ID code: '1FHK' 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' C A 3 alpha beta 73 93 79 76 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' G A 5 alpha beta 138 161 144 141 177 C1' U A 6 alpha beta 172 192 178 175 207 C1' G A 7 alpha beta 202 225 208 205 241 C1' A A 8 alpha beta 236 258 242 239 274 C1' A A 9 alpha beta 269 291 275 272 307 C1' A A 10 alpha beta 302 324 308 305 340 C1' U A 11 alpha beta 335 355 341 338 370 C1' G A 12 alpha beta 365 388 371 368 404 C1' C A 13 alpha beta 399 419 405 402 435 C1' C A 14 alpha beta 430 451 436 433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' G A 4 OK OK 109 105 125 108 141 C2' G A 5 OK OK 143 139 159 142 175 C2' U A 6 OK OK 177 173 190 176 205 C2' G A 7 OK OK 207 203 223 206 239 C2' A A 8 OK OK 241 237 256 240 272 C2' A A 9 OK OK 274 270 289 273 305 C2' A A 10 OK OK 307 303 322 306 338 C2' U A 11 OK OK 340 336 353 339 368 C2' G A 12 OK OK 370 366 386 369 402 C2' C A 13 OK OK 404 400 417 403 433 C2' C A 14 OK OK 435 431 449 434 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' G A 4 OK OK 103 124 106 107 139 C3' G A 5 OK OK 137 158 140 141 173 C3' U A 6 OK OK 171 189 174 175 203 C3' G A 7 OK OK 201 222 204 205 237 C3' A A 8 OK OK 235 255 238 239 270 C3' A A 9 OK OK 268 288 271 272 303 C3' A A 10 OK OK 301 321 304 305 336 C3' U A 11 OK OK 334 352 337 338 366 C3' G A 12 OK OK 364 385 367 368 400 C3' C A 13 OK OK 398 416 401 402 431 C3' C A 14 OK OK 429 447 432 433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' G A 4 OK OK 105 123 102 104 137 C4' G A 5 OK OK 139 157 136 138 171 C4' U A 6 OK OK 173 188 170 172 201 C4' G A 7 OK OK 203 221 200 202 235 C4' A A 8 OK OK 237 254 234 236 268 C4' A A 9 OK OK 270 287 267 269 301 C4' A A 10 OK OK 303 320 300 302 334 C4' U A 11 OK OK 336 351 333 335 364 C4' G A 12 OK OK 366 384 363 365 398 C4' C A 13 OK OK 400 415 397 399 429 C4' C A 14 OK OK 431 446 428 430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' G A 4 OK OK 101 121 122 103 136 C5' G A 5 OK OK 135 155 156 137 170 C5' U A 6 OK OK 169 186 187 171 200 C5' G A 7 OK OK 199 219 220 201 234 C5' A A 8 OK OK 233 252 253 235 267 C5' A A 9 OK OK 266 285 286 268 300 C5' A A 10 OK OK 299 318 319 301 333 C5' U A 11 OK OK 332 349 350 334 363 C5' G A 12 OK OK 362 382 383 364 397 C5' C A 13 OK OK 396 413 414 398 428 C5' C A 14 OK OK 427 444 445 429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 75 99 100 101 132 P G A 5 distorted distorted 106 133 134 135 166 P U A 6 distorted distorted 140 167 168 169 196 P G A 7 distorted distorted 174 197 198 199 230 P A A 8 distorted distorted 204 231 232 233 263 P A A 9 distorted distorted 238 264 265 266 296 P A A 10 distorted distorted 271 297 298 299 329 P U A 11 distorted distorted 304 330 331 332 359 P G A 12 distorted distorted 337 360 361 362 393 P C A 13 distorted distorted 367 394 395 396 424 P C A 14 distorted distorted 401 425 426 427 ---------------------------------------------------------------------------------