ID code: '2LPA' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' A A 5 alpha beta 140 162 146 143 178 C1' C A 6 alpha beta 173 193 179 176 209 C1' A A 7 alpha beta 204 226 210 207 242 C1' U A 8 alpha beta 237 257 243 240 272 C1' A A 9 alpha beta 267 289 273 270 305 C1' G A 10 alpha beta 300 323 306 303 339 C1' U A 11 alpha beta 334 354 340 337 369 C1' C A 12 alpha beta 364 384 370 367 400 C1' U A 13 alpha beta 395 415 401 398 430 C1' U A 14 alpha beta 425 445 431 428 460 C1' C A 15 alpha beta 455 476 461 458 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' G A 4 OK OK 111 107 127 110 143 C2' A A 5 OK OK 145 141 160 144 176 C2' C A 6 OK OK 178 174 191 177 207 C2' A A 7 OK OK 209 205 224 208 240 C2' U A 8 OK OK 242 238 255 241 270 C2' A A 9 OK OK 272 268 287 271 303 C2' G A 10 OK OK 305 301 321 304 337 C2' U A 11 OK OK 339 335 352 338 367 C2' C A 12 OK OK 369 365 382 368 398 C2' U A 13 OK OK 400 396 413 399 428 C2' U A 14 OK OK 430 426 443 429 458 C2' C A 15 OK OK 460 456 474 459 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' G A 4 OK OK 105 126 108 109 141 C3' A A 5 OK OK 139 159 142 143 174 C3' C A 6 OK OK 172 190 175 176 205 C3' A A 7 OK OK 203 223 206 207 238 C3' U A 8 OK OK 236 254 239 240 268 C3' A A 9 OK OK 266 286 269 270 301 C3' G A 10 OK OK 299 320 302 303 335 C3' U A 11 OK OK 333 351 336 337 365 C3' C A 12 OK OK 363 381 366 367 396 C3' U A 13 OK OK 394 412 397 398 426 C3' U A 14 OK OK 424 442 427 428 456 C3' C A 15 OK OK 454 472 457 458 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' G A 4 OK OK 107 125 104 106 139 C4' A A 5 OK OK 141 158 138 140 172 C4' C A 6 OK OK 174 189 171 173 203 C4' A A 7 OK OK 205 222 202 204 236 C4' U A 8 OK OK 238 253 235 237 266 C4' A A 9 OK OK 268 285 265 267 299 C4' G A 10 OK OK 301 319 298 300 333 C4' U A 11 OK OK 335 350 332 334 363 C4' C A 12 OK OK 365 380 362 364 394 C4' U A 13 OK OK 396 411 393 395 424 C4' U A 14 OK OK 426 441 423 425 454 C4' C A 15 OK OK 456 471 453 455 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' G A 4 OK OK 103 123 124 105 138 C5' A A 5 OK OK 137 156 157 139 171 C5' C A 6 OK OK 170 187 188 172 202 C5' A A 7 OK OK 201 220 221 203 235 C5' U A 8 OK OK 234 251 252 236 265 C5' A A 9 OK OK 264 283 284 266 298 C5' G A 10 OK OK 297 317 318 299 332 C5' U A 11 OK OK 331 348 349 333 362 C5' C A 12 OK OK 361 378 379 363 393 C5' U A 13 OK OK 392 409 410 394 423 C5' U A 14 OK OK 422 439 440 424 453 C5' C A 15 OK OK 452 469 470 454 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P G A 4 distorted distorted 74 101 102 103 134 P A A 5 distorted distorted 108 135 136 137 167 P C A 6 distorted distorted 142 168 169 170 198 P A A 7 distorted distorted 175 199 200 201 231 P U A 8 distorted distorted 206 232 233 234 261 P A A 9 distorted distorted 239 262 263 264 294 P G A 10 distorted distorted 269 295 296 297 328 P U A 11 distorted distorted 302 329 330 331 358 P C A 12 distorted distorted 336 359 360 361 389 P U A 13 distorted distorted 366 390 391 392 419 P U A 14 distorted distorted 397 420 421 422 449 P C A 15 distorted distorted 427 450 451 452 ---------------------------------------------------------------------------------