Contacts of the helix formed by residues 319 - 326 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293T ARG* 3.2 23.5 + - - +
279X VAL* 4.5 0.7 - - - +
281X TYR* 2.9 27.0 + - - -
313X PRO* 3.4 17.7 - - + +
316X ASP* 3.2 35.0 + - + +
317X LEU 3.2 0.2 - - - -
318X THR* 1.3 75.3 - - - +
320X PRO* 1.3 75.0 - - - +
321X ALA* 2.8 30.0 + - - +
322X PRO* 3.0 19.2 - - + +
323X ALA* 3.1 13.2 + - - +
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Residues in contact with PRO 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281U ARG* 6.0 4.3 - - - +
278X ALA* 4.1 13.5 - - + +
279X VAL* 4.0 28.0 - - + -
281X TYR* 4.0 19.1 - - + -
285X LEU* 3.6 16.6 - - + +
318X THR 3.2 7.4 - - - +
319X ASP* 1.3 93.4 - - - +
321X ALA* 1.3 60.0 + - - +
323X ALA* 4.1 3.4 - - + -
324X THR* 3.0 27.6 + - - +
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Residues in contact with ALA 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259X PHE* 3.3 30.7 - - + -
262X THR* 4.7 9.0 - - + +
281X TYR* 3.9 12.7 - - + -
285X LEU* 4.3 11.9 - - + -
289X MET* 3.8 9.8 - - + +
319X ASP* 2.8 11.6 + - - +
320X PRO* 1.3 81.4 - - - +
322X PRO* 1.3 70.1 - - + +
324X THR* 3.6 0.9 + - - -
325X THR* 2.9 20.5 + - - -
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Residues in contact with PRO 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X PHE* 4.1 5.6 - - + -
259X PHE* 4.7 0.4 - - + -
310X VAL* 4.3 10.8 - - + -
311X TYR 3.7 12.3 - - - +
312X VAL* 4.2 18.4 - - + -
313X PRO* 3.6 23.6 - - + -
316X ASP 4.4 5.4 - - - +
317X LEU* 4.9 5.2 - - - +
319X ASP* 3.0 25.8 - - + +
321X ALA* 1.3 87.7 - - + +
323X ALA* 1.3 62.6 - - - +
324X THR 3.0 3.1 - - - -
325X THR* 2.9 22.2 + - - +
326X PHE* 3.3 19.9 + - + -
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Residues in contact with ALA 323 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173U ARG* 5.3 2.8 - - - +
330U GLU* 4.2 14.2 - - - +
332U GLN* 3.7 23.0 + - - +
317X LEU 3.3 19.0 + - - +
318X THR 3.8 5.6 - - - +
319X ASP 3.1 20.8 + - - +
320X PRO* 4.3 4.3 - - + +
322X PRO* 1.3 76.5 - - - +
324X THR* 1.3 59.8 + - - +
326X PHE* 4.1 17.4 - - - +
327X ALA* 5.0 1.0 + - - +
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Residues in contact with THR 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275U LYS* 5.2 16.4 - - + +
285X LEU* 4.1 10.3 - - - +
286X ALA* 4.4 25.7 - - + +
289X MET* 4.4 8.3 - - - -
320X PRO* 3.0 20.1 + - - +
321X ALA 4.2 2.5 - - - -
322X PRO 3.0 0.4 - - - -
323X ALA* 1.3 76.4 - - - +
325X THR* 1.3 64.2 + - - +
326X PHE 3.1 3.0 + - - -
327X ALA* 3.6 15.0 + - + +
328X HIS* 3.6 13.9 - - + +
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Residues in contact with THR 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X PHE* 4.3 7.9 - - + -
258X ILE* 5.0 2.6 - - + +
289X MET* 3.3 21.3 - - + +
293X GLN* 3.8 22.9 - - - +
308X GLN* 5.4 0.2 - - - +
310X VAL* 3.8 30.7 - - + +
321X ALA 2.9 16.8 + - - -
322X PRO* 2.9 13.6 + - - +
324X THR* 1.3 77.0 - - - +
326X PHE* 1.3 65.2 + - - +
327X ALA 3.3 0.2 - - - -
328X HIS* 3.1 17.3 + - + +
329X LEU* 3.6 11.3 - - + +
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Residues in contact with PHE 326 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173U ARG* 3.2 61.5 - - + -
174U GLN* 4.9 17.1 - - + +
330U GLU* 6.1 0.2 - - - +
156X PHE* 3.4 47.8 - + - -
317X LEU* 5.1 12.6 - - + -
322X PRO* 3.3 28.0 + - + -
323X ALA* 4.1 13.0 - - - +
324X THR 3.1 0.4 - - - -
325X THR* 1.3 79.1 - - - +
327X ALA* 1.3 63.0 + - - +
329X LEU* 3.1 22.7 + - - +
332X THR* 4.0 25.1 - - + +
334X VAL* 4.0 10.8 - - + -
352X ASP* 4.7 0.7 - - - -
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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