ID code: '2KOC' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 alpha beta 8 31 14 11 48 C1' G A 2 alpha beta 43 66 49 46 82 C1' C A 3 alpha beta 77 97 83 80 113 C1' A A 4 alpha beta 108 130 114 111 146 C1' C A 5 alpha beta 141 161 147 144 177 C1' U A 6 alpha beta 172 192 178 175 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' C A 8 alpha beta 232 252 238 235 268 C1' G A 9 alpha beta 263 286 269 266 302 C1' G A 10 alpha beta 297 320 303 300 336 C1' U A 11 alpha beta 331 351 337 334 366 C1' G A 12 alpha beta 361 384 367 364 400 C1' C A 13 alpha beta 395 415 401 398 431 C1' C A 14 alpha beta 426 447 432 429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 29 12 46 C2' G A 2 OK OK 48 44 64 47 80 C2' C A 3 OK OK 82 78 95 81 111 C2' A A 4 OK OK 113 109 128 112 144 C2' C A 5 OK OK 146 142 159 145 175 C2' U A 6 OK OK 177 173 190 176 205 C2' U A 7 OK OK 207 203 220 206 235 C2' C A 8 OK OK 237 233 250 236 266 C2' G A 9 OK OK 268 264 284 267 300 C2' G A 10 OK OK 302 298 318 301 334 C2' U A 11 OK OK 336 332 349 335 364 C2' G A 12 OK OK 366 362 382 365 398 C2' C A 13 OK OK 400 396 413 399 429 C2' C A 14 OK OK 431 427 445 430 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' G A 2 OK OK 42 63 45 46 78 C3' C A 3 OK OK 76 94 79 80 109 C3' A A 4 OK OK 107 127 110 111 142 C3' C A 5 OK OK 140 158 143 144 173 C3' U A 6 OK OK 171 189 174 175 203 C3' U A 7 OK OK 201 219 204 205 233 C3' C A 8 OK OK 231 249 234 235 264 C3' G A 9 OK OK 262 283 265 266 298 C3' G A 10 OK OK 296 317 299 300 332 C3' U A 11 OK OK 330 348 333 334 362 C3' G A 12 OK OK 360 381 363 364 396 C3' C A 13 OK OK 394 412 397 398 427 C3' C A 14 OK OK 425 443 428 429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' G A 2 OK OK 44 62 41 43 76 C4' C A 3 OK OK 78 93 75 77 107 C4' A A 4 OK OK 109 126 106 108 140 C4' C A 5 OK OK 142 157 139 141 171 C4' U A 6 OK OK 173 188 170 172 201 C4' U A 7 OK OK 203 218 200 202 231 C4' C A 8 OK OK 233 248 230 232 262 C4' G A 9 OK OK 264 282 261 263 296 C4' G A 10 OK OK 298 316 295 297 330 C4' U A 11 OK OK 332 347 329 331 360 C4' G A 12 OK OK 362 380 359 361 394 C4' C A 13 OK OK 396 411 393 395 425 C4' C A 14 OK OK 427 442 424 426 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' G A 2 OK OK 40 60 61 42 75 C5' C A 3 OK OK 74 91 92 76 106 C5' A A 4 OK OK 105 124 125 107 139 C5' C A 5 OK OK 138 155 156 140 170 C5' U A 6 OK OK 169 186 187 171 200 C5' U A 7 OK OK 199 216 217 201 230 C5' C A 8 OK OK 229 246 247 231 261 C5' G A 9 OK OK 260 280 281 262 295 C5' G A 10 OK OK 294 314 315 296 329 C5' U A 11 OK OK 328 345 346 330 359 C5' G A 12 OK OK 358 378 379 360 393 C5' C A 13 OK OK 392 409 410 394 424 C5' C A 14 OK OK 423 440 441 425 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 37 P G A 2 distorted distorted 10 38 39 40 71 P C A 3 distorted distorted 45 72 73 74 102 P A A 4 distorted distorted 79 103 104 105 135 P C A 5 distorted distorted 110 136 137 138 166 P U A 6 distorted distorted 143 167 168 169 196 P U A 7 distorted distorted 174 197 198 199 226 P C A 8 distorted distorted 204 227 228 229 257 P G A 9 distorted distorted 234 258 259 260 291 P G A 10 distorted distorted 265 292 293 294 325 P U A 11 distorted distorted 299 326 327 328 355 P G A 12 distorted distorted 333 356 357 358 389 P C A 13 distorted distorted 363 390 391 392 420 P C A 14 distorted distorted 397 421 422 423 ---------------------------------------------------------------------------------