Contacts of the helix formed by residues 440 - 445 (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 SER 440 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413V PHE* 3.2 14.7 - - - -
436V ASP 3.9 11.2 - - - -
437V THR* 4.7 1.8 - - - -
438V VAL 3.4 0.8 - - - -
439V ALA* 1.3 77.9 - - - +
441V PHE* 1.3 75.3 + - - +
442V LYS 3.4 1.1 - - - +
443V ALA* 4.2 8.4 + - - +
444V VAL* 3.5 20.3 - - - +
449V TYR* 4.9 0.7 - - - -
462V GLY* 3.2 23.5 + - - -
463V ILE* 3.2 27.5 - - - +
466V VAL* 4.9 0.2 - - - +
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Residues in contact with PHE 441 (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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139V LYS* 4.4 12.3 - - + -
140V VAL* 5.7 1.3 - - - -
143V LEU* 5.0 9.0 - - + -
370V VAL* 4.1 18.8 - - + -
374V VAL* 4.1 12.6 - - + -
410V ILE* 4.0 31.9 - - + -
413V PHE* 3.3 54.7 - + - -
437V THR* 3.4 40.1 + - + -
438V VAL 4.5 0.2 + - - -
440V SER* 1.3 78.5 - - - +
442V LYS* 1.3 61.4 + - - +
443V ALA 3.1 6.2 + - - -
444V VAL* 3.6 6.2 + - - +
445V LEU* 3.2 34.6 + - + +
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Residues in contact with LYS 442 (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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366V GLU* 4.8 17.2 + - + +
370V VAL* 4.4 15.7 - - + +
438V VAL* 3.4 26.8 + - + +
439V ALA* 3.6 24.6 - - + +
440V SER 4.1 0.2 - - - +
441V PHE* 1.3 80.2 - - - +
443V ALA* 1.3 62.4 + - + +
445V LEU* 4.3 8.1 - - - +
446V GLU* 3.8 26.3 + - - +
448V LYS* 5.2 4.4 + - - +
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Residues in contact with ALA 443 (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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439V ALA 5.6 2.0 - - - +
440V SER* 4.2 7.5 + - - +
441V PHE 3.1 0.6 - - - -
442V LYS* 1.3 81.8 - - + +
444V VAL* 1.3 65.7 + - - +
445V LEU 3.2 1.3 - - - -
446V GLU* 3.3 8.5 + - - +
448V LYS* 3.2 54.5 + - + +
449V TYR* 3.6 22.0 - - + -
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Residues in contact with VAL 444 (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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406V ARG* 3.8 10.6 + - + -
409V LYS* 4.9 9.0 - - + -
410V ILE* 4.4 19.5 - - + -
413V PHE* 5.6 4.7 - - + -
440V SER 3.5 18.6 - - - +
441V PHE* 3.6 6.2 + - - +
443V ALA* 1.3 74.7 - - - +
445V LEU* 1.3 63.0 + - - +
446V GLU 3.2 1.2 + - - -
447V GLY 3.3 8.7 + - - -
449V TYR* 3.4 53.6 - - + +
450V ASP* 3.3 9.6 - - - +
457V PHE* 4.2 20.2 - - + -
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Residues in contact with LEU 445 (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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370V VAL* 4.2 13.7 - - + +
373V LYS* 3.7 39.8 - - + +
374V VAL* 4.3 9.9 - - + +
377V THR* 3.6 26.5 - - + +
406V ARG* 2.9 31.1 + - - +
410V ILE* 4.2 25.8 - - + -
441V PHE* 3.2 23.3 + - + +
442V LYS* 4.5 8.5 - - - +
443V ALA 3.2 0.8 - - - -
444V VAL* 1.3 79.5 - - - +
446V GLU* 1.3 61.4 + - + +
447V GLY 3.5 0.2 - - - -
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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