ID code: '1K4B' 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' U A 4 alpha beta 103 123 109 106 138 C1' C A 5 alpha beta 133 153 139 136 169 C1' A A 6 alpha beta 164 186 170 167 202 C1' G A 7 alpha beta 197 220 203 200 236 C1' U A 8 alpha beta 231 251 237 234 266 C1' U A 9 alpha beta 261 281 267 264 296 C1' G A 10 alpha beta 291 314 297 294 330 C1' A A 11 alpha beta 325 347 331 328 363 C1' A A 12 alpha beta 358 380 364 361 396 C1' C A 13 alpha beta 391 411 397 394 427 C1' C A 14 alpha beta 422 443 428 425 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 4 OK OK 108 104 121 107 136 C2' C A 5 OK OK 138 134 151 137 167 C2' A A 6 OK OK 169 165 184 168 200 C2' G A 7 OK OK 202 198 218 201 234 C2' U A 8 OK OK 236 232 249 235 264 C2' U A 9 OK OK 266 262 279 265 294 C2' G A 10 OK OK 296 292 312 295 328 C2' A A 11 OK OK 330 326 345 329 361 C2' A A 12 OK OK 363 359 378 362 394 C2' C A 13 OK OK 396 392 409 395 425 C2' C A 14 OK OK 427 423 441 426 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 102 120 105 106 134 C3' C A 5 OK OK 132 150 135 136 165 C3' A A 6 OK OK 163 183 166 167 198 C3' G A 7 OK OK 196 217 199 200 232 C3' U A 8 OK OK 230 248 233 234 262 C3' U A 9 OK OK 260 278 263 264 292 C3' G A 10 OK OK 290 311 293 294 326 C3' A A 11 OK OK 324 344 327 328 359 C3' A A 12 OK OK 357 377 360 361 392 C3' C A 13 OK OK 390 408 393 394 423 C3' C A 14 OK OK 421 439 424 425 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 104 119 101 103 132 C4' C A 5 OK OK 134 149 131 133 163 C4' A A 6 OK OK 165 182 162 164 196 C4' G A 7 OK OK 198 216 195 197 230 C4' U A 8 OK OK 232 247 229 231 260 C4' U A 9 OK OK 262 277 259 261 290 C4' G A 10 OK OK 292 310 289 291 324 C4' A A 11 OK OK 326 343 323 325 357 C4' A A 12 OK OK 359 376 356 358 390 C4' C A 13 OK OK 392 407 389 391 421 C4' C A 14 OK OK 423 438 420 422 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 100 117 118 102 131 C5' C A 5 OK OK 130 147 148 132 162 C5' A A 6 OK OK 161 180 181 163 195 C5' G A 7 OK OK 194 214 215 196 229 C5' U A 8 OK OK 228 245 246 230 259 C5' U A 9 OK OK 258 275 276 260 289 C5' G A 10 OK OK 288 308 309 290 323 C5' A A 11 OK OK 322 341 342 324 356 C5' A A 12 OK OK 355 374 375 357 389 C5' C A 13 OK OK 388 405 406 390 420 C5' C A 14 OK OK 419 436 437 421 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 4 distorted distorted 75 98 99 100 127 P C A 5 distorted distorted 105 128 129 130 158 P A A 6 distorted distorted 135 159 160 161 191 P G A 7 distorted distorted 166 192 193 194 225 P U A 8 distorted distorted 199 226 227 228 255 P U A 9 distorted distorted 233 256 257 258 285 P G A 10 distorted distorted 263 286 287 288 319 P A A 11 distorted distorted 293 320 321 322 352 P A A 12 distorted distorted 327 353 354 355 385 P C A 13 distorted distorted 360 386 387 388 416 P C A 14 distorted distorted 393 417 418 419 ---------------------------------------------------------------------------------