Contacts of the helix formed by residues 511 - 555 (chain A) in PDB entry 2KES
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 511 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLY* 1.3 72.5 - - - -
512A VAL* 1.3 52.0 + - - +
513A GLU* 3.3 18.2 + - - -
514A THR* 3.1 7.6 + - - -
515A CYS* 2.8 41.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLY* 2.8 21.6 + - - +
511A SER* 1.3 72.5 - - - +
513A GLU* 1.3 71.0 + - + +
515A CYS* 4.5 3.8 - - - +
516A MET* 2.7 61.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLY* 4.0 5.2 - - - -
511A SER* 3.3 25.8 + - - -
512A VAL* 1.3 90.2 + - + +
514A THR* 1.3 86.6 + - - +
516A MET* 4.0 7.1 - - - +
517A SER* 3.0 24.6 + - - -
----------------------------------------------------------
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Residues in contact with THR 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A SER* 3.6 7.5 - - - -
513A GLU* 1.3 100.3 + - - +
515A CYS* 1.3 64.4 + - - +
517A SER* 3.2 15.0 + - - -
518A LEU* 3.4 23.1 + - + +
----------------------------------------------------------
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Residues in contact with CYS 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A SER* 2.8 28.1 + - - +
512A VAL* 4.1 4.0 - - - +
514A THR* 1.3 72.7 - - - +
516A MET* 1.3 56.1 + - - +
518A LEU* 3.1 25.7 - - + +
519A ALA* 2.7 46.5 + - - +
----------------------------------------------------------
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Residues in contact with MET 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A VAL* 2.7 47.6 + - + +
513A GLU* 4.0 7.9 - - - +
515A CYS* 1.3 72.0 - - - +
517A SER* 1.3 51.1 + - - +
519A ALA* 4.1 5.8 - - - +
520A SER* 2.7 42.2 + - - +
----------------------------------------------------------
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Residues in contact with SER 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU 3.0 16.0 + - - -
514A THR* 3.2 9.0 + - - -
515A CYS 3.1 0.6 - - - -
516A MET* 1.3 76.1 - - - +
518A LEU* 1.3 63.3 + - - +
520A SER* 2.8 19.1 + - - -
521A GLN* 3.3 22.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 3.4 21.5 + - + +
515A CYS* 3.1 44.6 - - + +
517A SER* 1.3 78.9 - - - +
519A ALA* 1.3 70.3 + - + +
521A GLN* 3.3 13.0 + - - +
522A VAL* 3.1 29.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A CYS* 2.7 30.7 + - - +
516A MET* 4.1 4.7 - - - +
518A LEU* 1.3 83.5 - - + +
520A SER* 1.3 50.5 + - - +
522A VAL* 3.1 10.9 + - - +
523A VAL* 2.7 40.1 + - + +
----------------------------------------------------------
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Residues in contact with SER 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A MET* 2.7 27.6 + - - -
517A SER* 2.8 17.2 + - - -
519A ALA* 1.3 75.8 - - - +
521A GLN* 1.3 58.8 + - - +
523A VAL* 3.0 13.1 + - - +
524A LYS* 2.8 43.9 + - - +
----------------------------------------------------------
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Residues in contact with GLN 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A SER* 3.3 20.9 + - - +
518A LEU* 3.5 10.0 - - - +
519A ALA 3.3 0.2 - - - -
520A SER* 1.3 79.3 + - - +
522A VAL* 1.3 62.5 + - + +
524A LYS* 3.1 16.8 + - + +
525A LEU* 3.0 26.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 3.1 20.7 + - + +
519A ALA* 3.3 10.3 - - - +
521A GLN* 1.3 75.1 - - + +
523A VAL* 1.3 58.5 + - + +
525A LEU* 3.1 12.0 + - + +
526A THR* 2.8 33.7 + - + +
----------------------------------------------------------
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Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ALA* 2.7 23.8 + - + +
520A SER* 3.0 17.2 + - - +
522A VAL* 1.3 72.6 - - + +
524A LYS* 1.3 65.7 + - + +
526A THR* 3.1 12.9 - - + +
527A LYS* 2.8 41.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A SER* 2.8 39.3 + - - +
521A GLN* 3.1 12.8 + - + +
523A VAL* 1.3 81.3 - - + +
525A LEU* 1.3 65.9 + - + +
527A LYS* 3.5 5.8 - - - +
528A GLN* 3.0 39.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLN* 3.0 29.8 + - + +
522A VAL* 3.1 12.6 + - + +
524A LYS* 1.3 83.9 - - + +
526A THR* 1.3 57.3 + - - +
528A GLN* 3.2 10.1 + - - +
529A LEU* 2.9 40.4 + - + +
----------------------------------------------------------
