ID code: '2KBD' 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' --------------------------------------------------------------------------------- 7 C1' C A 1 beta 3 8 6 26 C1' T A 2 beta 22 27 25 46 C1' G A 3 beta 42 47 45 68 C1' G A 4 beta 64 69 67 90 C1' G A 5 beta 86 91 89 112 C1' G A 6 beta 108 113 111 134 C1' A A 7 beta 130 135 133 155 C1' C A 8 beta 151 156 154 174 C1' T A 9 beta 170 175 173 194 C1' T A 10 beta 190 195 193 214 C1' T A 11 beta 210 215 213 234 C1' C A 12 beta 230 235 233 253 C1' C A 13 beta 249 254 252 272 C1' A A 14 beta 268 273 271 293 C1' G A 15 beta 289 294 292 315 C1' G A 16 beta 311 316 314 334 C1' C B 32 beta 330 335 333 349 C1' C B 31 beta 345 350 348 368 C1' T B 30 beta 364 369 367 388 C1' G B 29 beta 384 389 387 410 C1' G B 28 beta 406 411 409 432 C1' A B 27 beta 428 433 431 453 C1' A B 26 beta 449 454 452 474 C1' A B 25 beta 470 475 473 495 C1' G B 24 beta 491 496 494 517 C1' T B 23 beta 513 518 516 537 C1' C B 22 beta 533 538 536 556 C1' C B 21 beta 552 557 555 575 C1' C B 20 beta 571 576 574 594 C1' C B 19 beta 590 595 593 613 C1' A B 18 beta 609 614 612 634 C1' G B 17 beta 630 635 633 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6 C2' C A 1 7 4 25 C2' T A 2 26 23 45 C2' G A 3 46 43 67 C2' G A 4 68 65 89 C2' G A 5 90 87 111 C2' G A 6 112 109 133 C2' A A 7 134 131 154 C2' C A 8 155 152 173 C2' T A 9 174 171 193 C2' T A 10 194 191 213 C2' T A 11 214 211 233 C2' C A 12 234 231 252 C2' C A 13 253 250 271 C2' A A 14 272 269 292 C2' G A 15 293 290 314 C2' G A 16 315 312 333 C2' C B 32 334 331 348 C2' C B 31 349 346 367 C2' T B 30 368 365 387 C2' G B 29 388 385 409 C2' G B 28 410 407 431 C2' A B 27 432 429 452 C2' A B 26 453 450 473 C2' A B 25 474 471 494 C2' G B 24 495 492 516 C2' T B 23 517 514 536 C2' C B 22 537 534 555 C2' C B 21 556 553 574 C2' C B 20 575 572 593 C2' C B 19 594 591 612 C2' A B 18 613 610 633 C2' G B 17 634 631 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4 C3' C A 1 OK 2 5 6 23 C3' T A 2 OK 21 24 25 43 C3' G A 3 OK 41 44 45 65 C3' G A 4 OK 63 66 67 87 C3' G A 5 OK 85 88 89 109 C3' G A 6 OK 107 110 111 131 C3' A A 7 OK 129 132 133 152 C3' C A 8 OK 150 153 154 171 C3' T A 9 OK 169 172 173 191 C3' T A 10 OK 189 192 193 211 C3' T A 11 OK 209 212 213 231 C3' C A 12 OK 229 232 233 250 C3' C A 13 OK 248 251 252 269 C3' A A 14 OK 267 270 271 290 C3' G A 15 OK 288 291 292 312 C3' G A 16 OK 310 313 314 331 C3' C B 32 OK 329 332 333 346 C3' C B 31 OK 344 347 348 365 C3' T B 30 OK 363 366 367 385 C3' G B 29 OK 383 386 387 407 C3' G B 28 OK 405 408 409 429 C3' A B 27 OK 427 430 431 450 C3' A B 26 OK 448 451 452 471 C3' A B 25 OK 469 472 473 492 C3' G B 24 OK 490 493 494 514 C3' T B 23 OK 512 515 516 534 C3' C B 22 OK 532 535 536 553 C3' C B 21 OK 551 554 555 572 C3' C B 20 OK 570 573 574 591 C3' C B 19 OK 589 592 593 610 C3' A B 18 OK 608 611 612 631 C3' G B 17 OK 629 632 633 