Contacts of the helix formed by residues 319 - 327 (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 ASP 319 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293U ARG* 5.5 1.7 + - - -
279V VAL* 4.7 5.9 - - - +
281V TYR* 2.8 22.1 + - - -
313V PRO* 3.5 26.9 - - + +
316V ASP* 3.3 33.2 + - + +
317V LEU 3.1 1.0 - - - +
318V THR* 1.3 77.9 - - - +
320V PRO* 1.3 72.5 - - - +
321V ALA* 2.7 31.7 + - - +
322V PRO* 3.1 14.5 - - + +
323V ALA* 3.2 15.5 + - - +
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Residues in contact with PRO 320 (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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281S ARG* 6.2 0.7 - - - +
278V ALA* 4.0 9.4 - - + +
279V VAL* 3.5 42.0 - - + -
281V TYR* 3.9 12.1 - - + -
285V LEU* 3.7 29.3 - - + +
318V THR 3.7 4.7 - - - +
319V ASP* 1.3 93.4 - - - +
321V ALA* 1.3 57.6 + - - +
323V ALA* 4.2 6.3 - - + -
324V THR* 2.9 26.5 + - - +
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Residues in contact with ALA 321 (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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259V PHE* 3.6 28.0 - - + -
262V THR* 4.7 11.7 + - - +
281V TYR* 2.9 31.2 + - + +
289V MET* 4.8 2.6 - - - +
310V VAL* 5.8 0.7 - - - -
319V ASP* 2.7 11.8 + - - +
320V PRO* 1.3 72.1 - - - +
322V PRO* 1.4 69.8 - - + +
323V ALA 3.2 1.8 + - - -
324V THR* 3.5 2.8 + - - -
325V THR* 2.8 24.4 + - - -
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Residues in contact with PRO 322 (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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156V PHE* 4.9 1.1 - - + -
310V VAL* 4.6 14.6 - - + -
311V TYR 4.2 2.7 - - - +
312V VAL* 3.9 9.4 - - + -
313V PRO* 3.6 22.7 - - + -
316V ASP 3.6 15.3 - - - +
317V LEU* 4.5 18.8 - - + -
319V ASP* 3.1 20.9 - - + +
321V ALA* 1.4 93.6 - - + +
323V ALA* 1.3 56.5 + - - +
325V THR* 3.8 9.9 - - - +
326V PHE* 3.1 37.1 + - + -
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Residues in contact with ALA 323 (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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330S GLU* 5.2 4.3 - - - +
332S GLN* 4.1 28.4 + - + +
317V LEU 3.9 14.7 + - - +
318V THR 4.9 1.3 - - - +
319V ASP 3.2 20.9 + - - +
320V PRO* 4.5 4.9 - - + +
321V ALA 3.2 1.2 - - - -
322V PRO* 1.3 78.0 - - - +
324V THR* 1.3 61.7 + - - +
325V THR 3.2 1.2 + - - -
326V PHE* 3.7 12.1 + - - +
327V ALA* 3.9 10.6 + - - +
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Residues in contact with THR 324 (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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285V LEU* 3.2 24.8 - - + +
286V ALA* 4.4 11.0 - - + -
289V MET* 3.7 29.9 - - + +
320V PRO* 2.9 19.6 + - - +
321V ALA 3.5 4.3 + - - -
323V ALA* 1.3 77.0 - - - +
325V THR* 1.3 60.3 + - - +
326V PHE 3.4 0.2 - - - -
327V ALA* 3.8 8.4 + - + +
328V HIS* 3.1 26.6 - - - +
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Residues in contact with THR 325 (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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156V PHE* 5.1 0.9 - - + -
258V ILE* 4.2 16.9 - - + +
259V PHE* 6.0 1.4 - - - -
262V THR* 5.0 1.0 + - - -
289V MET* 3.5 21.7 - - + +
293V GLN* 5.4 1.6 - - - +
308V GLN* 4.7 7.0 - - - +
310V VAL* 3.8 33.4 - - + +
321V ALA 2.8 18.0 + - - -
322V PRO* 3.9 9.1 - - - +
323V ALA 3.2 0.4 - - - -
324V THR* 1.3 77.6 - - - +
326V PHE* 1.3 62.4 + - - +
327V ALA 3.2 2.2 + - - -
328V HIS* 3.6 8.8 + - - +
329V LEU* 3.1 25.7 + - + +
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Residues in contact with PHE 326 (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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173S ARG* 3.2 51.8 - - - -
174S GLN* 5.1 6.1 - - - -
330S GLU* 5.9 0.4 - - - +
156V PHE* 3.4 38.4 - + - -
317V LEU* 3.7 24.7 - - + -
322V PRO 3.1 26.5 + - - +
323V ALA* 4.1 8.3 - - - +
324V THR 3.4 0.6 - - - -
325V THR* 1.3 75.6 - - - +
327V ALA* 1.3 62.3 + - - +
328V HIS 3.2 2.2 + - - -
329V LEU* 3.5 19.5 + - + +
332V THR* 3.5 28.3 - - + -
352V ASP* 4.2 13.9 - - - -
356V ARG* 4.8 3.6 + - - -
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Residues in contact with ALA 327 (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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209S GLY 5.7 2.7 - - - +
210S GLN* 6.1 0.7 - - - -
211S LYS* 5.0 8.1 + - - +
275S LYS* 4.6 25.4 + - - +
330S GLU* 5.2 11.4 + - - +
323V ALA 3.9 10.2 + - - +
324V THR* 3.8 15.0 + - + +
325V THR 3.2 0.8 - - - -
326V PHE* 1.3 78.8 - - - +
328V HIS* 1.3 66.0 + - + +
329V LEU 4.8 0.4 - - - -
356V ARG* 4.3 13.3 + - - +
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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