ID code: '4FTE' 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' --------------------------------------------------------------------------------- 7398 C1' U R 1 beta 7393 7399 7396 7418 C1' U R 2 beta 7413 7419 7416 7438 C1' U R 3 beta 7433 7439 7436 7458 C1' C R 4 beta 7453 7459 7456 7478 C1' U R 5 beta 7473 7479 7476 7498 C1' C R 6 beta 7493 7499 7496 7518 C1' U R 7 beta 7513 7519 7516 7538 C1' U R 8 beta 7533 7539 7536 7558 C1' U R 9 beta 7553 7559 7556 7578 C1' U R 10 beta 7573 7579 7576 7598 C1' A R 11 beta 7593 7599 7596 7620 C1' U R 12 beta 7615 7621 7618 7640 C1' C R 13 beta 7635 7641 7638 7660 C1' U R 14 beta 7655 7661 7658 7680 C1' U R 15 beta 7675 7681 7678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7396 C2' U R 1 OK 7398 7394 7397 7416 C2' U R 2 OK 7418 7414 7417 7436 C2' U R 3 OK 7438 7434 7437 7456 C2' C R 4 OK 7458 7454 7457 7476 C2' U R 5 OK 7478 7474 7477 7496 C2' C R 6 OK 7498 7494 7497 7516 C2' U R 7 OK 7518 7514 7517 7536 C2' U R 8 OK 7538 7534 7537 7556 C2' U R 9 OK 7558 7554 7557 7576 C2' U R 10 OK 7578 7574 7577 7596 C2' A R 11 OK 7598 7594 7597 7618 C2' U R 12 OK 7620 7616 7619 7638 C2' C R 13 OK 7640 7636 7639 7658 C2' U R 14 OK 7660 7656 7659 7678 C2' U R 15 OK 7680 7676 7679 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7394 C3' U R 1 OK 7392 7395 7396 7414 C3' U R 2 OK 7412 7415 7416 7434 C3' U R 3 OK 7432 7435 7436 7454 C3' C R 4 OK 7452 7455 7456 7474 C3' U R 5 OK 7472 7475 7476 7494 C3' C R 6 OK 7492 7495 7496 7514 C3' U R 7 OK 7512 7515 7516 7534 C3' U R 8 OK 7532 7535 7536 7554 C3' U R 9 OK 7552 7555 7556 7574 C3' U R 10 OK 7572 7575 7576 7594 C3' A R 11 OK 7592 7595 7596 7616 C3' U R 12 OK 7614 7617 7618 7636 C3' C R 13 OK 7634 7637 7638 7656 C3' U R 14 OK 7654 7657 7658 7676 C3' U R 15 OK 7674 7677 7678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7392 C4' U R 1 OK 7394 7391 7393 7412 C4' U R 2 OK 7414 7411 7413 7432 C4' U R 3 OK 7434 7431 7433 7452 C4' C R 4 OK 7454 7451 7453 7472 C4' U R 5 OK 7474 7471 7473 7492 C4' C R 6 OK 7494 7491 7493 7512 C4' U R 7 OK 7514 7511 7513 7532 C4' U R 8 OK 7534 7531 7533 7552 C4' U R 9 OK 7554 7551 7553 7572 C4' U R 10 OK 7574 7571 7573 7592 C4' A R 11 OK 7594 7591 7593 7614 C4' U R 12 OK 7616 7613 7615 7634 C4' C R 13 OK 7636 7633 7635 7654 C4' U R 14 OK 7656 7653 7655 7674 C4' U R 15 OK 7676 7673 7675 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7391 C5' U R 1 7390 7392 7411 C5' U R 2 7410 7412 7431 C5' U R 3 7430 7432 7451 C5' C R 4 7450 7452 7471 C5' U R 5 7470 7472 7491 C5' C R 6 7490 7492 7511 C5' U R 7 7510 7512 7531 C5' U R 8 7530 7532 7551 C5' U R 9 7550 7552 7571 C5' U R 10 7570 7572 7591 C5' A R 11 7590 7592 7613 C5' U R 12 7612 7614 7633 C5' C R 13 7632 7634 7653 C5' U R 14 7652 7654 7673 C5' U R 15 7672 7674 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7387 P U R 1 distorted distorted 7388 7389 7390 7407 P U R 2 distorted distorted 7395 7408 7409 7410 7427 P U R 3 distorted distorted 7415 7428 7429 7430 7447 P C R 4 distorted distorted 7435 7448 7449 7450 7467 P U R 5 distorted distorted 7455 7468 7469 7470 7487 P C R 6 distorted distorted 7475 7488 7489 7490 7507 P U R 7 distorted distorted 7495 7508 7509 7510 7527 P U R 8 distorted distorted 7515 7528 7529 7530 7547 P U R 9 distorted distorted 7535 7548 7549 7550 7567 P U R 10 distorted distorted 7555 7568 7569 7570 7587 P A R 11 distorted distorted 7575 7588 7589 7590 7609 P U R 12 distorted distorted 7595 7610 7611 7612 7629 P C R 13 distorted distorted 7617 7630 7631 7632 7649 P U R 14 distorted distorted 7637 7650 7651 7652 7669 P U R 15 distorted distorted 7657 7670 7671 7672 ---------------------------------------------------------------------------------