ID code: '1PBL' 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' --------------------------------------------------------------------------------- 9 C1' OMC A 1 alpha beta 15 23 1 10 45 C1' OMG A 2 alpha beta 39 65 46 42 78 C1' OMC A 3 alpha beta 84 95 70 79 116 C1' OMG A 4 alpha beta 110 136 117 113 149 C1' OMC A 5 alpha beta 155 166 141 150 187 C1' OMG A 6 alpha beta 181 208 188 184 222 C1' OMC B 7 alpha beta 228 236 214 223 258 C1' OMG B 8 alpha beta 252 278 259 255 291 C1' OMC B 9 alpha beta 297 308 283 292 329 C1' OMG B 10 alpha beta 323 349 330 326 362 C1' OMC B 11 alpha beta 368 379 354 363 400 C1' OMG B 12 alpha beta 394 421 401 397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' OMC A 1 OK OK 9 13 24 11 42 C2' OMG A 2 OK OK 45 40 61 43 79 C2' OMC A 3 OK OK 78 82 96 80 113 C2' OMG A 4 OK OK 116 111 132 114 150 C2' OMC A 5 OK OK 149 153 167 151 184 C2' OMG A 6 OK OK 187 182 204 185 223 C2' OMC B 7 OK OK 222 226 237 224 255 C2' OMG B 8 OK OK 258 253 274 256 292 C2' OMC B 9 OK OK 291 295 309 293 326 C2' OMG B 10 OK OK 329 324 345 327 363 C2' OMC B 11 OK OK 362 366 380 364 397 C2' OMG B 12 OK OK 400 395 417 398 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 13 C3' OMC A 1 OK OK 14 28 16 10 40 C3' OMG A 2 OK OK 38 60 41 42 82 C3' OMC A 3 OK OK 83 100 85 79 111 C3' OMG A 4 OK OK 109 131 112 113 153 C3' OMC A 5 OK OK 154 171 156 150 182 C3' OMG A 6 OK OK 180 202 183 184 226 C3' OMC B 7 OK OK 227 241 229 223 253 C3' OMG B 8 OK OK 251 273 254 255 295 C3' OMC B 9 OK OK 296 313 298 292 324 C3' OMG B 10 OK OK 322 344 325 326 366 C3' OMC B 11 OK OK 367 384 369 363 395 C3' OMG B 12 OK OK 393 415 396 397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 14 C4' OMC A 1 OK OK 13 29 17 15 38 C4' OMG A 2 OK OK 40 59 37 39 83 C4' OMC A 3 OK OK 82 101 86 84 109 C4' OMG A 4 OK OK 111 130 108 110 154 C4' OMC A 5 OK OK 153 172 157 155 180 C4' OMG A 6 OK OK 182 201 179 181 227 C4' OMC B 7 OK OK 226 242 230 228 251 C4' OMG B 8 OK OK 253 272 250 252 296 C4' OMC B 9 OK OK 295 314 299 297 322 C4' OMG B 10 OK OK 324 343 321 323 367 C4' OMC B 11 OK OK 366 385 370 368 393 C4' OMG B 12 OK OK 395 414 392 394 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 17 C5' OMC A 1 OK OK 18 30 31 14 37 C5' OMG A 2 OK OK 36 57 58 38 86 C5' OMC A 3 OK OK 87 102 103 83 108 C5' OMG A 4 OK OK 107 128 129 109 157 C5' OMC A 5 OK OK 158 173 174 154 179 C5' OMG A 6 OK OK 178 199 200 180 230 C5' OMC B 7 OK OK 231 243 244 227 250 C5' OMG B 8 OK OK 249 270 271 251 299 C5' OMC B 9 OK OK 300 315 316 296 321 C5' OMG B 10 OK OK 320 341 342 322 370 C5' OMC B 11 OK OK 371 386 387 367 392 C5' OMG B 12 OK OK 391 412 413 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P OMG A 2 distorted distorted 16 34 35 36 88 P OMC A 3 distorted distorted 41 89 90 87 104 P OMG A 4 distorted distorted 85 105 106 107 159 P OMC A 5 distorted distorted 112 160 161 158 175 P OMG A 6 distorted distorted 156 176 177 178 246 P OMG B 8 distorted distorted 229 247 248 249 301 P OMC B 9 distorted distorted 254 302 303 300 317 P OMG B 10 distorted distorted 298 318 319 320 372 P OMC B 11 distorted distorted 325 373 374 371 388 P OMG B 12 distorted distorted 369 389 390 391 ---------------------------------------------------------------------------------