ID code: '1L3U' 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 19 beta 4 9 7 30 C1' C B 20 beta 26 31 29 49 C1' G B 21 beta 45 50 48 71 C1' A B 22 beta 67 72 70 92 C1' T B 23 beta 88 93 91 112 C1' C B 24 beta 108 113 111 131 C1' A B 25 beta 127 132 130 152 C1' C B 26 beta 148 153 151 171 C1' G B 27 beta 167 172 170 193 C1' T B 28 beta 189 194 192 213 C1' A B 29 beta 209 214 212 235 C1' T C 4 beta 231 236 234 255 C1' A C 5 beta 251 256 254 276 C1' C C 6 beta 272 277 275 295 C1' G C 7 beta 291 296 294 317 C1' T C 8 beta 313 318 316 337 C1' G C 9 beta 333 338 336 359 C1' A C 10 beta 355 360 358 380 C1' T C 11 beta 376 381 379 400 C1' C C 12 beta 396 401 399 419 C1' G C 13 beta 415 420 418 441 C1' C C 14 beta 437 442 440 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 19 8 5 29 C2' C B 20 30 27 48 C2' G B 21 49 46 70 C2' A B 22 71 68 91 C2' T B 23 92 89 111 C2' C B 24 112 109 130 C2' A B 25 131 128 151 C2' C B 26 152 149 170 C2' G B 27 171 168 192 C2' T B 28 193 190 212 C2' A B 29 213 210 234 C2' T C 4 235 232 254 C2' A C 5 255 252 275 C2' C C 6 276 273 294 C2' G C 7 295 292 316 C2' T C 8 317 314 336 C2' G C 9 337 334 358 C2' A C 10 359 356 379 C2' T C 11 380 377 399 C2' C C 12 400 397 418 C2' G C 13 419 416 440 C2' C C 14 441 438 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 19 OK 3 6 7 27 C3' C B 20 OK 25 28 29 46 C3' G B 21 OK 44 47 48 68 C3' A B 22 OK 66 69 70 89 C3' T B 23 OK 87 90 91 109 C3' C B 24 OK 107 110 111 128 C3' A B 25 OK 126 129 130 149 C3' C B 26 OK 147 150 151 168 C3' G B 27 OK 166 169 170 190 C3' T B 28 OK 188 191 192 210 C3' A B 29 OK 208 211 212 232 C3' T C 4 OK 230 233 234 252 C3' A C 5 OK 250 253 254 273 C3' C C 6 OK 271 274 275 292 C3' G C 7 OK 290 293 294 314 C3' T C 8 OK 312 315 316 334 C3' G C 9 OK 332 335 336 356 C3' A C 10 OK 354 357 358 377 C3' T C 11 OK 375 378 379 397 C3' C C 12 OK 395 398 399 416 C3' G C 13 OK 414 417 418 438 C3' C C 14 OK 436 439 440 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 19 OK 5 2 4 25 C4' C B 20 OK 27 24 26 44 C4' G B 21 OK 46 43 45 66 C4' A B 22 OK 68 65 67 87 C4' T B 23 OK 89 86 88 107 C4' C B 24 OK 109 106 108 126 C4' A B 25 OK 128 125 127 147 C4' C B 26 OK 149 146 148 166 C4' G B 27 OK 168 165 167 188 C4' T B 28 OK 190 187 189 208 C4' A B 29 OK 210 207 209 230 C4' T C 4 OK 232 229 231 250 C4' A C 5 OK 252 249 251 271 C4' C C 6 OK 273 270 272 290 C4' G C 7 OK 292 289 291 312 C4' T C 8 OK 314 311 313 332 C4' G C 9 OK 334 331 333 354 C4' A C 10 OK 356 353 355 375 C4' T C 11 OK 377 374 376 395 C4' C C 12 OK 397 394 396 414 C4' G C 13 OK 416 413 415 436 C4' C C 14 OK 438 435 437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 19 1 3 24 C5' C B 20 23 25 43 C5' G B 21 42 44 65 C5' A B 22 64 66 86 C5' T B 23 85 87 106 C5' C B 24 105 107 125 C5' A B 25 124 126 146 C5' C B 26 145 147 165 C5' G B 27 164 166 187 C5' T B 28 186 188 207 C5' A B 29 206 208 229 C5' T C 4 228 230 249 C5' A C 5 248 250 270 C5' C C 6 269 271 289 C5' G C 7 288 290 311 C5' T C 8 310 312 331 C5' G C 9 330 332 353 C5' A C 10 352 354 374 C5' T C 11 373 375 394 C5' C C 12 393 395 413 C5' G C 13 412 414 435 C5' C C 14 434 436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 20 distorted distorted 6 21 22 23 39 P G B 21 distorted distorted 28 40 41 42 61 P A B 22 distorted distorted 47 62 63 64 82 P T B 23 distorted distorted 69 83 84 85 102 P C B 24 distorted distorted 90 103 104 105 121 P A B 25 distorted distorted 110 122 123 124 142 P C B 26 distorted distorted 129 143 144 145 161 P G B 27 distorted distorted 150 162 163 164 183 P T B 28 distorted distorted 169 184 185 186 203 P A B 29 distorted distorted 191 204 205 206 225 P T C 4 distorted distorted 226 227 228 245 P A C 5 distorted distorted 233 246 247 248 266 P C C 6 distorted distorted 253 267 268 269 285 P G C 7 distorted distorted 274 286 287 288 307 P T C 8 distorted distorted 293 308 309 310 327 P G C 9 distorted distorted 315 328 329 330 349 P A C 10 distorted distorted 335 350 351 352 370 P T C 11 distorted distorted 357 371 372 373 390 P C C 12 distorted distorted 378 391 392 393 409 P G C 13 distorted distorted 398 410 411 412 431 P C C 14 distorted distorted 417 432 433 434 ---------------------------------------------------------------------------------