ID code: '3FS0' 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 44 beta 4 10 7 32 C1' G A 45 beta 27 33 30 55 C1' U A 46 beta 50 56 53 75 C1' G A 47 beta 70 76 73 98 C1' A A 48 beta 93 99 96 120 C1' G A 49 beta 115 121 118 143 C1' G A 50 beta 138 144 141 166 C1' C A 51 beta 161 167 164 186 C1' U A 52 beta 181 187 184 206 C1' G A 53 beta 201 207 204 227 C1' C B -6 beta 222 228 225 247 C1' C B -5 beta 242 248 245 267 C1' A B -4 beta 262 268 265 289 C1' G B -3 beta 284 290 287 312 C1' U B -2 beta 307 313 310 332 C1' C B -1 beta 327 333 330 352 C1' G B 1 beta 347 353 350 375 C1' G B 2 beta 370 376 373 398 C1' A B 3 beta 393 399 396 420 C1' A B 4 beta 415 421 418 442 C1' C B 5 beta 437 443 440 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 44 OK 9 5 8 30 C2' G A 45 OK 32 28 31 53 C2' U A 46 OK 55 51 54 73 C2' G A 47 OK 75 71 74 96 C2' A A 48 OK 98 94 97 118 C2' G A 49 OK 120 116 119 141 C2' G A 50 OK 143 139 142 164 C2' C A 51 OK 166 162 165 184 C2' U A 52 OK 186 182 185 204 C2' G A 53 OK 206 202 205 225 C2' C B -6 OK 227 223 226 245 C2' C B -5 OK 247 243 246 265 C2' A B -4 OK 267 263 266 287 C2' G B -3 OK 289 285 288 310 C2' U B -2 OK 312 308 311 330 C2' C B -1 OK 332 328 331 350 C2' G B 1 OK 352 348 351 373 C2' G B 2 OK 375 371 374 396 C2' A B 3 OK 398 394 397 418 C2' A B 4 OK 420 416 419 440 C2' C B 5 OK 442 438 441 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 44 OK 3 6 7 28 C3' G A 45 OK 26 29 30 51 C3' U A 46 OK 49 52 53 71 C3' G A 47 OK 69 72 73 94 C3' A A 48 OK 92 95 96 116 C3' G A 49 OK 114 117 118 139 C3' G A 50 OK 137 140 141 162 C3' C A 51 OK 160 163 164 182 C3' U A 52 OK 180 183 184 202 C3' G A 53 OK 200 203 204 223 C3' C B -6 OK 221 224 225 243 C3' C B -5 OK 241 244 245 263 C3' A B -4 OK 261 264 265 285 C3' G B -3 OK 283 286 287 308 C3' U B -2 OK 306 309 310 328 C3' C B -1 OK 326 329 330 348 C3' G B 1 OK 346 349 350 371 C3' G B 2 OK 369 372 373 394 C3' A B 3 OK 392 395 396 416 C3' A B 4 OK 414 417 418 438 C3' C B 5 OK 436 439 440 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 44 OK 5 2 4 26 C4' G A 45 OK 28 25 27 49 C4' U A 46 OK 51 48 50 69 C4' G A 47 OK 71 68 70 92 C4' A A 48 OK 94 91 93 114 C4' G A 49 OK 116 113 115 137 C4' G A 50 OK 139 136 138 160 C4' C A 51 OK 162 159 161 180 C4' U A 52 OK 182 179 181 200 C4' G A 53 OK 202 199 201 221 C4' C B -6 OK 223 220 222 241 C4' C B -5 OK 243 240 242 261 C4' A B -4 OK 263 260 262 283 C4' G B -3 OK 285 282 284 306 C4' U B -2 OK 308 305 307 326 C4' C B -1 OK 328 325 327 346 C4' G B 1 OK 348 345 347 369 C4' G B 2 OK 371 368 370 392 C4' A B 3 OK 394 391 393 414 C4' A B 4 OK 416 413 415 436 C4' C B 5 OK 438 435 437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 44 1 3 25 C5' G A 45 24 26 48 C5' U A 46 47 49 68 C5' G A 47 67 69 91 C5' A A 48 90 92 113 C5' G A 49 112 114 136 C5' G A 50 135 137 159 C5' C A 51 158 160 179 C5' U A 52 178 180 199 C5' G A 53 198 200 220 C5' C B -6 219 221 240 C5' C B -5 239 241 260 C5' A B -4 259 261 282 C5' G B -3 281 283 305 C5' U B -2 304 306 325 C5' C B -1 324 326 345 C5' G B 1 344 346 368 C5' G B 2 367 369 391 C5' A B 3 390 392 413 C5' A B 4 412 414 435 C5' C B 5 434 436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 45 distorted distorted 6 22 23 24 44 P U A 46 distorted distorted 29 45 46 47 64 P G A 47 distorted distorted 52 65 66 67 87 P A A 48 distorted distorted 72 88 89 90 109 P G A 49 distorted distorted 95 110 111 112 132 P G A 50 distorted distorted 117 133 134 135 155 P C A 51 distorted distorted 140 156 157 158 175 P U A 52 distorted distorted 163 176 177 178 195 P G A 53 distorted distorted 183 196 197 198 236 P C B -5 distorted distorted 224 237 238 239 256 P A B -4 distorted distorted 244 257 258 259 278 P G B -3 distorted distorted 264 279 280 281 301 P U B -2 distorted distorted 286 302 303 304 321 P C B -1 distorted distorted 309 322 323 324 341 P G B 1 OK OK 342 343 344 364 P G B 2 distorted distorted 349 365 366 367 387 P A B 3 distorted distorted 372 388 389 390 409 P A B 4 distorted distorted 395 410 411 412 431 P C B 5 distorted distorted 417 432 433 434 ---------------------------------------------------------------------------------