ID code: '3CGP' 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 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' G A 3 beta 47 53 50 75 C1' C A 4 beta 70 76 73 95 C1' G A 5 beta 90 96 93 115 C1' PSU A 6 beta 121 111 116 138 C1' A A 7 beta 133 139 136 160 C1' G A 8 beta 155 161 158 183 C1' U A 9 beta 178 184 181 203 C1' A A 10 beta 198 204 201 225 C1' G A 11 beta 220 226 223 248 C1' C A 12 beta 243 249 246 266 C1' C B 13 beta 261 267 264 286 C1' G B 14 beta 281 287 284 309 C1' C B 15 beta 304 310 307 329 C1' U B 16 beta 324 330 327 349 C1' A B 17 beta 344 350 347 371 C1' C B 18 beta 366 372 369 391 C1' U B 19 beta 386 392 389 411 C1' A B 20 beta 406 412 409 433 C1' A B 21 beta 428 434 431 455 C1' C B 22 beta 450 456 453 475 C1' G B 23 beta 470 476 473 498 C1' C B 24 beta 493 499 496 518 C1' G B 25 beta 513 519 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' G A 3 OK 52 48 51 73 C2' C A 4 OK 75 71 74 93 C2' G A 5 OK 95 91 94 116 C2' PSU A 6 OK 115 118 117 136 C2' A A 7 OK 138 134 137 158 C2' G A 8 OK 160 156 159 181 C2' U A 9 OK 183 179 182 201 C2' A A 10 OK 203 199 202 223 C2' G A 11 OK 225 221 224 246 C2' C A 12 OK 248 244 247 264 C2' C B 13 OK 266 262 265 284 C2' G B 14 OK 286 282 285 307 C2' C B 15 OK 309 305 308 327 C2' U B 16 OK 329 325 328 347 C2' A B 17 OK 349 345 348 369 C2' C B 18 OK 371 367 370 389 C2' U B 19 OK 391 387 390 409 C2' A B 20 OK 411 407 410 431 C2' A B 21 OK 433 429 432 453 C2' C B 22 OK 455 451 454 473 C2' G B 23 OK 475 471 474 496 C2' C B 24 OK 498 494 497 516 C2' G B 25 OK 518 514 517 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' G A 3 OK 46 49 50 71 C3' C A 4 OK 69 72 73 91 C3' G A 5 OK 89 92 93 118 C3' PSU A 6 OK 119 120 116 134 C3' A A 7 OK 132 135 136 156 C3' G A 8 OK 154 157 158 179 C3' U A 9 OK 177 180 181 199 C3' A A 10 OK 197 200 201 221 C3' G A 11 OK 219 222 223 244 C3' C A 12 OK 242 245 246 262 C3' C B 13 OK 260 263 264 282 C3' G B 14 OK 280 283 284 305 C3' C B 15 OK 303 306 307 325 C3' U B 16 OK 323 326 327 345 C3' A B 17 OK 343 346 347 367 C3' C B 18 OK 365 368 369 387 C3' U B 19 OK 385 388 389 407 C3' A B 20 OK 405 408 409 429 C3' A B 21 OK 427 430 431 451 C3' C B 22 OK 449 452 453 471 C3' G B 23 OK 469 472 473 494 C3' C B 24 OK 492 495 496 514 C3' G B 25 OK 512 515 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' G A 3 OK 48 45 47 69 C4' C A 4 OK 71 68 70 89 C4' G A 5 OK 91 88 90 119 C4' PSU A 6 OK 118 122 121 132 C4' A A 7 OK 134 131 133 154 C4' G A 8 OK 156 153 155 177 C4' U A 9 OK 179 176 178 197 C4' A A 10 OK 199 196 198 219 C4' G A 11 OK 221 218 220 242 C4' C A 12 OK 244 241 243 260 C4' C B 13 OK 262 259 261 280 C4' G B 14 OK 282 279 281 303 C4' C B 15 OK 305 302 304 323 C4' U B 16 OK 325 322 324 343 C4' A B 17 OK 345 342 344 365 C4' C B 18 OK 367 364 366 385 C4' U B 19 OK 387 384 386 405 C4' A B 20 OK 407 404 406 427 C4' A B 21 OK 429 426 428 449 C4' C B 22 OK 451 448 450 469 C4' G B 23 OK 471 468 470 492 C4' C B 24 OK 494 491 493 512 C4' G B 25 OK 514 511 513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' G A 3 44 46 68 C5' C A 4 67 69 88 C5' G A 5 87 89 122 C5' PSU A 6 123 119 131 C5' A A 7 130 132 153 C5' G A 8 152 154 176 C5' U A 9 175 177 196 C5' A A 10 195 197 218 C5' G A 11 217 219 241 C5' C A 12 240 242 259 C5' C B 13 258 260 279 C5' G B 14 278 280 302 C5' C B 15 301 303 322 C5' U B 16 321 323 342 C5' A B 17 341 343 364 C5' C B 18 363 365 384 C5' U B 19 383 385 404 C5' A B 20 403 405 426 C5' A B 21 425 427 448 C5' C B 22 447 449 468 C5' G B 23 467 469 491 C5' C B 24 490 492 511 C5' G B 25 510 512 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P C A 4 distorted distorted 49 65 66 67 84 P G A 5 distorted distorted 72 85 86 87 124 P PSU A 6 distorted distorted 92 125 126 123 127 P A A 7 distorted distorted 120 128 129 130 149 P G A 8 distorted distorted 135 150 151 152 172 P U A 9 distorted distorted 157 173 174 175 192 P A A 10 distorted distorted 180 193 194 195 214 P G A 11 distorted distorted 200 215 216 217 237 P C A 12 distorted distorted 222 238 239 240 275 P G B 14 distorted distorted 263 276 277 278 298 P C B 15 distorted distorted 283 299 300 301 318 P U B 16 distorted distorted 306 319 320 321 338 P A B 17 distorted distorted 326 339 340 341 360 P C B 18 distorted distorted 346 361 362 363 380 P U B 19 distorted distorted 368 381 382 383 400 P A B 20 distorted distorted 388 401 402 403 422 P A B 21 distorted distorted 408 423 424 425 444 P C B 22 distorted distorted 430 445 446 447 464 P G B 23 distorted distorted 452 465 466 467 487 P C B 24 distorted distorted 472 488 489 490 507 P G B 25 distorted distorted 495 508 509 510 ---------------------------------------------------------------------------------