ID code: '4BW0' 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' G A 2 beta 27 33 30 55 C1' G A 3 beta 50 56 53 78 C1' G A 4 beta 73 79 76 101 C1' G A 5 beta 96 102 99 124 C1' A A 6 beta 119 125 122 146 C1' G A 7 beta 141 147 144 169 C1' C A 8 beta 164 170 167 189 C1' C A 9 beta 184 190 187 209 C1' G A 10 beta 204 210 207 232 C1' A A 11 beta 227 233 230 254 C1' A A 12 beta 249 255 252 276 C1' A A 13 beta 271 277 274 298 C1' G A 14 beta 293 299 296 321 C1' G A 15 beta 316 322 319 344 C1' C A 16 beta 339 345 342 364 C1' G A 17 beta 359 365 362 387 C1' A A 18 beta 382 388 385 409 C1' A A 19 beta 404 410 407 431 C1' G A 20 beta 426 432 429 454 C1' A A 21 beta 449 455 452 476 C1' A A 22 beta 471 477 474 498 C1' C A 23 beta 493 499 496 518 C1' C A 24 beta 513 519 516 538 C1' C A 25 beta 533 539 536 558 C1' A A 26 beta 553 559 556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK 32 28 31 53 C2' G A 3 OK 55 51 54 76 C2' G A 4 OK 78 74 77 99 C2' G A 5 OK 101 97 100 122 C2' A A 6 OK 124 120 123 144 C2' G A 7 OK 146 142 145 167 C2' C A 8 OK 169 165 168 187 C2' C A 9 OK 189 185 188 207 C2' G A 10 OK 209 205 208 230 C2' A A 11 OK 232 228 231 252 C2' A A 12 OK 254 250 253 274 C2' A A 13 OK 276 272 275 296 C2' G A 14 OK 298 294 297 319 C2' G A 15 OK 321 317 320 342 C2' C A 16 OK 344 340 343 362 C2' G A 17 OK 364 360 363 385 C2' A A 18 OK 387 383 386 407 C2' A A 19 OK 409 405 408 429 C2' G A 20 OK 431 427 430 452 C2' A A 21 OK 454 450 453 474 C2' A A 22 OK 476 472 475 496 C2' C A 23 OK 498 494 497 516 C2' C A 24 OK 518 514 517 536 C2' C A 25 OK 538 534 537 556 C2' A A 26 OK 558 554 557 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' G A 3 OK 49 52 53 74 C3' G A 4 OK 72 75 76 97 C3' G A 5 OK 95 98 99 120 C3' A A 6 OK 118 121 122 142 C3' G A 7 OK 140 143 144 165 C3' C A 8 OK 163 166 167 185 C3' C A 9 OK 183 186 187 205 C3' G A 10 OK 203 206 207 228 C3' A A 11 OK 226 229 230 250 C3' A A 12 OK 248 251 252 272 C3' A A 13 OK 270 273 274 294 C3' G A 14 OK 292 295 296 317 C3' G A 15 OK 315 318 319 340 C3' C A 16 OK 338 341 342 360 C3' G A 17 OK 358 361 362 383 C3' A A 18 OK 381 384 385 405 C3' A A 19 OK 403 406 407 427 C3' G A 20 OK 425 428 429 450 C3' A A 21 OK 448 451 452 472 C3' A A 22 OK 470 473 474 494 C3' C A 23 OK 492 495 496 514 C3' C A 24 OK 512 515 516 534 C3' C A 25 OK 532 535 536 554 C3' A A 26 OK 552 555 556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' G A 3 OK 51 48 50 72 C4' G A 4 OK 74 71 73 95 C4' G A 5 OK 97 94 96 118 C4' A A 6 OK 120 117 119 140 C4' G A 7 OK 142 139 141 163 C4' C A 8 OK 165 162 164 183 C4' C A 9 OK 185 182 184 203 C4' G A 10 OK 205 202 204 226 C4' A A 11 OK 228 225 227 248 C4' A A 12 OK 250 247 249 270 C4' A A 13 OK 272 269 271 292 C4' G A 14 OK 294 291 293 315 C4' G A 15 OK 317 314 316 338 C4' C A 16 OK 340 337 339 358 C4' G A 17 OK 360 357 359 381 C4' A A 18 OK 383 380 382 403 C4' A A 19 OK 405 402 404 425 C4' G A 20 OK 427 424 426 448 C4' A A 21 OK 450 447 449 470 C4' A A 22 OK 472 469 471 492 C4' C A 23 OK 494 491 493 512 C4' C A 24 OK 514 511 513 532 C4' C A 25 OK 534 531 533 552 C4' A A 26 OK 554 551 553 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' G A 3 47 49 71 C5' G A 4 70 72 94 C5' G A 5 93 95 117 C5' A A 6 116 118 139 C5' G A 7 138 140 162 C5' C A 8 161 163 182 C5' C A 9 181 183 202 C5' G A 10 201 203 225 C5' A A 11 224 226 247 C5' A A 12 246 248 269 C5' A A 13 268 270 291 C5' G A 14 290 292 314 C5' G A 15 313 315 337 C5' C A 16 336 338 357 C5' G A 17 356 358 380 C5' A A 18 379 381 402 C5' A A 19 401 403 424 C5' G A 20 423 425 447 C5' A A 21 446 448 469 C5' A A 22 468 470 491 C5' C A 23 490 492 511 C5' C A 24 510 512 531 C5' C A 25 530 532 551 C5' A A 26 550 552 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P G A 3 distorted distorted 29 45 46 47 67 P G A 4 distorted distorted 52 68 69 70 90 P G A 5 distorted distorted 75 91 92 93 113 P A A 6 distorted distorted 98 114 115 116 135 P G A 7 distorted distorted 121 136 137 138 158 P C A 8 distorted distorted 143 159 160 161 178 P C A 9 OK OK 166 179 180 181 198 P G A 10 distorted distorted 186 199 200 201 221 P A A 11 OK OK 206 222 223 224 243 P A A 12 distorted distorted 229 244 245 246 265 P A A 13 distorted distorted 251 266 267 268 287 P G A 14 distorted distorted 273 288 289 290 310 P G A 15 distorted distorted 295 311 312 313 333 P C A 16 distorted distorted 318 334 335 336 353 P G A 17 OK OK 341 354 355 356 376 P A A 18 distorted distorted 361 377 378 379 398 P A A 19 distorted distorted 384 399 400 401 420 P G A 20 distorted distorted 406 421 422 423 443 P A A 21 distorted distorted 428 444 445 446 465 P A A 22 distorted distorted 451 466 467 468 487 P C A 23 distorted distorted 473 488 489 490 507 P C A 24 distorted distorted 495 508 509 510 527 P C A 25 distorted distorted 515 528 529 530 547 P A A 26 distorted distorted 535 548 549 550 ---------------------------------------------------------------------------------