Contacts of the helix formed by residues 384 - 391 (chain F) 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 LEU 384 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407C GLN* 3.8 25.1 - - - +
380F THR* 3.3 31.5 + - + +
381F TYR* 3.5 6.3 + - - +
382F LYS 3.0 1.0 - - - -
383F SER* 1.3 82.2 - - - +
385F GLN* 1.3 66.0 + - - +
386F ASP 3.0 3.7 + - - -
387F ILE* 3.0 33.8 + - + -
388F ILE* 2.9 29.1 + - + +
396F LEU* 3.6 34.3 - - + -
400F ASP* 4.5 8.1 - - + -
404F VAL* 4.3 11.4 - - + -
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Residues in contact with GLN 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F TYR* 3.2 52.0 + - - +
382F LYS* 3.1 27.4 + - + +
384F LEU* 1.3 76.4 - - - +
386F ASP* 1.3 62.5 + - - +
388F ILE* 4.1 5.0 - - - +
389F ALA* 3.1 30.0 + - - +
411F GLN* 5.4 3.0 + - - +
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Residues in contact with ASP 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F LYS 6.1 0.2 - - - -
383F SER 5.3 1.0 - - - +
384F LEU 3.0 0.8 - - - -
385F GLN* 1.3 78.9 - - - +
387F ILE* 1.3 75.2 + - + +
389F ALA* 3.0 15.9 + - - +
390F ILE* 3.1 22.1 + - + +
9G ARG* 4.3 14.5 + - - -
13G ILE* 6.1 4.9 - - + -
247G MET* 3.8 24.3 - - + +
251G TYR* 4.5 8.5 + - - -
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Residues in contact with ILE 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C GLN* 4.9 11.4 - - + +
408C PHE* 6.1 0.7 - - + -
383F SER 3.8 13.9 - - - +
384F LEU* 3.0 31.8 + - + +
386F ASP* 1.3 81.1 - - + +
388F ILE* 1.3 59.4 + - - +
390F ILE* 5.4 0.7 - - - -
391F LEU* 2.9 49.9 + - + +
392F GLY 3.3 7.2 + - - +
395F GLU* 5.5 2.7 - - + -
396F LEU* 4.2 28.9 - - + -
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Residues in contact with ILE 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B PHE* 5.6 9.6 - - + -
381F TYR* 5.0 17.0 - - + +
384F LEU* 2.9 20.1 + - + +
385F GLN* 4.1 4.5 - - - +
387F ILE* 1.3 75.5 - - - +
389F ALA* 1.3 64.4 + - - +
390F ILE 3.0 1.9 + - - -
391F LEU 4.0 0.2 - - - -
392F GLY* 3.1 22.7 + - - +
393F MET* 3.6 43.3 - - + +
396F LEU* 3.4 32.1 - - + -
404F VAL* 4.8 5.4 - - + -
408F ARG* 6.1 2.5 - - - +
243G ASN* 5.2 1.4 + - - -
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Residues in contact with ALA 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385F GLN 3.1 19.8 + - - +
386F ASP* 3.0 8.5 + - - +
388F ILE* 1.3 79.8 - - - +
390F ILE* 1.3 60.4 + - + +
243G ASN* 3.2 27.7 + - - +
247G MET* 5.0 12.3 - - - +
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Residues in contact with ILE 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386F ASP* 3.1 16.6 + - + +
387F ILE* 4.4 1.1 - - - +
388F ILE 3.1 0.4 - - - -
389F ALA* 1.3 83.9 - - + +
391F LEU* 1.3 80.2 + - + +
392F GLY 3.7 0.2 - - - -
13G ILE* 4.4 16.2 - - + -
16G ILE* 4.4 23.8 - - + -
20G THR* 5.1 2.2 - - + -
239G ASN 4.8 0.2 - - - -
240G ALA* 3.7 32.6 - - + +
243G ASN* 3.5 29.5 + - - +
244G ALA* 4.7 7.4 - - + +
247G MET* 4.1 28.7 - - + -
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Residues in contact with LEU 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C PHE* 3.5 33.7 - - + -
390D ILE* 4.6 13.0 - - + -
387F ILE* 2.9 31.8 + - + +
390F ILE* 1.3 92.4 - - + +
392F GLY* 1.3 61.4 + - - +
394F ASP* 5.5 4.0 - - - +
395F GLU* 4.1 23.6 - - + +
16G ILE* 6.4 0.4 - - + -
20G THR* 5.1 10.5 - - + -
83G LEU* 3.7 23.3 - - + -
236G ALA 5.1 6.8 - - - +
240G ALA* 5.3 5.4 - - + -
243G ASN* 5.6 0.8 + - - -
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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