ID code: '1I4B' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' U A 6 alpha beta 168 188 174 171 203 C1' U A 7 alpha beta 198 218 204 201 233 C1' A A 8 alpha beta 228 250 234 231 266 C1' G A 9 alpha beta 261 284 267 264 300 C1' C A 10 alpha beta 295 315 301 298 331 C1' A A 11 alpha beta 326 348 332 329 364 C1' C A 12 alpha beta 359 379 365 362 395 C1' C A 13 alpha beta 390 411 396 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' C A 5 OK OK 142 138 155 141 171 C2' U A 6 OK OK 173 169 186 172 201 C2' U A 7 OK OK 203 199 216 202 231 C2' A A 8 OK OK 233 229 248 232 264 C2' G A 9 OK OK 266 262 282 265 298 C2' C A 10 OK OK 300 296 313 299 329 C2' A A 11 OK OK 331 327 346 330 362 C2' C A 12 OK OK 364 360 377 363 393 C2' C A 13 OK OK 395 391 409 394 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' C A 5 OK OK 136 154 139 140 169 C3' U A 6 OK OK 167 185 170 171 199 C3' U A 7 OK OK 197 215 200 201 229 C3' A A 8 OK OK 227 247 230 231 262 C3' G A 9 OK OK 260 281 263 264 296 C3' C A 10 OK OK 294 312 297 298 327 C3' A A 11 OK OK 325 345 328 329 360 C3' C A 12 OK OK 358 376 361 362 391 C3' C A 13 OK OK 389 407 392 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' C A 5 OK OK 138 153 135 137 167 C4' U A 6 OK OK 169 184 166 168 197 C4' U A 7 OK OK 199 214 196 198 227 C4' A A 8 OK OK 229 246 226 228 260 C4' G A 9 OK OK 262 280 259 261 294 C4' C A 10 OK OK 296 311 293 295 325 C4' A A 11 OK OK 327 344 324 326 358 C4' C A 12 OK OK 360 375 357 359 389 C4' C A 13 OK OK 391 406 388 390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' C A 5 OK OK 134 151 152 136 166 C5' U A 6 OK OK 165 182 183 167 196 C5' U A 7 OK OK 195 212 213 197 226 C5' A A 8 OK OK 225 244 245 227 259 C5' G A 9 OK OK 258 278 279 260 293 C5' C A 10 OK OK 292 309 310 294 324 C5' A A 11 OK OK 323 342 343 325 357 C5' C A 12 OK OK 356 373 374 358 388 C5' C A 13 OK OK 387 404 405 389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P C A 5 distorted distorted 105 132 133 134 162 P U A 6 distorted distorted 139 163 164 165 192 P U A 7 distorted distorted 170 193 194 195 222 P A A 8 distorted distorted 200 223 224 225 255 P G A 9 distorted distorted 230 256 257 258 289 P C A 10 distorted distorted 263 290 291 292 320 P A A 11 distorted distorted 297 321 322 323 353 P C A 12 distorted distorted 328 354 355 356 384 P C A 13 distorted distorted 361 385 386 387 ---------------------------------------------------------------------------------