Contacts of the helix formed by residues 365 - 378 (chain A) in PDB entry 3PEY
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 GLN 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ASP 3.9 1.3 + - - +
364A LEU* 1.3 75.5 - - - +
366A THR* 1.3 66.4 + - - +
367A GLN* 3.3 27.8 + - - +
368A GLU* 3.1 24.3 + - + +
369A ARG* 2.9 20.3 + - - +
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Residues in contact with THR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ARG* 3.5 36.9 + - - +
198A PRO* 4.2 10.8 - - + -
199A ASP* 2.7 32.7 + - - +
364A LEU 3.7 2.2 + - - +
365A GLN* 1.3 72.2 - - - +
367A GLN* 1.3 74.4 + - - +
369A ARG* 3.3 11.0 + - - +
370A ASP* 3.0 29.2 + - - +
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASP* 4.9 0.9 - - - +
365A GLN* 3.6 27.4 + - + +
366A THR* 1.3 92.1 + - - +
368A GLU* 1.3 68.0 + - + +
370A ASP* 3.5 9.0 + - - +
371A ARG* 3.1 27.2 + - - +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A LEU* 4.4 7.9 - - + -
365A GLN* 3.1 37.1 + - + +
367A GLN* 1.3 82.5 - - + +
369A ARG* 1.3 65.3 - - - +
371A ARG* 2.9 41.1 + - - +
372A LEU* 2.9 39.7 + - + +
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Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ARG* 3.5 20.2 - - - +
173A GLU* 2.9 44.7 + - - +
360A LEU* 3.6 16.1 - - + +
361A HIS 3.8 17.1 + - - +
362A GLY* 3.6 21.4 + - - -
364A LEU* 3.7 22.2 + - + -
365A GLN 2.9 13.3 + - - +
366A THR* 3.3 13.0 + - - +
368A GLU* 1.3 76.1 - - - +
370A ASP* 1.3 62.7 + - - +
372A LEU* 4.5 3.1 - - - -
373A ILE* 3.0 27.9 + - - +
389A VAL* 3.5 12.1 - - - +
4B U 2.9 40.6 + - - -
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Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ARG* 2.8 42.4 + - - -
173A GLU* 5.0 0.5 - - - +
176A ARG* 3.3 36.2 + - - +
366A THR 3.0 17.5 + - - +
367A GLN* 3.8 8.1 - - - +
368A GLU 3.2 0.2 - - - -
369A ARG* 1.3 78.4 - - - +
371A ARG* 1.3 64.1 + - - +
374A ASP* 3.0 33.0 + - - +
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Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A GLN 3.1 18.3 + - - +
368A GLU* 2.9 38.9 + - - +
370A ASP* 1.3 74.8 - - - +
372A LEU* 1.3 79.8 + - - +
374A ASP* 3.4 4.6 + - - +
375A ASP* 2.9 52.2 + - - +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A SER* 3.4 25.9 + - - +
359A ILE* 3.3 25.4 - - + +
360A LEU* 4.2 9.4 - - + -
364A LEU* 3.5 23.1 - - + -
368A GLU* 2.9 29.0 + - + +
369A ARG* 3.8 4.3 - - - +
371A ARG* 1.3 101.3 - - - +
373A ILE* 1.3 65.4 + - - +
375A ASP* 3.4 8.7 + - + +
376A PHE* 3.1 22.5 + - - +
381A SER* 4.5 1.4 + - - -
384A LEU* 5.2 3.4 - - + +
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU* 3.9 22.4 - - + -
176A ARG* 3.2 30.3 - - - +
360A LEU* 3.8 12.3 - - + +
369A ARG 3.0 19.1 + - - +
370A ASP 3.5 0.4 - - - +
372A LEU* 1.3 77.6 - - - +
374A ASP* 1.3 57.7 + - - +
376A PHE* 3.2 4.5 + - + +
377A ARG* 2.7 53.3 + - - +
384A LEU* 4.4 9.9 - - + -
390A LEU* 4.0 28.5 - - + -
394A ILE* 4.7 6.5 - - + -
396A ILE* 4.3 18.4 - - + -
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Residues in contact with ASP 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG* 3.1 37.1 + - - -
370A ASP* 3.0 21.8 + - - +
371A ARG* 3.7 5.7 - - - +
373A ILE* 1.3 79.4 - - - +
375A ASP* 1.3 63.1 + - - +
377A ARG* 3.3 12.4 + - - +
378A GLU* 2.9 32.0 + - + +
380A ARG* 3.8 11.7 - - - +
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Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A SER* 6.0 1.1 - - - +
371A ARG* 2.9 49.2 + - - +
372A LEU* 3.6 9.4 - - + +
373A ILE 3.3 0.2 - - - -
374A ASP* 1.3 75.1 - - - +
376A PHE* 1.3 57.2 + - - +
378A GLU 3.7 0.2 - - - -
379A GLY 3.1 6.6 + - - -
380A ARG* 2.8 69.9 + - + +
381A SER* 3.4 13.3 + - - +
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Residues in contact with PHE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A SER* 3.9 21.9 + - - -
333A SER 3.5 20.0 - - - -
334A ILE* 3.6 26.0 - - + -
372A LEU 3.1 15.7 + - - +
373A ILE* 3.6 6.7 - - + +
375A ASP* 1.3 75.2 - - - +
377A ARG* 1.3 63.7 + - - +
378A GLU 3.2 0.7 + - - -
379A GLY* 3.2 11.8 + - - -
381A SER* 3.1 31.3 + - - +
382A LYS 3.4 23.6 - - - -
384A LEU* 3.7 35.7 - - + -
396A ILE* 3.6 30.5 - - + +
398A THR* 5.0 0.7 + - - -
399A VAL* 3.8 15.0 - - + -
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Residues in contact with ARG 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU 4.7 5.1 + - - -
177A GLN* 2.9 41.2 + - - +
373A ILE* 2.7 31.5 + - - +
374A ASP* 3.7 14.3 + - - +
376A PHE* 1.3 73.6 - - - +
378A GLU* 1.3 77.0 + - - +
379A GLY 3.6 0.5 + - - -
394A ILE* 4.3 13.1 - - - +
395A ASP 2.9 26.9 + - - -
396A ILE* 3.7 31.4 - - + +
397A PRO* 5.7 0.6 - - + +
398A THR* 5.0 2.6 + - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A ASP* 2.9 22.6 + - + +
375A ASP 4.3 0.7 - - - +
377A ARG* 1.3 97.2 - - + +
379A GLY* 1.3 61.4 + - - +
380A ARG* 3.4 35.4 + - + +
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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