ID code: '5LQT' 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 beta 4 10 7 33 C1' CBV A 2 beta 28 34 31 54 C1' C A 3 beta 49 55 52 74 C1' G A 4 beta 69 75 72 97 C1' G A 5 beta 92 98 95 126 C1' 6MZ A 6 beta 125 114 127 144 C1' C A 7 beta 139 145 142 164 C1' G A 8 beta 159 165 162 187 C1' G A 9 beta 182 188 185 210 C1' C A 10 beta 205 211 208 228 C1' G B 1 beta 223 229 226 252 C1' CBV B 2 beta 247 253 250 273 C1' C B 3 beta 268 274 271 293 C1' G B 4 beta 288 294 291 316 C1' G B 5 beta 311 317 314 345 C1' 6MZ B 6 beta 344 333 346 363 C1' C B 7 beta 358 364 361 383 C1' G B 8 beta 378 384 381 406 C1' G B 9 beta 401 407 404 429 C1' C B 10 beta 424 430 427 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 31 C2' CBV A 2 OK 33 29 32 52 C2' C A 3 OK 54 50 53 72 C2' G A 4 OK 74 70 73 95 C2' G A 5 OK 97 93 96 127 C2' 6MZ A 6 OK 126 129 128 142 C2' C A 7 OK 144 140 143 162 C2' G A 8 OK 164 160 163 185 C2' G A 9 OK 187 183 186 208 C2' C A 10 OK 210 206 209 226 C2' G B 1 OK 228 224 227 250 C2' CBV B 2 OK 252 248 251 271 C2' C B 3 OK 273 269 272 291 C2' G B 4 OK 293 289 292 314 C2' G B 5 OK 316 312 315 346 C2' 6MZ B 6 OK 345 348 347 361 C2' C B 7 OK 363 359 362 381 C2' G B 8 OK 383 379 382 404 C2' G B 9 OK 406 402 405 427 C2' C B 10 OK 429 425 428 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 29 C3' CBV A 2 OK 27 30 31 50 C3' C A 3 OK 48 51 52 70 C3' G A 4 OK 68 71 72 93 C3' G A 5 OK 91 94 95 129 C3' 6MZ A 6 OK 124 130 127 140 C3' C A 7 OK 138 141 142 160 C3' G A 8 OK 158 161 162 183 C3' G A 9 OK 181 184 185 206 C3' C A 10 OK 204 207 208 224 C3' G B 1 OK 222 225 226 248 C3' CBV B 2 OK 246 249 250 269 C3' C B 3 OK 267 270 271 289 C3' G B 4 OK 287 290 291 312 C3' G B 5 OK 310 313 314 348 C3' 6MZ B 6 OK 343 349 346 359 C3' C B 7 OK 357 360 361 379 C3' G B 8 OK 377 380 381 402 C3' G B 9 OK 400 403 404 425 C3' C B 10 OK 423 426 427 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 27 C4' CBV A 2 OK 29 26 28 48 C4' C A 3 OK 50 47 49 68 C4' G A 4 OK 70 67 69 91 C4' G A 5 OK 93 90 92 124 C4' 6MZ A 6 OK 129 123 125 138 C4' C A 7 OK 140 137 139 158 C4' G A 8 OK 160 157 159 181 C4' G A 9 OK 183 180 182 204 C4' C A 10 OK 206 203 205 222 C4' G B 1 OK 224 221 223 246 C4' CBV B 2 OK 248 245 247 267 C4' C B 3 OK 269 266 268 287 C4' G B 4 OK 289 286 288 310 C4' G B 5 OK 312 309 311 343 C4' 6MZ B 6 OK 348 342 344 357 C4' C B 7 OK 359 356 358 377 C4' G B 8 OK 379 376 378 400 C4' G B 9 OK 402 399 401 423 C4' C B 10 OK 425 422 424 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 26 C5' CBV A 2 25 27 47 C5' C A 3 46 48 67 C5' G A 4 66 68 90 C5' G A 5 89 91 123 C5' 6MZ A 6 122 124 137 C5' C A 7 136 138 157 C5' G A 8 156 158 180 C5' G A 9 179 181 203 C5' C A 10 202 204 221 C5' G B 1 220 222 245 C5' CBV B 2 244 246 266 C5' C B 3 265 267 286 C5' G B 4 285 287 309 C5' G B 5 308 310 342 C5' 6MZ B 6 341 343 356 C5' C B 7 355 357 376 C5' G B 8 375 377 399 C5' G B 9 398 400 422 C5' C B 10 421 423 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 22 P CBV A 2 distorted distorted 6 23 24 25 43 P C A 3 distorted distorted 30 44 45 46 63 P G A 4 distorted distorted 51 64 65 66 86 P G A 5 distorted distorted 71 87 88 89 131 P 6MZ A 6 OK OK 94 112 113 122 133 P C A 7 distorted distorted 130 134 135 136 153 P G A 8 distorted distorted 141 154 155 156 176 P G A 9 distorted distorted 161 177 178 179 199 P C A 10 distorted distorted 184 200 201 202 241 P CBV B 2 distorted distorted 225 242 243 244 262 P C B 3 distorted distorted 249 263 264 265 282 P G B 4 distorted distorted 270 283 284 285 305 P G B 5 distorted distorted 290 306 307 308 350 P 6MZ B 6 distorted distorted 313 331 332 341 352 P C B 7 distorted distorted 349 353 354 355 372 P G B 8 distorted distorted 360 373 374 375 395 P G B 9 distorted distorted 380 396 397 398 418 P C B 10 distorted distorted 403 419 420 421 ---------------------------------------------------------------------------------