ID code: '1NK8' 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' G B 26 beta 148 153 151 174 C1' C B 27 beta 170 175 173 193 C1' G B 28 beta 189 194 192 215 C1' C B 29 beta 211 216 214 235 C1' G C 4 beta 231 236 234 257 C1' T C 5 beta 253 258 256 277 C1' G C 6 beta 273 278 276 299 C1' C C 7 beta 295 300 298 318 C1' T C 8 beta 314 319 317 338 C1' G C 9 beta 334 339 337 360 C1' A C 10 beta 356 361 359 381 C1' T C 11 beta 377 382 380 401 C1' C C 12 beta 397 402 400 420 C1' G C 13 beta 416 421 419 442 C1' C C 14 beta 438 443 441 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G B 26 152 149 173 C2' C B 27 174 171 192 C2' G B 28 193 190 214 C2' C B 29 215 212 234 C2' G C 4 235 232 256 C2' T C 5 257 254 276 C2' G C 6 277 274 298 C2' C C 7 299 296 317 C2' T C 8 318 315 337 C2' G C 9 338 335 359 C2' A C 10 360 357 380 C2' T C 11 381 378 400 C2' C C 12 401 398 419 C2' G C 13 420 417 441 C2' C C 14 442 439 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G B 26 OK 147 150 151 171 C3' C B 27 OK 169 172 173 190 C3' G B 28 OK 188 191 192 212 C3' C B 29 OK 210 213 214 232 C3' G C 4 OK 230 233 234 254 C3' T C 5 OK 252 255 256 274 C3' G C 6 OK 272 275 276 296 C3' C C 7 OK 294 297 298 315 C3' T C 8 OK 313 316 317 335 C3' G C 9 OK 333 336 337 357 C3' A C 10 OK 355 358 359 378 C3' T C 11 OK 376 379 380 398 C3' C C 12 OK 396 399 400 417 C3' G C 13 OK 415 418 419 439 C3' C C 14 OK 437 440 441 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G B 26 OK 149 146 148 169 C4' C B 27 OK 171 168 170 188 C4' G B 28 OK 190 187 189 210 C4' C B 29 OK 212 209 211 230 C4' G C 4 OK 232 229 231 252 C4' T C 5 OK 254 251 253 272 C4' G C 6 OK 274 271 273 294 C4' C C 7 OK 296 293 295 313 C4' T C 8 OK 315 312 314 333 C4' G C 9 OK 335 332 334 355 C4' A C 10 OK 357 354 356 376 C4' T C 11 OK 378 375 377 396 C4' C C 12 OK 398 395 397 415 C4' G C 13 OK 417 414 416 437 C4' C C 14 OK 439 436 438 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G B 26 145 147 168 C5' C B 27 167 169 187 C5' G B 28 186 188 209 C5' C B 29 208 210 229 C5' G C 4 228 230 251 C5' T C 5 250 252 271 C5' G C 6 270 272 293 C5' C C 7 292 294 312 C5' T C 8 311 313 332 C5' G C 9 331 333 354 C5' A C 10 353 355 375 C5' T C 11 374 376 395 C5' C C 12 394 396 414 C5' G C 13 413 415 436 C5' C C 14 435 437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G B 26 distorted distorted 129 143 144 145 164 P C B 27 distorted distorted 150 165 166 167 183 P G B 28 distorted distorted 172 184 185 186 205 P C B 29 distorted distorted 191 206 207 208 225 P G C 4 distorted distorted 226 227 228 247 P T C 5 distorted distorted 233 248 249 250 267 P G C 6 distorted distorted 255 268 269 270 289 P C C 7 distorted distorted 275 290 291 292 308 P T C 8 distorted distorted 297 309 310 311 328 P G C 9 distorted distorted 316 329 330 331 350 P A C 10 distorted distorted 336 351 352 353 371 P T C 11 distorted distorted 358 372 373 374 391 P C C 12 distorted distorted 379 392 393 394 410 P G C 13 distorted distorted 399 411 412 413 432 P C C 14 distorted distorted 418 433 434 435 ---------------------------------------------------------------------------------