ID code: '1YTU' 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' A C 1 beta 8 14 11 35 C1' G C 2 beta 30 36 33 58 C1' A C 3 beta 53 59 56 80 C1' C C 4 beta 75 81 78 100 C1' A C 5 beta 95 101 98 123 C1' U D 15 beta 118 124 121 143 C1' G D 16 beta 138 144 141 166 C1' U D 17 beta 161 167 164 186 C1' C D 18 beta 181 187 184 208 C1' A E 1 beta 203 209 206 230 C1' G E 2 beta 225 231 228 253 C1' A E 3 beta 248 254 251 275 C1' C E 4 beta 270 276 273 295 C1' A E 5 beta 290 296 293 317 C1' G E 6 beta 312 318 315 341 C1' U F 15 beta 336 342 339 361 C1' G F 16 beta 356 362 359 384 C1' U F 17 beta 379 385 382 404 C1' C F 18 beta 399 405 402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' A C 1 OK 13 9 12 33 C2' G C 2 OK 35 31 34 56 C2' A C 3 OK 58 54 57 78 C2' C C 4 OK 80 76 79 98 C2' A C 5 OK 100 96 99 121 C2' U D 15 OK 123 119 122 141 C2' G D 16 OK 143 139 142 164 C2' U D 17 OK 166 162 165 184 C2' C D 18 OK 186 182 185 206 C2' A E 1 OK 208 204 207 228 C2' G E 2 OK 230 226 229 251 C2' A E 3 OK 253 249 252 273 C2' C E 4 OK 275 271 274 293 C2' A E 5 OK 295 291 294 315 C2' G E 6 OK 317 313 316 339 C2' U F 15 OK 341 337 340 359 C2' G F 16 OK 361 357 360 382 C2' U F 17 OK 384 380 383 402 C2' C F 18 OK 404 400 403 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' A C 1 OK 7 10 11 31 C3' G C 2 OK 29 32 33 54 C3' A C 3 OK 52 55 56 76 C3' C C 4 OK 74 77 78 96 C3' A C 5 OK 94 97 98 119 C3' U D 15 OK 117 120 121 139 C3' G D 16 OK 137 140 141 162 C3' U D 17 OK 160 163 164 182 C3' C D 18 OK 180 183 184 204 C3' A E 1 OK 202 205 206 226 C3' G E 2 OK 224 227 228 249 C3' A E 3 OK 247 250 251 271 C3' C E 4 OK 269 272 273 291 C3' A E 5 OK 289 292 293 313 C3' G E 6 OK 311 314 315 337 C3' U F 15 OK 335 338 339 357 C3' G F 16 OK 355 358 359 380 C3' U F 17 OK 378 381 382 400 C3' C F 18 OK 398 401 402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' A C 1 OK 9 6 8 29 C4' G C 2 OK 31 28 30 52 C4' A C 3 OK 54 51 53 74 C4' C C 4 OK 76 73 75 94 C4' A C 5 OK 96 93 95 117 C4' U D 15 OK 119 116 118 137 C4' G D 16 OK 139 136 138 160 C4' U D 17 OK 162 159 161 180 C4' C D 18 OK 182 179 181 202 C4' A E 1 OK 204 201 203 224 C4' G E 2 OK 226 223 225 247 C4' A E 3 OK 249 246 248 269 C4' C E 4 OK 271 268 270 289 C4' A E 5 OK 291 288 290 311 C4' G E 6 OK 313 310 312 335 C4' U F 15 OK 337 334 336 355 C4' G F 16 OK 357 354 356 378 C4' U F 17 OK 380 377 379 398 C4' C F 18 OK 400 397 399 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' A C 1 5 7 28 C5' G C 2 27 29 51 C5' A C 3 50 52 73 C5' C C 4 72 74 93 C5' A C 5 92 94 116 C5' U D 15 115 117 136 C5' G D 16 135 137 159 C5' U D 17 158 160 179 C5' C D 18 178 180 201 C5' A E 1 200 202 223 C5' G E 2 222 224 246 C5' A E 3 245 247 268 C5' C E 4 267 269 288 C5' A E 5 287 289 310 C5' G E 6 309 311 334 C5' U F 15 333 335 354 C5' G F 16 353 355 377 C5' U F 17 376 378 397 C5' C F 18 396 398 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P A C 1 distorted distorted 3 4 5 24 P G C 2 distorted distorted 10 25 26 27 47 P A C 3 distorted distorted 32 48 49 50 69 P C C 4 distorted distorted 55 70 71 72 89 P A C 5 distorted distorted 77 90 91 92 112 P U D 15 OK OK 113 114 115 132 P G D 16 distorted distorted 120 133 134 135 155 P U D 17 distorted distorted 140 156 157 158 175 P C D 18 distorted distorted 163 176 177 178 197 P A E 1 distorted distorted 198 199 200 219 P G E 2 distorted distorted 205 220 221 222 242 P A E 3 distorted distorted 227 243 244 245 264 P C E 4 distorted distorted 250 265 266 267 284 P A E 5 distorted distorted 272 285 286 287 306 P G E 6 distorted distorted 292 307 308 309 330 P U F 15 distorted distorted 331 332 333 350 P G F 16 distorted distorted 338 351 352 353 373 P U F 17 distorted distorted 358 374 375 376 393 P C F 18 distorted distorted 381 394 395 396 ---------------------------------------------------------------------------------