ID code: '5KIB' 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' --------------------------------------------------------------------------------- 8 C1' DT A 1 alpha beta 4 24 9 7 41 C1' DT A 2 alpha beta 37 57 42 40 73 C1' DA A 3 alpha beta 69 90 74 72 105 C1' DG A 4 alpha beta 101 123 106 104 139 C1' G A 5 alpha beta 134 157 140 137 172 C1' DC A 6 alpha beta 168 187 173 171 202 C1' DC A 7 alpha beta 198 217 203 201 232 C1' DT A 8 alpha beta 228 248 233 231 264 C1' DG A 9 alpha beta 260 283 265 263 296 C1' DC B 10 alpha beta 292 311 297 295 327 C1' DA B 11 alpha beta 323 344 328 326 359 C1' DG B 12 alpha beta 355 377 360 358 392 C1' DG B 13 alpha beta 388 410 393 391 425 C1' DC B 14 alpha beta 421 440 426 424 455 C1' DC B 15 alpha beta 451 470 456 454 485 C1' DT B 16 alpha beta 481 501 486 484 517 C1' DA B 17 alpha beta 513 534 518 516 549 C1' DA B 18 alpha beta 545 567 550 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DT A 1 OK OK 8 5 22 23 40 C2' DT A 2 OK OK 41 38 55 56 72 C2' DA A 3 OK OK 73 70 88 89 104 C2' DG A 4 OK OK 105 102 121 122 137 C2' G A 5 OK OK 139 135 155 138 171 C2' DC A 6 OK OK 172 169 185 186 201 C2' DC A 7 OK OK 202 199 215 216 231 C2' DT A 8 OK OK 232 229 246 247 263 C2' DG A 9 OK OK 264 261 281 282 295 C2' DC B 10 OK OK 296 293 309 310 326 C2' DA B 11 OK OK 327 324 342 343 358 C2' DG B 12 OK OK 359 356 375 376 391 C2' DG B 13 OK OK 392 389 408 409 424 C2' DC B 14 OK OK 425 422 438 439 454 C2' DC B 15 OK OK 455 452 468 469 484 C2' DT B 16 OK OK 485 482 499 500 516 C2' DA B 17 OK OK 517 514 532 533 548 C2' DA B 18 OK OK 549 546 565 566 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DT A 1 OK OK 3 21 6 7 38 C3' DT A 2 OK OK 36 54 39 40 70 C3' DA A 3 OK OK 68 87 71 72 102 C3' DG A 4 OK OK 100 120 103 104 135 C3' G A 5 OK OK 133 154 136 137 169 C3' DC A 6 OK OK 167 184 170 171 199 C3' DC A 7 OK OK 197 214 200 201 229 C3' DT A 8 OK OK 227 245 230 231 261 C3' DG A 9 OK OK 259 279 262 263 293 C3' DC B 10 OK OK 291 308 294 295 324 C3' DA B 11 OK OK 322 341 325 326 356 C3' DG B 12 OK OK 354 374 357 358 389 C3' DG B 13 OK OK 387 407 390 391 422 C3' DC B 14 OK OK 420 437 423 424 452 C3' DC B 15 OK OK 450 467 453 454 482 C3' DT B 16 OK OK 480 498 483 484 514 C3' DA B 17 OK OK 512 531 515 516 546 C3' DA B 18 OK OK 544 563 547 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DT A 1 OK OK 5 20 2 4 36 C4' DT A 2 OK OK 38 53 35 37 68 C4' DA A 3 OK OK 70 86 67 69 100 C4' DG A 4 OK OK 102 119 99 101 133 C4' G A 5 OK OK 135 153 132 134 167 C4' DC A 6 OK OK 169 183 166 168 197 C4' DC A 7 OK OK 199 213 196 198 227 C4' DT A 8 OK OK 229 244 226 228 259 C4' DG A 9 OK OK 261 278 258 260 291 C4' DC B 10 OK OK 293 307 290 292 322 C4' DA B 11 OK OK 324 340 321 323 354 C4' DG B 12 OK OK 356 373 353 355 387 C4' DG B 13 OK OK 389 406 386 388 420 C4' DC B 14 OK OK 422 436 419 421 450 C4' DC B 15 OK OK 452 466 449 451 480 C4' DT B 16 OK OK 482 497 479 481 512 C4' DA B 17 OK OK 514 530 511 513 544 C4' DA B 18 OK OK 546 562 543 545 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DT A 1 OK OK 1 18 19 3 35 C5' DT A 2 OK OK 34 51 52 36 67 C5' DA A 3 OK OK 66 84 85 68 99 C5' DG A 4 OK OK 98 117 118 100 132 C5' G A 5 OK OK 131 151 152 133 166 C5' DC A 6 OK OK 165 181 182 167 196 C5' DC A 7 OK OK 195 211 212 197 226 C5' DT A 8 OK OK 225 242 243 227 258 C5' DG A 9 OK OK 257 276 277 259 290 C5' DC B 10 OK OK 289 305 306 291 321 C5' DA B 11 OK OK 320 338 339 322 353 C5' DG B 12 OK OK 352 371 372 354 386 C5' DG B 13 OK OK 385 404 405 387 419 C5' DC B 14 OK OK 418 434 435 420 449 C5' DC B 15 OK OK 448 464 465 450 479 C5' DT B 16 OK OK 478 495 496 480 511 C5' DA B 17 OK OK 510 528 529 512 543 C5' DA B 18 OK OK 542 560 561 544 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 31 P DT A 2 distorted distorted 6 32 33 34 63 P DA A 3 distorted distorted 39 64 65 66 95 P DG A 4 distorted distorted 71 96 97 98 128 P G A 5 distorted distorted 103 129 130 131 162 P DC A 6 distorted distorted 136 163 164 165 192 P DC A 7 distorted distorted 170 193 194 195 222 P DT A 8 distorted distorted 200 223 224 225 254 P DG A 9 distorted distorted 230 255 256 257 317 P DA B 11 distorted distorted 294 318 319 320 349 P DG B 12 distorted distorted 325 350 351 352 382 P DG B 13 distorted distorted 357 383 384 385 415 P DC B 14 distorted distorted 390 416 417 418 445 P DC B 15 distorted distorted 423 446 447 448 475 P DT B 16 distorted distorted 453 476 477 478 507 P DA B 17 distorted distorted 483 508 509 510 539 P DA B 18 distorted distorted 515 540 541 542 ---------------------------------------------------------------------------------