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Residues in contact with THR 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A VAL* 2.8 25.2 + - + +
523A VAL* 3.1 27.8 - - + +
525A LEU* 1.3 73.7 - - - +
527A LYS* 1.3 58.4 + - - +
529A LEU* 3.5 14.7 - - - +
530A LYS* 2.9 50.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A VAL* 2.8 27.8 + - + +
524A LYS* 3.5 8.1 - - - +
526A THR* 1.3 79.2 - - - +
528A GLN* 1.3 59.2 + - + +
530A LYS* 3.2 11.1 + - + +
531A GLU* 2.8 54.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A LYS* 3.0 26.3 + - - +
525A LEU* 3.2 7.8 + - - +
527A LYS* 1.3 73.2 - - + +
529A LEU* 1.3 61.3 + - + +
531A GLU* 3.6 17.4 - - - +
532A GLN* 2.9 31.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LEU* 2.9 32.0 + - + +
526A THR* 3.5 17.0 - - - +
528A GLN* 1.3 76.9 - - + +
530A LYS* 1.3 57.0 + - + +
532A GLN* 3.4 18.5 + - - +
533A THR* 2.6 38.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A THR* 2.9 33.4 + - + +
527A LYS* 3.5 10.5 - - + +
529A LEU* 1.3 79.6 - - - +
531A GLU* 1.3 52.4 + - + +
533A THR* 3.1 8.4 + - + +
534A VAL* 2.7 47.0 + - + +
----------------------------------------------------------
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Residues in contact with GLU 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A LYS* 2.8 44.3 + - + +
528A GLN* 3.6 17.4 - - - +
530A LYS* 1.3 75.8 - - + +
532A GLN* 1.3 62.3 + - - +
534A VAL* 3.1 25.0 - - + +
535A GLU* 3.1 18.6 - - - +
----------------------------------------------------------
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Residues in contact with GLN 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A GLN 2.9 16.9 + - - +
529A LEU* 3.7 20.4 + - - +
531A GLU* 1.3 75.9 - - - +
533A THR* 1.3 58.5 + - - +
535A GLU* 3.2 16.3 - - + +
536A ARG* 3.1 35.0 + - + +
----------------------------------------------------------
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Residues in contact with THR 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 2.6 23.7 + - - +
530A LYS* 3.5 11.8 - - + +
532A GLN* 1.3 77.4 + - - +
534A VAL* 1.3 58.7 + - + +
536A ARG* 3.1 31.4 + - - +
537A VAL* 2.7 53.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LYS* 2.7 30.5 + - + +
531A GLU* 3.1 24.9 - - + +
533A THR* 1.3 73.0 - - + +
535A GLU* 1.3 55.4 + - + +
537A VAL* 3.1 10.4 - - + +
538A THR* 2.6 39.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A GLU* 3.1 22.7 + - - +
532A GLN* 3.2 18.0 - - - +
534A VAL* 1.3 78.2 - - + +
536A ARG* 1.3 58.3 + - + +
538A THR* 3.6 6.2 - - - +
539A LEU* 2.8 35.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLN* 3.1 24.9 + - + +
533A THR* 3.6 31.0 + - - +
535A GLU* 1.3 76.9 - - + +
537A VAL* 1.3 75.8 + - - +
539A LEU* 3.2 7.3 + - + +
540A GLN* 2.8 51.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A THR* 2.7 32.6 + - + +
534A VAL* 3.1 21.3 - - + +
536A ARG* 1.3 94.1 - - - +
538A THR* 1.3 58.6 + - - +
540A GLN* 3.3 9.1 + - - +
541A ASN* 2.7 32.9 + - - +
----------------------------------------------------------
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Residues in contact with THR 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 2.6 22.5 + - - +
535A GLU* 3.6 6.7 - - - +
537A VAL* 1.3 81.5 - - - +
539A LEU* 1.3 60.2 + - - +
541A ASN* 3.1 11.2 - - + +
542A GLN* 2.8 43.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLU 2.8 21.6 + - - +
536A ARG* 3.4 9.2 - - + +
538A THR* 1.3 74.0 - - - +
540A GLN* 1.3 80.3 + - - +
542A GLN* 3.0 25.0 + - + +
543A LEU* 2.8 32.8 + - + +
----------------------------------------------------------
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Residues in contact with GLN 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ARG* 2.8 38.6 + - - +
537A VAL* 3.6 7.0 - - - +
539A LEU* 1.3 94.0 - - - +
541A ASN* 1.3 52.0 + - - +
543A LEU* 3.2 26.2 + - - +
544A GLN* 2.7 33.3 + - - +
----------------------------------------------------------
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Residues in contact with ASN 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A VAL 2.7 19.0 + - - +
538A THR* 3.1 19.1 - - + +
540A GLN* 1.3 71.8 - - - +
542A GLN* 1.3 57.2 + - - +
544A GLN* 3.1 27.8 + - - +
