Contacts of the helix formed by residues 463 - 474 (chain V) in PDB entry 3FKS
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 ILE 463 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436V ASP* 4.4 12.1 + - - +
439V ALA 4.2 9.0 - - - +
440V SER* 3.2 37.0 - - - +
443V ALA* 6.4 0.2 - - + -
449V TYR* 3.2 33.2 - - + +
462V GLY* 1.3 71.6 - - - -
464V GLU* 1.3 80.3 + - + +
465V ASP 3.3 1.6 - - - -
466V VAL* 3.3 15.1 + - + +
467V VAL* 3.2 19.6 - - + +
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Residues in contact with GLU 464 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436V ASP* 5.7 3.4 - - - +
463V ILE* 1.3 88.9 - - + +
465V ASP* 1.3 68.2 + - - +
467V VAL* 3.3 17.6 + - - +
468V ALA* 3.5 11.3 + - - +
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Residues in contact with ASP 465 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430V LYS* 3.0 46.8 + - - +
460V VAL* 4.1 7.8 - - + +
461V GLY* 3.6 20.3 + - - +
462V GLY 4.1 4.2 + - - -
463V ILE* 3.3 0.8 - - - +
464V GLU* 1.3 82.0 + - - +
466V VAL* 1.3 64.0 + - - +
468V ALA* 3.3 9.3 + - - +
469V LYS* 3.2 23.7 + - - +
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Residues in contact with VAL 466 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413V PHE* 3.6 17.5 - - + -
440V SER* 4.9 1.1 - - - +
449V TYR* 5.4 9.2 - - + -
452V ILE* 6.2 1.1 - - + -
456V ALA* 3.7 23.7 - - + +
457V PHE* 3.8 29.6 - - + -
460V VAL* 3.7 11.9 - - + -
462V GLY 3.3 27.1 - - - +
463V ILE* 3.5 14.1 - - + +
464V GLU 3.2 0.6 - - - -
465V ASP* 1.3 80.0 - - - +
467V VAL* 1.3 60.4 + - + +
469V LYS* 3.6 3.6 + - - +
470V ALA* 3.5 18.5 + - - +
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Residues in contact with VAL 467 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449V TYR* 4.4 15.3 - - + +
463V ILE* 3.2 32.5 - - + +
464V GLU* 3.8 8.7 - - - +
465V ASP 3.2 0.4 - - - -
466V VAL* 1.3 77.6 - - + +
468V ALA* 1.3 62.2 + - - +
470V ALA* 3.4 18.6 + - + +
471V GLU* 3.8 7.8 + - - +
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Residues in contact with ALA 468 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464V GLU 3.5 8.8 + - - +
465V ASP* 3.3 11.4 + - - +
467V VAL* 1.3 76.7 - - - +
469V LYS* 1.3 58.3 + - - +
470V ALA 3.1 5.7 + - - -
471V GLU* 3.8 4.2 + - - +
472V LYS* 3.6 20.8 + - - +
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Residues in contact with LYS 469 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455V HIS* 3.6 33.8 + - - +
456V ALA* 3.8 24.5 - - - +
458V TYR 4.9 5.2 - - - -
459V MET 5.4 3.6 + - - -
460V VAL* 4.1 10.1 - - + -
465V ASP 3.2 16.5 + - - +
466V VAL 4.1 1.8 - - - +
467V VAL 3.3 0.4 - - - -
468V ALA* 1.3 75.6 - - - +
470V ALA* 1.3 57.1 + - - +
471V GLU 3.5 0.2 - - - -
472V LYS* 4.2 13.2 - - + +
473V LEU* 3.3 41.9 - - + +
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Residues in contact with ALA 470 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452V ILE* 3.7 32.1 - - + -
466V VAL 3.5 11.6 + - - +
467V VAL* 3.4 17.3 - - + +
468V ALA 3.1 0.6 - - - -
469V LYS* 1.3 79.7 - - - +
471V GLU* 1.3 59.3 + - - +
474V ALA* 3.0 32.9 + - - +
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Residues in contact with GLU 471 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467V VAL 3.8 6.8 + - - +
468V ALA* 3.8 6.8 + - - +
470V ALA* 1.3 78.3 - - - +
472V LYS* 1.3 64.7 + - - +
473V LEU 3.2 1.7 + - - -
474V ALA 3.7 16.6 - - - -
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Residues in contact with LYS 472 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468V ALA 3.6 16.3 + - - +
469V LYS* 4.5 14.4 - - + +
471V GLU* 1.3 79.3 - - - +
473V LEU* 1.3 66.1 + - + +
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Residues in contact with LEU 473 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452V ILE* 5.5 0.2 - - + -
453V PRO* 5.3 15.0 - - + -
455V HIS* 3.7 27.6 - - + +
456V ALA* 3.5 29.6 - - + +
469V LYS* 3.3 34.7 + - + +
470V ALA* 4.6 1.1 - - - +
471V GLU 4.2 0.2 - - - -
472V LYS* 1.3 85.7 - - + +
474V ALA* 1.3 61.1 + - + +
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Residues in contact with ALA 474 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452V ILE* 4.6 4.7 - - + -
453V PRO* 4.6 20.4 - - + -
470V ALA 3.0 23.3 + - - +
471V GLU* 3.7 15.0 - - - -
473V LEU* 1.3 79.5 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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