ID code: '4JRT' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 beta 8 14 11 36 C1' G A 2 beta 31 37 34 59 C1' G A 3 beta 54 60 57 82 C1' U A 4 beta 77 83 80 102 C1' G A 5 beta 97 103 100 125 C1' G A 6 beta 120 126 123 148 C1' U A 7 beta 143 149 146 168 C1' G A 8 beta 163 169 166 191 C1' C A 9 beta 186 192 189 211 C1' G A 10 beta 206 212 209 234 C1' G A 11 beta 229 235 232 257 C1' G A 12 beta 252 258 255 282 C1' C B 13 beta 277 283 280 302 C1' C B 14 beta 297 303 300 322 C1' U B 15 beta 317 323 320 342 C1' G B 16 beta 337 343 340 365 C1' C B 17 beta 360 366 363 385 C1' A B 18 beta 380 386 383 407 C1' C B 19 beta 402 408 405 427 C1' U B 20 beta 422 428 425 447 C1' G B 21 beta 442 448 445 470 C1' C B 22 beta 465 471 468 490 C1' C B 23 beta 485 491 488 510 C1' C B 24 beta 505 511 508 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK 13 9 12 34 C2' G A 2 OK 36 32 35 57 C2' G A 3 OK 59 55 58 80 C2' U A 4 OK 82 78 81 100 C2' G A 5 OK 102 98 101 123 C2' G A 6 OK 125 121 124 146 C2' U A 7 OK 148 144 147 166 C2' G A 8 OK 168 164 167 189 C2' C A 9 OK 191 187 190 209 C2' G A 10 OK 211 207 210 232 C2' G A 11 OK 234 230 233 255 C2' G A 12 OK 257 253 256 280 C2' C B 13 OK 282 278 281 300 C2' C B 14 OK 302 298 301 320 C2' U B 15 OK 322 318 321 340 C2' G B 16 OK 342 338 341 363 C2' C B 17 OK 365 361 364 383 C2' A B 18 OK 385 381 384 405 C2' C B 19 OK 407 403 406 425 C2' U B 20 OK 427 423 426 445 C2' G B 21 OK 447 443 446 468 C2' C B 22 OK 470 466 469 488 C2' C B 23 OK 490 486 489 508 C2' C B 24 OK 510 506 509 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK 7 10 11 32 C3' G A 2 OK 30 33 34 55 C3' G A 3 OK 53 56 57 78 C3' U A 4 OK 76 79 80 98 C3' G A 5 OK 96 99 100 121 C3' G A 6 OK 119 122 123 144 C3' U A 7 OK 142 145 146 164 C3' G A 8 OK 162 165 166 187 C3' C A 9 OK 185 188 189 207 C3' G A 10 OK 205 208 209 230 C3' G A 11 OK 228 231 232 253 C3' G A 12 OK 251 254 255 278 C3' C B 13 OK 276 279 280 298 C3' C B 14 OK 296 299 300 318 C3' U B 15 OK 316 319 320 338 C3' G B 16 OK 336 339 340 361 C3' C B 17 OK 359 362 363 381 C3' A B 18 OK 379 382 383 403 C3' C B 19 OK 401 404 405 423 C3' U B 20 OK 421 424 425 443 C3' G B 21 OK 441 444 445 466 C3' C B 22 OK 464 467 468 486 C3' C B 23 OK 484 487 488 506 C3' C B 24 OK 504 507 508 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK 9 6 8 30 C4' G A 2 OK 32 29 31 53 C4' G A 3 OK 55 52 54 76 C4' U A 4 OK 78 75 77 96 C4' G A 5 OK 98 95 97 119 C4' G A 6 OK 121 118 120 142 C4' U A 7 OK 144 141 143 162 C4' G A 8 OK 164 161 163 185 C4' C A 9 OK 187 184 186 205 C4' G A 10 OK 207 204 206 228 C4' G A 11 OK 230 227 229 251 C4' G A 12 OK 253 250 252 276 C4' C B 13 OK 278 275 277 296 C4' C B 14 OK 298 295 297 316 C4' U B 15 OK 318 315 317 336 C4' G B 16 OK 338 335 337 359 C4' C B 17 OK 361 358 360 379 C4' A B 18 OK 381 378 380 401 C4' C B 19 OK 403 400 402 421 C4' U B 20 OK 423 420 422 441 C4' G B 21 OK 443 440 442 464 C4' C B 22 OK 466 463 465 484 C4' C B 23 OK 486 483 485 504 C4' C B 24 OK 506 503 505 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 5 7 29 C5' G A 2 28 30 52 C5' G A 3 51 53 75 C5' U A 4 74 76 95 C5' G A 5 94 96 118 C5' G A 6 117 119 141 C5' U A 7 140 142 161 C5' G A 8 160 162 184 C5' C A 9 183 185 204 C5' G A 10 203 205 227 C5' G A 11 226 228 250 C5' G A 12 249 251 275 C5' C B 13 274 276 295 C5' C B 14 294 296 315 C5' U B 15 314 316 335 C5' G B 16 334 336 358 C5' C B 17 357 359 378 C5' A B 18 377 379 400 C5' C B 19 399 401 420 C5' U B 20 419 421 440 C5' G B 21 439 441 463 C5' C B 22 462 464 483 C5' C B 23 482 484 503 C5' C B 24 502 504 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 25 P G A 2 distorted distorted 10 26 27 28 48 P G A 3 distorted distorted 33 49 50 51 71 P U A 4 distorted distorted 56 72 73 74 91 P G A 5 distorted distorted 79 92 93 94 114 P G A 6 distorted distorted 99 115 116 117 137 P U A 7 distorted distorted 122 138 139 140 157 P G A 8 distorted distorted 145 158 159 160 180 P C A 9 distorted distorted 165 181 182 183 200 P G A 10 distorted distorted 188 201 202 203 223 P G A 11 distorted distorted 208 224 225 226 246 P G A 12 distorted distorted 231 247 248 249 271 P C B 13 distorted distorted 272 273 274 291 P C B 14 distorted distorted 279 292 293 294 311 P U B 15 distorted distorted 299 312 313 314 331 P G B 16 distorted distorted 319 332 333 334 354 P C B 17 distorted distorted 339 355 356 357 374 P A B 18 distorted distorted 362 375 376 377 396 P C B 19 distorted distorted 382 397 398 399 416 P U B 20 distorted distorted 404 417 418 419 436 P G B 21 distorted distorted 424 437 438 439 459 P C B 22 distorted distorted 444 460 461 462 479 P C B 23 distorted distorted 467 480 481 482 499 P C B 24 distorted distorted 487 500 501 502 ---------------------------------------------------------------------------------