ID code: '1L3T' 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 20 beta 4 9 7 30 C1' C B 21 beta 26 31 29 49 C1' G B 22 beta 45 50 48 71 C1' A B 23 beta 67 72 70 92 C1' T B 24 beta 88 93 91 112 C1' C B 25 beta 108 113 111 131 C1' A B 26 beta 127 132 130 152 C1' C B 27 beta 148 153 151 171 C1' G B 28 beta 167 172 170 193 C1' T B 29 beta 189 194 192 214 C1' A C 4 beta 210 215 213 235 C1' C C 5 beta 231 236 234 254 C1' G C 6 beta 250 255 253 276 C1' T C 7 beta 272 277 275 296 C1' G C 8 beta 292 297 295 318 C1' A C 9 beta 314 319 317 339 C1' T C 10 beta 335 340 338 359 C1' C C 11 beta 355 360 358 378 C1' G C 12 beta 374 379 377 400 C1' C C 13 beta 396 401 399 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 20 8 5 29 C2' C B 21 30 27 48 C2' G B 22 49 46 70 C2' A B 23 71 68 91 C2' T B 24 92 89 111 C2' C B 25 112 109 130 C2' A B 26 131 128 151 C2' C B 27 152 149 170 C2' G B 28 171 168 192 C2' T B 29 193 190 213 C2' A C 4 214 211 234 C2' C C 5 235 232 253 C2' G C 6 254 251 275 C2' T C 7 276 273 295 C2' G C 8 296 293 317 C2' A C 9 318 315 338 C2' T C 10 339 336 358 C2' C C 11 359 356 377 C2' G C 12 378 375 399 C2' C C 13 400 397 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 20 OK 3 6 7 27 C3' C B 21 OK 25 28 29 46 C3' G B 22 OK 44 47 48 68 C3' A B 23 OK 66 69 70 89 C3' T B 24 OK 87 90 91 109 C3' C B 25 OK 107 110 111 128 C3' A B 26 OK 126 129 130 149 C3' C B 27 OK 147 150 151 168 C3' G B 28 OK 166 169 170 190 C3' T B 29 OK 188 191 192 211 C3' A C 4 OK 209 212 213 232 C3' C C 5 OK 230 233 234 251 C3' G C 6 OK 249 252 253 273 C3' T C 7 OK 271 274 275 293 C3' G C 8 OK 291 294 295 315 C3' A C 9 OK 313 316 317 336 C3' T C 10 OK 334 337 338 356 C3' C C 11 OK 354 357 358 375 C3' G C 12 OK 373 376 377 397 C3' C C 13 OK 395 398 399 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 20 OK 5 2 4 25 C4' C B 21 OK 27 24 26 44 C4' G B 22 OK 46 43 45 66 C4' A B 23 OK 68 65 67 87 C4' T B 24 OK 89 86 88 107 C4' C B 25 OK 109 106 108 126 C4' A B 26 OK 128 125 127 147 C4' C B 27 OK 149 146 148 166 C4' G B 28 OK 168 165 167 188 C4' T B 29 OK 190 187 189 209 C4' A C 4 OK 211 208 210 230 C4' C C 5 OK 232 229 231 249 C4' G C 6 OK 251 248 250 271 C4' T C 7 OK 273 270 272 291 C4' G C 8 OK 293 290 292 313 C4' A C 9 OK 315 312 314 334 C4' T C 10 OK 336 333 335 354 C4' C C 11 OK 356 353 355 373 C4' G C 12 OK 375 372 374 395 C4' C C 13 OK 397 394 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 20 1 3 24 C5' C B 21 23 25 43 C5' G B 22 42 44 65 C5' A B 23 64 66 86 C5' T B 24 85 87 106 C5' C B 25 105 107 125 C5' A B 26 124 126 146 C5' C B 27 145 147 165 C5' G B 28 164 166 187 C5' T B 29 186 188 208 C5' A C 4 207 209 229 C5' C C 5 228 230 248 C5' G C 6 247 249 270 C5' T C 7 269 271 290 C5' G C 8 289 291 312 C5' A C 9 311 313 333 C5' T C 10 332 334 353 C5' C C 11 352 354 372 C5' G C 12 371 373 394 C5' C C 13 393 395 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 21 distorted distorted 6 21 22 23 39 P G B 22 distorted distorted 28 40 41 42 61 P A B 23 distorted distorted 47 62 63 64 82 P T B 24 distorted distorted 69 83 84 85 102 P C B 25 distorted distorted 90 103 104 105 121 P A B 26 distorted distorted 110 122 123 124 142 P C B 27 distorted distorted 129 143 144 145 161 P G B 28 distorted distorted 150 162 163 164 183 P T B 29 distorted distorted 169 184 185 186 204 P A C 4 distorted distorted 205 206 207 225 P C C 5 distorted distorted 212 226 227 228 244 P G C 6 distorted distorted 233 245 246 247 266 P T C 7 distorted distorted 252 267 268 269 286 P G C 8 distorted distorted 274 287 288 289 308 P A C 9 distorted distorted 294 309 310 311 329 P T C 10 distorted distorted 316 330 331 332 349 P C C 11 distorted distorted 337 350 351 352 368 P G C 12 distorted distorted 357 369 370 371 390 P C C 13 distorted distorted 376 391 392 393 ---------------------------------------------------------------------------------