3 distorted distorted 28 40 41 42 59 P C B 4 distorted distorted 47 60 61 62 78 P A B 5 distorted distorted 67 79 80 81 99 P A B 6 distorted distorted 86 100 101 102 120 P G B 7 distorted distorted 107 121 122 123 142 P G B 8 distorted distorted 128 143 144 145 164 P T B 9 distorted distorted 150 165 166 167 184 P C B 10 distorted distorted 172 185 186 187 203 P A B 11 distorted distorted 192 204 205 206 224 P C B 12 distorted distorted 211 225 226 227 243 P G B 13 distorted distorted 232 244 245 246 282 P G C 15 distorted distorted 271 283 284 285 304 P T C 16 distorted distorted 290 305 306 307 324 P G C 17 distorted distorted 312 325 326 327 346 P A C 18 distorted distorted 332 347 348 349 367 P C C 19 distorted distorted 354 368 369 370 386 P C C 20 distorted distorted 375 387 388 389 405 P T C 21 distorted distorted 394 406 407 408 425 P T C 22 distorted distorted 413 426 427 428 445 P G C 23 distorted distorted 433 446 447 448 467 P A C 24 distorted distorted 453 468 469 470 488 P G C 25 distorted distorted 475 489 490 491 510 P C C 26 distorted distorted 496 511 512 513 ---------------------------------------------------------------------------------