545A GLN* 2.9 61.0 + - - +
----------------------------------------------------------
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Residues in contact with GLN 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A THR* 2.8 25.8 + - + +
539A LEU* 3.3 33.8 + - + +
541A ASN* 1.3 75.9 - - - +
543A LEU* 1.3 58.4 + - - +
545A GLN* 3.2 21.7 + - - +
546A PHE* 2.8 26.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 2.8 20.3 + - + +
540A GLN* 3.4 31.9 - - - +
542A GLN* 1.3 74.0 - - - +
544A GLN* 1.3 55.5 + - - +
546A PHE* 3.2 28.5 - - + +
547A LEU* 2.7 49.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A GLN 2.7 16.3 + - - +
541A ASN* 3.1 31.0 + - - +
543A LEU* 1.3 74.2 - - - +
545A GLN* 1.3 57.6 + - + +
547A LEU* 3.1 21.5 - - + +
548A GLU* 2.8 42.4 + - + +
----------------------------------------------------------
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Residues in contact with GLN 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ASN* 2.9 40.5 + - - +
542A GLN* 3.2 20.5 + - - +
544A GLN* 1.3 76.2 - - + +
546A PHE* 1.3 57.9 + - - +
548A GLU* 3.5 7.9 + - - +
549A ALA* 2.8 28.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A GLN 2.8 13.8 + - - +
543A LEU* 3.2 36.8 - - + +
545A GLN* 1.3 74.9 - - - +
547A LEU* 1.3 73.7 + - + +
549A ALA* 3.1 8.8 + - + +
550A GLN* 2.9 58.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 2.7 28.1 + - + +
544A GLN* 3.1 35.7 - - + +
546A PHE* 1.3 81.1 - - + +
548A GLU* 1.3 72.8 + - + +
550A GLN* 3.2 11.6 + - - +
551A LYS* 2.8 33.1 + - + +
----------------------------------------------------------
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Residues in contact with GLU 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A GLN* 2.8 30.9 + - + +
545A GLN* 3.5 9.0 - - - +
547A LEU* 1.3 84.8 - - + +
549A ALA* 1.3 52.5 + - - +
551A LYS* 2.7 41.7 + - - +
552A SER* 2.6 45.1 + - - +
555A LYS* 5.5 1.7 + - - -
----------------------------------------------------------
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Residues in contact with ALA 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLN 2.8 16.8 + - - +
546A PHE* 3.1 12.5 + - + +
548A GLU* 1.3 72.6 - - - +
550A GLN* 1.3 66.0 + - - +
552A SER* 3.4 11.1 - - - -
553A GLU* 3.4 24.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A PHE* 2.9 53.9 + - + +
547A LEU* 3.3 10.5 - - - +
548A GLU 3.1 0.2 - - - -
549A ALA* 1.3 81.0 - - - +
551A LYS* 1.3 56.2 + - - +
553A GLU* 2.9 27.4 + - - +
554A GLY* 3.0 9.9 + - - -
----------------------------------------------------------
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Residues in contact with LYS 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A LEU* 2.8 18.2 + - + +
548A GLU* 2.7 50.6 + - - +
550A GLN* 1.3 70.2 - - - +
552A SER* 1.3 58.9 + - - +
553A GLU 3.1 0.2 - - - -
554A GLY* 3.6 4.9 - - - +
555A LYS* 2.8 61.6 + - + +
----------------------------------------------------------
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Residues in contact with SER 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLU* 2.6 29.0 + - - +
549A ALA* 3.4 12.3 - - - -
550A GLN 3.1 0.2 - - - -
551A LYS* 1.3 81.0 - - - +
553A GLU* 1.3 61.7 + - - +
555A LYS* 3.2 44.0 + - - +
556A SER* 3.6 10.6 - - - -
----------------------------------------------------------
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Residues in contact with GLU 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ALA 3.4 15.2 - - - +
550A GLN* 2.9 14.8 + - - +
552A SER* 1.3 82.7 - - - +
554A GLY* 1.3 63.6 + - - +
555A LYS 3.3 0.4 - - - -
556A SER* 3.1 26.8 + - - +
----------------------------------------------------------
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Residues in contact with GLY 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A GLN 3.0 12.4 + - - -
551A LYS* 3.2 6.4 + - - -
553A GLU* 1.3 73.4 - - - +
555A LYS* 1.3 58.0 + - - +
556A SER 3.1 12.1 + - - +
557A LEU* 5.5 1.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLU* 5.5 1.6 + - - -
551A LYS* 2.8 33.4 + - + +
552A SER* 3.2 43.6 + - - +
554A GLY* 1.3 76.4 - - - +
556A SER* 1.3 59.4 - - - +
557A LEU* 5.1 4.0 - - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il