ID code: '2KYE' 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 43 C1' A A 2 alpha beta 38 60 44 41 76 C1' G A 3 alpha beta 71 94 77 74 110 C1' A A 4 alpha beta 105 127 111 108 143 C1' G A 5 alpha beta 138 161 144 141 174 C1' PSU A 6 alpha beta 180 189 170 175 204 C1' PSU A 7 alpha beta 210 219 200 205 237 C1' G A 8 alpha beta 232 255 238 235 271 C1' G A 9 alpha beta 266 289 272 269 305 C1' G A 10 alpha beta 300 323 306 303 339 C1' C A 11 alpha beta 334 354 340 337 367 C1' PSU A 12 alpha beta 373 382 363 368 400 C1' C A 13 alpha beta 395 415 401 398 428 C1' PSU A 14 alpha beta 434 443 424 429 461 C1' C A 15 alpha beta 456 476 462 459 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' A A 2 OK OK 43 39 58 42 74 C2' G A 3 OK OK 76 72 92 75 108 C2' A A 4 OK OK 110 106 125 109 141 C2' G A 5 OK OK 143 139 159 142 175 C2' PSU A 6 OK OK 174 177 190 176 205 C2' PSU A 7 OK OK 204 207 220 206 235 C2' G A 8 OK OK 237 233 253 236 269 C2' G A 9 OK OK 271 267 287 270 303 C2' G A 10 OK OK 305 301 321 304 337 C2' C A 11 OK OK 339 335 352 338 368 C2' PSU A 12 OK OK 367 370 383 369 398 C2' C A 13 OK OK 400 396 413 399 429 C2' PSU A 14 OK OK 428 431 444 430 459 C2' C A 15 OK OK 461 457 474 460 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' A A 2 OK OK 37 57 40 41 72 C3' G A 3 OK OK 70 91 73 74 106 C3' A A 4 OK OK 104 124 107 108 139 C3' G A 5 OK OK 137 158 140 141 177 C3' PSU A 6 OK OK 178 192 179 175 207 C3' PSU A 7 OK OK 208 222 209 205 233 C3' G A 8 OK OK 231 252 234 235 267 C3' G A 9 OK OK 265 286 268 269 301 C3' G A 10 OK OK 299 320 302 303 335 C3' C A 11 OK OK 333 351 336 337 370 C3' PSU A 12 OK OK 371 385 372 368 396 C3' C A 13 OK OK 394 412 397 398 431 C3' PSU A 14 OK OK 432 446 433 429 457 C3' C A 15 OK OK 455 473 458 459 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' A A 2 OK OK 39 56 36 38 70 C4' G A 3 OK OK 72 90 69 71 104 C4' A A 4 OK OK 106 123 103 105 137 C4' G A 5 OK OK 139 157 136 138 178 C4' PSU A 6 OK OK 177 193 181 180 208 C4' PSU A 7 OK OK 207 223 211 210 231 C4' G A 8 OK OK 233 251 230 232 265 C4' G A 9 OK OK 267 285 264 266 299 C4' G A 10 OK OK 301 319 298 300 333 C4' C A 11 OK OK 335 350 332 334 371 C4' PSU A 12 OK OK 370 386 374 373 394 C4' C A 13 OK OK 396 411 393 395 432 C4' PSU A 14 OK OK 431 447 435 434 455 C4' C A 15 OK OK 457 472 454 456 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 36 C5' A A 2 OK OK 35 54 55 37 69 C5' G A 3 OK OK 68 88 89 70 103 C5' A A 4 OK OK 102 121 122 104 136 C5' G A 5 OK OK 135 155 156 137 181 C5' PSU A 6 OK OK 182 194 195 178 211 C5' PSU A 7 OK OK 212 224 225 208 230 C5' G A 8 OK OK 229 249 250 231 264 C5' G A 9 OK OK 263 283 284 265 298 C5' G A 10 OK OK 297 317 318 299 332 C5' C A 11 OK OK 331 348 349 333 374 C5' PSU A 12 OK OK 375 387 388 371 393 C5' C A 13 OK OK 392 409 410 394 435 C5' PSU A 14 OK OK 436 448 449 432 454 C5' C A 15 OK OK 453 470 471 455 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P A A 2 distorted distorted 6 33 34 35 65 P G A 3 distorted distorted 40 66 67 68 99 P A A 4 distorted distorted 73 100 101 102 132 P G A 5 distorted distorted 107 133 134 135 183 P PSU A 6 distorted distorted 140 184 185 182 213 P PSU A 7 distorted distorted 179 214 215 212 226 P G A 8 distorted distorted 209 227 228 229 260 P G A 9 distorted distorted 234 261 262 263 294 P G A 10 distorted distorted 268 295 296 297 328 P C A 11 distorted distorted 302 329 330 331 376 P PSU A 12 distorted distorted 336 377 378 375 389 P C A 13 distorted distorted 372 390 391 392 437 P PSU A 14 distorted distorted 397 438 439 436 450 P C A 15 distorted distorted 433 451 452 453 ---------------------------------------------------------------------------------