ID code: '1JKQ' 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' --------------------------------------------------------------------------------- 11 C1' G A 3 beta 7 12 10 33 C1' T A 4 beta 29 34 32 53 C1' T A 5 beta 49 54 52 73 C1' T A 6 beta 69 74 72 93 C1' T A 7 beta 89 94 92 113 C1' T A 8 beta 109 114 112 133 C1' T A 9 beta 129 134 132 153 C1' A A 10 beta 149 154 152 174 C1' T A 11 beta 170 175 173 194 C1' A A 12 beta 190 195 193 215 C1' A A 13 beta 211 216 214 236 C1' G A 14 beta 232 237 235 259 C1' C B 18 beta 255 260 258 278 C1' T B 19 beta 274 279 277 298 C1' T B 20 beta 294 299 297 318 C1' A B 21 beta 314 319 317 339 C1' T B 22 beta 335 340 338 359 C1' A B 23 beta 355 360 358 380 C1' A B 24 beta 376 381 379 401 C1' A B 25 beta 397 402 400 422 C1' A B 26 beta 418 423 421 443 C1' A B 27 beta 439 444 442 464 C1' A B 28 beta 460 465 463 485 C1' C B 29 beta 481 486 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 3 11 8 32 C2' T A 4 33 30 52 C2' T A 5 53 50 72 C2' T A 6 73 70 92 C2' T A 7 93 90 112 C2' T A 8 113 110 132 C2' T A 9 133 130 152 C2' A A 10 153 150 173 C2' T A 11 174 171 193 C2' A A 12 194 191 214 C2' A A 13 215 212 235 C2' G A 14 236 233 258 C2' C B 18 259 256 277 C2' T B 19 278 275 297 C2' T B 20 298 295 317 C2' A B 21 318 315 338 C2' T B 22 339 336 358 C2' A B 23 359 356 379 C2' A B 24 380 377 400 C2' A B 25 401 398 421 C2' A B 26 422 419 442 C2' A B 27 443 440 463 C2' A B 28 464 461 484 C2' C B 29 485 482 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 3 OK 6 9 10 30 C3' T A 4 OK 28 31 32 50 C3' T A 5 OK 48 51 52 70 C3' T A 6 OK 68 71 72 90 C3' T A 7 OK 88 91 92 110 C3' T A 8 OK 108 111 112 130 C3' T A 9 OK 128 131 132 150 C3' A A 10 OK 148 151 152 171 C3' T A 11 OK 169 172 173 191 C3' A A 12 OK 189 192 193 212 C3' A A 13 OK 210 213 214 233 C3' G A 14 OK 231 234 235 256 C3' C B 18 OK 254 257 258 275 C3' T B 19 OK 273 276 277 295 C3' T B 20 OK 293 296 297 315 C3' A B 21 OK 313 316 317 336 C3' T B 22 OK 334 337 338 356 C3' A B 23 OK 354 357 358 377 C3' A B 24 OK 375 378 379 398 C3' A B 25 OK 396 399 400 419 C3' A B 26 OK 417 420 421 440 C3' A B 27 OK 438 441 442 461 C3' A B 28 OK 459 462 463 482 C3' C B 29 OK 480 483 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 3 OK 8 5 7 28 C4' T A 4 OK 30 27 29 48 C4' T A 5 OK 50 47 49 68 C4' T A 6 OK 70 67 69 88 C4' T A 7 OK 90 87 89 108 C4' T A 8 OK 110 107 109 128 C4' T A 9 OK 130 127 129 148 C4' A A 10 OK 150 147 149 169 C4' T A 11 OK 171 168 170 189 C4' A A 12 OK 191 188 190 210 C4' A A 13 OK 212 209 211 231 C4' G A 14 OK 233 230 232 254 C4' C B 18 OK 256 253 255 273 C4' T B 19 OK 275 272 274 293 C4' T B 20 OK 295 292 294 313 C4' A B 21 OK 315 312 314 334 C4' T B 22 OK 336 333 335 354 C4' A B 23 OK 356 353 355 375 C4' A B 24 OK 377 374 376 396 C4' A B 25 OK 398 395 397 417 C4' A B 26 OK 419 416 418 438 C4' A B 27 OK 440 437 439 459 C4' A B 28 OK 461 458 460 480 C4' C B 29 OK 482 479 481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 3 4 6 27 C5' T A 4 26 28 47 C5' T A 5 46 48 67 C5' T A 6 66 68 87 C5' T A 7 86 88 107 C5' T A 8 106 108 127 C5' T A 9 126 128 147 C5' A A 10 146 148 168 C5' T A 11 167 169 188 C5' A A 12 187 189 209 C5' A A 13 208 210 230 C5' G A 14 229 231 253 C5' C B 18 252 254 272 C5' T B 19 271 273 292 C5' T B 20 291 293 312 C5' A B 21 311 313 333 C5' T B 22 332 334 353 C5' A B 23 352 354 374 C5' A B 24 373 375 395 C5' A B 25 394 396 416 C5' A B 26 415 417 437 C5' A B 27 436 438 458 C5' A B 28 457 459 479 C5' C B 29 478 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 3 distorted distorted 2 3 4 23 P T A 4 distorted distorted 9 24 25 26 43 P T A 5 distorted distorted 31 44 45 46 63 P T A 6 distorted distorted 51 64 65 66 83 P T A 7 distorted distorted 71 84 85 86 103 P T A 8 distorted distorted 91 104 105 106 123 P T A 9 distorted distorted 111 124 125 126 143 P A A 10 distorted distorted 131 144 145 146 164 P T A 11 distorted distorted 151 165 166 167 184 P A A 12 distorted distorted 172 185 186 187 205 P A A 13 distorted distorted 192 206 207 208 226 P G A 14 distorted distorted 213 227 228 229 249 P C B 18 distorted distorted 250 251 252 268 P T B 19 distorted distorted 257 269 270 271 288 P T B 20 distorted distorted 276 289 290 291 308 P A B 21 distorted distorted 296 309 310 311 329 P T B 22 distorted distorted 316 330 331 332 349 P A B 23 distorted distorted 337 350 351 352 370 P A B 24 distorted distorted 357 371 372 373 391 P A B 25 distorted distorted 378 392 393 394 412 P A B 26 distorted distorted 399 413 414 415 433 P A B 27 distorted distorted 420 434 435 436 454 P A B 28 distorted distorted 441 455 456 457 475 P C B 29 distorted distorted 462 476 477 478 ---------------------------------------------------------------------------------