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2 C4' C A 1 OK 4 1 3 21 C4' T A 2 OK 23 20 22 41 C4' G A 3 OK 43 40 42 63 C4' G A 4 OK 65 62 64 85 C4' G A 5 OK 87 84 86 107 C4' G A 6 OK 109 106 108 129 C4' A A 7 OK 131 128 130 150 C4' C A 8 OK 152 149 151 169 C4' T A 9 OK 171 168 170 189 C4' T A 10 OK 191 188 190 209 C4' T A 11 OK 211 208 210 229 C4' C A 12 OK 231 228 230 248 C4' C A 13 OK 250 247 249 267 C4' A A 14 OK 269 266 268 288 C4' G A 15 OK 290 287 289 310 C4' G A 16 OK 312 309 311 329 C4' C B 32 OK 331 328 330 344 C4' C B 31 OK 346 343 345 363 C4' T B 30 OK 365 362 364 383 C4' G B 29 OK 385 382 384 405 C4' G B 28 OK 407 404 406 427 C4' A B 27 OK 429 426 428 448 C4' A B 26 OK 450 447 449 469 C4' A B 25 OK 471 468 470 490 C4' G B 24 OK 492 489 491 512 C4' T B 23 OK 514 511 513 532 C4' C B 22 OK 534 531 533 551 C4' C B 21 OK 553 550 552 570 C4' C B 20 OK 572 569 571 589 C4' C B 19 OK 591 588 590 608 C4' A B 18 OK 610 607 609 629 C4' G B 17 OK 631 628 630 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1 C5' C A 1 2 20 C5' T A 2 19 21 40 C5' G A 3 39 41 62 C5' G A 4 61 63 84 C5' G A 5 83 85 106 C5' G A 6 105 107 128 C5' A A 7 127 129 149 C5' C A 8 148 150 168 C5' T A 9 167 169 188 C5' T A 10 187 189 208 C5' T A 11 207 209 228 C5' C A 12 227 229 247 C5' C A 13 246 248 266 C5' A A 14 265 267 287 C5' G A 15 286 288 309 C5' G A 16 308 310 328 C5' C B 32 329 343 C5' C B 31 361 344 362 C5' T B 30 381 363 382 C5' G B 29 403 383 404 C5' G B 28 425 405 426 C5' A B 27 446 427 447 C5' A B 26 467 448 468 C5' A B 25 488 469 489 C5' G B 24 510 490 511 C5' T B 23 530 512 531 C5' C B 22 549 532 550 C5' C B 21 568 551 569 C5' C B 20 587 570 588 C5' C B 19 606 589 607 C5' A B 18 627 608 628 C5' G B 17 649 629 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 16 P T A 2 OK OK 5 17 18 19 36 P G A 3 OK OK 24 37 38 39 58 P G A 4 OK OK 44 59 60 61 80 P G A 5 OK OK 66 81 82 83 102 P G A 6 OK OK 88 103 104 105 124 P A A 7 OK OK 110 125 126 127 145 P C A 8 OK OK 132 146 147 148 164 P T A 9 OK OK 153 165 166 167 184 P T A 10 OK OK 172 185 186 187 204 P T A 11 OK OK 192 205 206 207 224 P C A 12 OK OK 212 225 226 227 243 P C A 13 OK OK 232 244 245 246 262 P A A 14 OK OK 251 263 264 265 283 P G A 15 OK OK 270 284 285 286 305 P G A 16 OK OK 291 306 307 308 358 P C B 31 OK OK 332 359 360 361 378 P T B 30 OK OK 347 379 380 381 400 P G B 29 OK OK 366 401 402 403 422 P G B 28 OK OK 386 423 424 425 443 P A B 27 OK OK 408 444 445 446 464 P A B 26 OK OK 430 465 466 467 485 P A B 25 OK OK 451 486 487 488 507 P G B 24 OK OK 472 508 509 510 527 P T B 23 OK OK 493 528 529 530 546 P C B 22 OK OK 515 547 548 549 565 P C B 21 OK OK 535 566 567 568 584 P C B 20 OK OK 554 585 586 587 603 P C B 19 OK OK 573 604 605 606 624 P A B 18 OK OK 592 625 626 627 646 P G B 17 OK OK 611 647 648 649 ---------------------------------------------------------------------------------