ID code: '1NJX' 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' A B 21 beta 45 50 48 70 C1' T B 22 beta 66 71 69 90 C1' G B 23 beta 86 91 89 112 C1' A B 24 beta 108 113 111 133 C1' T B 25 beta 129 134 132 153 C1' G B 26 beta 149 154 152 175 C1' C B 27 beta 171 176 174 194 C1' T B 28 beta 190 195 193 214 C1' T B 29 beta 210 215 213 235 C1' G C 4 beta 231 236 234 257 C1' A C 5 beta 253 258 256 278 C1' G C 6 beta 274 279 277 300 C1' C C 7 beta 296 301 299 319 C1' A C 8 beta 315 320 318 340 C1' T C 9 beta 336 341 339 360 C1' C C 10 beta 356 361 359 379 C1' A C 11 beta 375 380 378 400 C1' T C 12 beta 396 401 399 420 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' A B 21 49 46 69 C2' T B 22 70 67 89 C2' G B 23 90 87 111 C2' A B 24 112 109 132 C2' T B 25 133 130 152 C2' G B 26 153 150 174 C2' C B 27 175 172 193 C2' T B 28 194 191 213 C2' T B 29 214 211 234 C2' G C 4 235 232 256 C2' A C 5 257 254 277 C2' G C 6 278 275 299 C2' C C 7 300 297 318 C2' A C 8 319 316 339 C2' T C 9 340 337 359 C2' C C 10 360 357 378 C2' A C 11 379 376 399 C2' T C 12 400 397 419 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' A B 21 OK 44 47 48 67 C3' T B 22 OK 65 68 69 87 C3' G B 23 OK 85 88 89 109 C3' A B 24 OK 107 110 111 130 C3' T B 25 OK 128 131 132 150 C3' G B 26 OK 148 151 152 172 C3' C B 27 OK 170 173 174 191 C3' T B 28 OK 189 192 193 211 C3' T B 29 OK 209 212 213 232 C3' G C 4 OK 230 233 234 254 C3' A C 5 OK 252 255 256 275 C3' G C 6 OK 273 276 277 297 C3' C C 7 OK 295 298 299 316 C3' A C 8 OK 314 317 318 337 C3' T C 9 OK 335 338 339 357 C3' C C 10 OK 355 358 359 376 C3' A C 11 OK 374 377 378 397 C3' T C 12 OK 395 398 399 417 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' A B 21 OK 46 43 45 65 C4' T B 22 OK 67 64 66 85 C4' G B 23 OK 87 84 86 107 C4' A B 24 OK 109 106 108 128 C4' T B 25 OK 130 127 129 148 C4' G B 26 OK 150 147 149 170 C4' C B 27 OK 172 169 171 189 C4' T B 28 OK 191 188 190 209 C4' T B 29 OK 211 208 210 230 C4' G C 4 OK 232 229 231 252 C4' A C 5 OK 254 251 253 273 C4' G C 6 OK 275 272 274 295 C4' C C 7 OK 297 294 296 314 C4' A C 8 OK 316 313 315 335 C4' T C 9 OK 337 334 336 355 C4' C C 10 OK 357 354 356 374 C4' A C 11 OK 376 373 375 395 C4' T C 12 OK 397 394 396 415 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' A B 21 42 44 64 C5' T B 22 63 65 84 C5' G B 23 83 85 106 C5' A B 24 105 107 127 C5' T B 25 126 128 147 C5' G B 26 146 148 169 C5' C B 27 168 170 188 C5' T B 28 187 189 208 C5' T B 29 207 209 229 C5' G C 4 228 230 251 C5' A C 5 250 252 272 C5' G C 6 271 273 294 C5' C C 7 293 295 313 C5' A C 8 312 314 334 C5' T C 9 333 335 354 C5' C C 10 353 355 373 C5' A C 11 372 374 394 C5' T C 12 393 395 414 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 A B 21 distorted distorted 28 40 41 42 60 P T B 22 distorted distorted 47 61 62 63 80 P G B 23 distorted distorted 68 81 82 83 102 P A B 24 distorted distorted 88 103 104 105 123 P T B 25 distorted distorted 110 124 125 126 143 P G B 26 distorted distorted 131 144 145 146 165 P C B 27 distorted distorted 151 166 167 168 184 P T B 28 distorted distorted 173 185 186 187 204 P T B 29 distorted distorted 192 205 206 207 225 P G C 4 distorted distorted 226 227 228 247 P A C 5 distorted distorted 233 248 249 250 268 P G C 6 distorted distorted 255 269 270 271 290 P C C 7 distorted distorted 276 291 292 293 309 P A C 8 distorted distorted 298 310 311 312 330 P T C 9 distorted distorted 317 331 332 333 350 P C C 10 distorted distorted 338 351 352 353 369 P A C 11 distorted distorted 358 370 371 372 390 P T C 12 distorted distorted 377 391 392 393 410 P G C 13 distorted distorted 398 411 412 413 432 P C C 14 distorted distorted 418 433 434 435 ---------------------------------------------------------------------------------