Contacts of the helix formed by residues 319 - 329 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279W VAL* 4.4 4.5 - - - +
281W TYR* 2.8 31.3 + - - -
313W PRO* 3.7 15.1 - - + +
316W ASP* 3.3 30.4 + - + +
318W THR* 1.3 75.9 - - - +
320W PRO* 1.3 80.7 - - - +
321W ALA 2.9 18.7 + - - -
322W PRO* 2.9 21.8 - - + +
323W ALA* 2.9 13.3 + - - +
259Y ARG* 3.4 22.2 + - - +
260Y GLN* 3.8 2.5 - - - +
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Residues in contact with PRO 320 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281T ARG* 6.3 0.9 - - - +
278W ALA* 4.3 9.4 - - + +
279W VAL* 3.9 29.4 - - + -
281W TYR* 3.9 14.8 - - + -
285W LEU* 3.5 22.1 - - + +
318W THR 3.3 4.7 - - - +
319W ASP* 1.3 93.9 - - - +
321W ALA* 1.3 60.5 + - - +
323W ALA* 3.9 7.9 - - + -
324W THR* 2.8 29.7 + - - +
260Y GLN* 4.2 6.7 - - - +
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Residues in contact with ALA 321 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259W PHE* 3.9 23.8 - - + -
262W THR* 4.4 14.2 + - + +
281W TYR* 3.1 37.6 - - + +
289W MET* 4.9 0.9 - - - +
313W PRO* 4.2 1.3 - - + -
319W ASP* 2.9 4.9 + - - -
320W PRO* 1.3 81.7 - - - +
322W PRO* 1.3 68.0 - - + +
324W THR* 3.6 2.3 + - - -
325W THR* 3.0 22.8 + - - -
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Residues in contact with PRO 322 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310W VAL* 4.7 6.3 - - + -
311W TYR 4.8 1.6 - - - +
312W VAL* 3.9 30.1 - - + -
313W PRO* 3.9 6.7 - - + -
316W ASP 3.5 21.8 - - - +
317W LEU* 4.3 6.7 - - - +
319W ASP* 2.9 28.5 - - + +
321W ALA* 1.3 87.8 - - + +
323W ALA* 1.3 57.2 + - - +
324W THR 3.2 0.2 - - - -
325W THR* 4.1 7.2 - - - +
326W PHE* 2.8 47.5 + - + -
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Residues in contact with ALA 323 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T ARG* 5.9 1.6 - - - -
332T GLN* 4.6 19.5 + - + +
317W LEU 4.1 10.8 - - - +
318W THR 3.7 12.8 - - - +
319W ASP 2.9 21.4 + - - +
320W PRO* 4.0 5.6 - - + +
322W PRO* 1.3 80.3 - - - +
324W THR* 1.3 60.6 + - - +
326W PHE* 3.8 4.9 + - - +
327W ALA* 3.7 17.0 + - - +
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Residues in contact with THR 324 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285W LEU* 3.3 22.2 - - + +
286W ALA* 4.2 20.2 - - + +
289W MET* 3.7 29.9 - - + +
320W PRO* 2.8 22.6 + - - +
321W ALA 4.2 2.2 - - - -
323W ALA* 1.3 75.8 - - - +
325W THR* 1.3 65.2 + - - +
327W ALA* 3.7 9.2 - - + +
328W HIS* 3.6 19.1 - - + +
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Residues in contact with THR 325 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258W ILE* 4.0 34.7 - - + +
259W PHE* 5.8 1.0 - - - -
262W THR* 4.5 2.6 + - - -
289W MET* 3.6 20.2 - - - +
293W GLN* 5.0 2.9 + - - +
308W GLN* 4.5 6.7 - - - +
310W VAL* 4.1 16.9 - - + +
321W ALA 3.0 15.5 + - - -
322W PRO* 3.1 11.0 + - - +
324W THR* 1.3 76.6 - - - +
326W PHE* 1.3 68.0 + - - +
327W ALA 3.1 2.8 + - - -
328W HIS* 3.1 15.2 + - - +
329W LEU* 3.4 17.8 + - + +
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Residues in contact with PHE 326 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T ARG* 3.6 45.9 + - - +
156W PHE* 3.6 33.7 - + - -
310W VAL* 4.6 4.0 - - + -
312W VAL* 4.8 0.2 - - + -
317W LEU* 4.1 29.6 - - + -
322W PRO* 2.8 40.1 + - + +
323W ALA* 4.1 6.1 - - - +
325W THR* 1.3 74.6 - - - +
327W ALA* 1.3 64.5 + - - +
329W LEU* 2.9 38.3 + - + +
332W THR* 4.6 15.0 - - + -
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Residues in contact with ALA 327 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T ARG* 4.8 9.6 - - - +
211T LYS* 4.0 11.2 - - - +
275T LYS* 5.3 14.6 - - - +
323W ALA 3.7 10.6 + - - +
324W THR* 3.7 15.5 - - + +
325W THR 3.1 0.2 - - - -
326W PHE* 1.3 78.9 - - - +
328W HIS* 1.3 64.9 - - + +
329W LEU 4.2 3.3 - - - +
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Residues in contact with HIS 328 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209T GLY 5.6 1.1 - - - -
211T LYS* 3.4 40.2 + - + +
238T ALA* 4.0 25.3 - - + +
152W LYS* 3.5 27.4 + - + +
286W ALA 5.1 1.6 + - - -
289W MET* 3.7 24.4 + - + +
290W GLY* 4.2 9.3 + - - -
293W GLN* 3.5 30.2 - - + +
294W GLU* 4.7 6.8 + - + -
324W THR* 3.6 19.6 + - - +
325W THR 3.1 6.7 + - - +
326W PHE 3.1 0.6 - - - -
327W ALA* 1.3 81.4 - - + +
329W LEU* 1.3 67.6 + - - +
330W ASP 3.4 1.2 + - - -
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Residues in contact with LEU 329 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T ARG* 4.5 6.9 + - - +
174T GLN* 5.8 1.4 + - - -
152W LYS* 3.4 24.7 - - + +
153W ILE 3.6 5.8 - - - +
154W GLY* 3.5 31.4 - - - +
156W PHE* 5.2 0.7 - - + -
293W GLN* 5.7 0.4 - - - +
308W GLN* 4.3 14.4 - - + +
310W VAL* 4.2 8.7 - - + -
325W THR* 3.4 22.2 + - + +
326W PHE* 2.9 48.0 + - + +
327W ALA 4.2 2.6 - - - +
328W HIS* 1.3 80.1 - - - +
330W ASP* 1.3 61.9 + - - +
331W ALA 4.5 4.5 - - - +
332W THR* 4.8 6.5 - - + -
356W ARG* 5.6 1.4 - - - -
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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