ID code: '1LRR' 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' --------------------------------------------------------------------------------- 8 C1' C B 1 beta 4 9 7 27 C1' A B 2 beta 23 28 26 48 C1' C B 3 beta 44 49 47 67 C1' C B 4 beta 63 68 66 86 C1' G B 5 beta 82 87 85 108 C1' A B 6 beta 104 109 107 129 C1' T B 7 beta 125 130 128 149 C1' C B 8 beta 145 150 148 168 C1' G B 9 beta 164 169 167 190 C1' A B 10 beta 186 191 189 211 C1' C B 11 beta 207 212 210 230 C1' T B 12 beta 226 231 229 248 C1' A C 1 beta 244 249 247 269 C1' G C 2 beta 265 270 268 291 C1' T C 3 beta 287 292 290 311 C1' C C 4 beta 307 312 310 330 C1' G C 5 beta 326 331 329 352 C1' +A C 6 beta 348 353 351 373 C1' T C 7 beta 369 374 372 393 C1' C C 8 beta 389 394 392 412 C1' G C 9 beta 408 413 411 434 C1' G C 10 beta 430 435 433 456 C1' T C 11 beta 452 457 455 476 C1' G C 12 beta 472 477 475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C B 1 8 5 26 C2' A B 2 27 24 47 C2' C B 3 48 45 66 C2' C B 4 67 64 85 C2' G B 5 86 83 107 C2' A B 6 108 105 128 C2' T B 7 129 126 148 C2' C B 8 149 146 167 C2' G B 9 168 165 189 C2' A B 10 190 187 210 C2' C B 11 211 208 229 C2' T B 12 230 227 247 C2' A C 1 248 245 268 C2' G C 2 269 266 290 C2' T C 3 291 288 310 C2' C C 4 311 308 329 C2' G C 5 330 327 351 C2' +A C 6 352 349 372 C2' T C 7 373 370 392 C2' C C 8 393 390 411 C2' G C 9 412 409 433 C2' G C 10 434 431 455 C2' T C 11 456 453 475 C2' G C 12 476 473 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C B 1 OK 3 6 7 24 C3' A B 2 OK 22 25 26 45 C3' C B 3 OK 43 46 47 64 C3' C B 4 OK 62 65 66 83 C3' G B 5 OK 81 84 85 105 C3' A B 6 OK 103 106 107 126 C3' T B 7 OK 124 127 128 146 C3' C B 8 OK 144 147 148 165 C3' G B 9 OK 163 166 167 187 C3' A B 10 OK 185 188 189 208 C3' C B 11 OK 206 209 210 227 C3' T B 12 OK 225 228 229 245 C3' A C 1 OK 243 246 247 266 C3' G C 2 OK 264 267 268 288 C3' T C 3 OK 286 289 290 308 C3' C C 4 OK 306 309 310 327 C3' G C 5 OK 325 328 329 349 C3' +A C 6 OK 347 350 351 370 C3' T C 7 OK 368 371 372 390 C3' C C 8 OK 388 391 392 409 C3' G C 9 OK 407 410 411 431 C3' G C 10 OK 429 432 433 453 C3' T C 11 OK 451 454 455 473 C3' G C 12 OK 471 474 475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C B 1 OK 5 2 4 22 C4' A B 2 OK 24 21 23 43 C4' C B 3 OK 45 42 44 62 C4' C B 4 OK 64 61 63 81 C4' G B 5 OK 83 80 82 103 C4' A B 6 OK 105 102 104 124 C4' T B 7 OK 126 123 125 144 C4' C B 8 OK 146 143 145 163 C4' G B 9 OK 165 162 164 185 C4' A B 10 OK 187 184 186 206 C4' C B 11 OK 208 205 207 225 C4' T B 12 OK 227 224 226 243 C4' A C 1 OK 245 242 244 264 C4' G C 2 OK 266 263 265 286 C4' T C 3 OK 288 285 287 306 C4' C C 4 OK 308 305 307 325 C4' G C 5 OK 327 324 326 347 C4' +A C 6 OK 349 346 348 368 C4' T C 7 OK 370 367 369 388 C4' C C 8 OK 390 387 389 407 C4' G C 9 OK 409 406 408 429 C4' G C 10 OK 431 428 430 451 C4' T C 11 OK 453 450 452 471 C4' G C 12 OK 473 470 472 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C B 1 1 3 21 C5' A B 2 20 22 42 C5' C B 3 41 43 61 C5' C B 4 60 62 80 C5' G B 5 79 81 102 C5' A B 6 101 103 123 C5' T B 7 122 124 143 C5' C B 8 142 144 162 C5' G B 9 161 163 184 C5' A B 10 183 185 205 C5' C B 11 204 206 224 C5' T B 12 223 225 242 C5' A C 1 241 243 263 C5' G C 2 262 264 285 C5' T C 3 284 286 305 C5' C C 4 304 306 324 C5' G C 5 323 325 346 C5' +A C 6 345 347 367 C5' T C 7 366 368 387 C5' C C 8 386 388 406 C5' G C 9 405 407 428 C5' G C 10 427 429 450 C5' T C 11 449 451 470 C5' G C 12 469 471 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A B 2 distorted distorted 6 18 19 20 38 P C B 3 distorted distorted 25 39 40 41 57 P C B 4 distorted distorted 46 58 59 60 76 P G B 5 distorted distorted 65 77 78 79 98 P A B 6 distorted distorted 84 99 100 101 119 P T B 7 distorted distorted 106 120 121 122 139 P C B 8 distorted distorted 127 140 141 142 158 P G B 9 distorted distorted 147 159 160 161 180 P A B 10 distorted distorted 166 181 182 183 201 P C B 11 distorted distorted 188 202 203 204 220 P T B 12 distorted distorted 209 221 222 223 259 P G C 2 distorted distorted 246 260 261 262 281 P T C 3 distorted distorted 267 282 283 284 301 P C C 4 distorted distorted 289 302 303 304 320 P G C 5 distorted distorted 309 321 322 323 342 P +A C 6 OK OK 328 343 344 345 363 P T C 7 distorted distorted 350 364 365 366 383 P C C 8 distorted distorted 371 384 385 386 402 P G C 9 distorted distorted 391 403 404 405 424 P G C 10 distorted distorted 410 425 426 427 446 P T C 11 distorted distorted 432 447 448 449 466 P G C 12 distorted distorted 454 467 468 469 ---------------------------------------------------------------------------------