ID code: '1CW0' 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' A M 301 beta 4 9 7 29 C1' C M 302 beta 25 30 28 48 C1' G M 303 beta 44 49 47 70 C1' T M 304 beta 66 71 69 90 C1' A M 305 beta 86 91 89 111 C1' C M 306 beta 107 112 110 130 C1' C M 307 beta 126 131 129 149 C1' T M 308 beta 145 150 148 169 C1' G M 309 beta 165 170 168 191 C1' G M 310 beta 187 192 190 213 C1' C M 311 beta 209 214 212 232 C1' T M 312 beta 228 233 231 250 C1' A N 351 beta 246 251 249 271 C1' G N 352 beta 267 272 270 293 C1' C N 353 beta 289 294 292 314 C1' T O 354 beta 310 315 313 334 C1' A O 355 beta 330 335 333 355 C1' G O 356 beta 351 356 354 377 C1' G O 357 beta 373 378 376 399 C1' T O 358 beta 395 400 398 419 C1' A O 359 beta 415 420 418 440 C1' C O 360 beta 436 441 439 459 C1' G O 361 beta 455 460 458 481 C1' T O 362 beta 477 482 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A M 301 8 5 28 C2' C M 302 29 26 47 C2' G M 303 48 45 69 C2' T M 304 70 67 89 C2' A M 305 90 87 110 C2' C M 306 111 108 129 C2' C M 307 130 127 148 C2' T M 308 149 146 168 C2' G M 309 169 166 190 C2' G M 310 191 188 212 C2' C M 311 213 210 231 C2' T M 312 232 229 249 C2' A N 351 250 247 270 C2' G N 352 271 268 292 C2' C N 353 293 290 313 C2' T O 354 314 311 333 C2' A O 355 334 331 354 C2' G O 356 355 352 376 C2' G O 357 377 374 398 C2' T O 358 399 396 418 C2' A O 359 419 416 439 C2' C O 360 440 437 458 C2' G O 361 459 456 480 C2' T O 362 481 478 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A M 301 OK 3 6 7 26 C3' C M 302 OK 24 27 28 45 C3' G M 303 OK 43 46 47 67 C3' T M 304 OK 65 68 69 87 C3' A M 305 OK 85 88 89 108 C3' C M 306 OK 106 109 110 127 C3' C M 307 OK 125 128 129 146 C3' T M 308 OK 144 147 148 166 C3' G M 309 OK 164 167 168 188 C3' G M 310 OK 186 189 190 210 C3' C M 311 OK 208 211 212 229 C3' T M 312 OK 227 230 231 247 C3' A N 351 OK 245 248 249 268 C3' G N 352 OK 266 269 270 290 C3' C N 353 OK 288 291 292 311 C3' T O 354 OK 309 312 313 331 C3' A O 355 OK 329 332 333 352 C3' G O 356 OK 350 353 354 374 C3' G O 357 OK 372 375 376 396 C3' T O 358 OK 394 397 398 416 C3' A O 359 OK 414 417 418 437 C3' C O 360 OK 435 438 439 456 C3' G O 361 OK 454 457 458 478 C3' T O 362 OK 476 479 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A M 301 OK 5 2 4 24 C4' C M 302 OK 26 23 25 43 C4' G M 303 OK 45 42 44 65 C4' T M 304 OK 67 64 66 85 C4' A M 305 OK 87 84 86 106 C4' C M 306 OK 108 105 107 125 C4' C M 307 OK 127 124 126 144 C4' T M 308 OK 146 143 145 164 C4' G M 309 OK 166 163 165 186 C4' G M 310 OK 188 185 187 208 C4' C M 311 OK 210 207 209 227 C4' T M 312 OK 229 226 228 245 C4' A N 351 OK 247 244 246 266 C4' G N 352 OK 268 265 267 288 C4' C N 353 OK 290 287 289 309 C4' T O 354 OK 311 308 310 329 C4' A O 355 OK 331 328 330 350 C4' G O 356 OK 352 349 351 372 C4' G O 357 OK 374 371 373 394 C4' T O 358 OK 396 393 395 414 C4' A O 359 OK 416 413 415 435 C4' C O 360 OK 437 434 436 454 C4' G O 361 OK 456 453 455 476 C4' T O 362 OK 478 475 477 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A M 301 1 3 23 C5' C M 302 22 24 42 C5' G M 303 41 43 64 C5' T M 304 63 65 84 C5' A M 305 83 85 105 C5' C M 306 104 106 124 C5' C M 307 123 125 143 C5' T M 308 142 144 163 C5' G M 309 162 164 185 C5' G M 310 184 186 207 C5' C M 311 206 208 226 C5' T M 312 225 227 244 C5' A N 351 243 245 265 C5' G N 352 264 266 287 C5' C N 353 286 288 308 C5' T O 354 307 309 328 C5' A O 355 327 329 349 C5' G O 356 348 350 371 C5' G O 357 370 372 393 C5' T O 358 392 394 413 C5' A O 359 412 414 434 C5' C O 360 433 435 453 C5' G O 361 452 454 475 C5' T O 362 474 476 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P C M 302 distorted distorted 6 20 21 22 38 P G M 303 distorted distorted 27 39 40 41 60 P T M 304 distorted distorted 46 61 62 63 80 P A M 305 distorted distorted 68 81 82 83 101 P C M 306 distorted distorted 88 102 103 104 120 P C M 307 distorted distorted 109 121 122 123 139 P T M 308 distorted distorted 128 140 141 142 159 P G M 309 distorted distorted 147 160 161 162 181 P G M 310 distorted distorted 167 182 183 184 203 P C M 311 distorted distorted 189 204 205 206 222 P T M 312 distorted distorted 211 223 224 225 261 P G N 352 distorted distorted 248 262 263 264 283 P C N 353 distorted distorted 269 284 285 286 304 P T O 354 OK OK 305 306 307 324 P A O 355 distorted distorted 312 325 326 327 345 P G O 356 distorted distorted 332 346 347 348 367 P G O 357 distorted distorted 353 368 369 370 389 P T O 358 distorted distorted 375 390 391 392 409 P A O 359 distorted distorted 397 410 411 412 430 P C O 360 distorted distorted 417 431 432 433 449 P G O 361 distorted distorted 438 450 451 452 471 P T O 362 distorted distorted 457 472 473 474 ---------------------------------------------------------------------------------