Contacts of the helix formed by residues 371 - 379 (chain A) in PDB entry 2EYQ
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 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A VAL* 3.5 31.9 - - + -
369A ALA 3.3 0.6 - - - -
370A PRO* 1.3 79.2 - - + +
372A ASP* 1.3 57.9 + - - +
373A ALA 3.3 2.9 - - - -
374A LEU* 3.2 17.2 + - + +
375A ARG* 2.8 34.1 + - - +
401A LEU* 3.8 32.8 - - + +
404A ARG* 3.3 44.6 - - + +
405A ILE* 3.8 28.2 - - + +
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Residues in contact with ASP 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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369A ALA* 3.6 29.7 + - + +
370A PRO 3.5 3.0 - - - -
371A LEU* 1.3 74.1 - - - +
373A ALA* 1.3 68.5 + - - +
375A ARG* 3.3 32.7 + - - +
376A LYS* 2.8 46.0 + - - +
379A GLU* 4.9 2.8 - - - +
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Residues in contact with ALA 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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360A ASP 3.9 21.1 - - - +
361A LEU* 3.6 7.7 - - + +
362A ALA 4.1 17.3 - - - +
364A GLN* 5.0 6.3 - - - +
369A ALA 5.2 0.2 + - - -
370A PRO 4.8 2.6 + - - +
371A LEU 3.3 1.3 - - - -
372A ASP* 1.3 78.3 - - - +
374A LEU* 1.3 57.9 + - - +
376A LYS* 3.5 22.2 - - - +
377A PHE* 3.2 25.6 + - - +
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Residues in contact with LEU 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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361A LEU* 4.3 22.4 + - + +
363A VAL* 5.9 0.7 - - + -
371A LEU* 3.2 21.4 + - + +
373A ALA* 1.3 79.5 - - - +
375A ARG* 1.3 63.8 + - - +
377A PHE* 3.5 0.7 + - - +
378A LEU* 3.1 43.9 + - + +
387A PHE* 4.2 11.0 - - + -
401A LEU* 4.8 6.5 - - + -
402A LEU* 4.1 13.9 - - + -
405A ILE* 3.8 16.4 - - + -
444A ILE* 5.3 1.3 - - + -
449A LEU* 3.7 40.6 - - + -
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Residues in contact with ARG 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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369A ALA* 5.2 9.9 - - - +
370A PRO* 5.9 1.2 - - - +
371A LEU* 2.8 24.8 + - - +
372A ASP* 2.9 26.6 + - - +
374A LEU* 1.3 76.7 - - - +
376A LYS* 1.3 59.7 + - - +
378A LEU* 3.2 11.1 + - - +
379A GLU* 2.9 37.6 + - - +
404A ARG 3.7 19.4 + - - -
405A ILE* 3.9 42.5 - - + +
406A LYS* 5.9 2.6 - - - +
407A ILE* 6.3 0.2 - - + -
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Residues in contact with LYS 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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372A ASP* 2.8 34.7 + - + +
373A ALA* 3.5 29.9 - - - +
375A ARG* 1.3 69.2 - - - +
377A PHE* 1.3 65.8 + - + +
378A LEU 3.0 2.9 + - - -
379A GLU* 3.2 17.8 + - + +
380A THR* 2.7 31.9 + - + +
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Residues in contact with PHE 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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358A LEU* 4.7 2.5 - - + -
359A PRO* 3.4 39.3 - - + -
361A LEU* 3.6 26.9 - - + -
373A ALA 3.2 18.0 + - - +
374A LEU 3.8 2.9 - - - +
375A ARG 3.3 0.2 - - - -
376A LYS* 1.3 84.3 - - + +
378A LEU* 1.3 79.6 + - + +
380A THR* 3.1 22.9 - - + +
381A PHE* 3.5 49.0 - + - +
385A VAL* 4.7 1.3 - - + -
435A VAL* 6.0 1.3 - - + -
442A ALA* 4.4 12.8 - - + -
444A ILE* 4.4 7.9 - - + -
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Residues in contact with LEU 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 LEU* 3.1 37.2 + - + +
375A ARG 3.6 4.9 - - - +
376A LYS 3.0 0.8 - - - -
377A PHE* 1.3 109.2 - - + +
379A GLU* 1.3 55.9 + - - +
380A THR 3.2 6.7 + - - -
381A PHE* 3.9 3.4 + - - +
385A VAL* 4.0 20.6 - - + -
387A PHE* 4.1 14.6 - - + -
405A ILE* 4.7 0.2 - - + -
407A ILE* 3.1 36.8 - - + -
423A ARG* 2.8 43.9 + - - +
444A ILE* 4.9 0.7 - - + -
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Residues in contact with GLU 379 (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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372A ASP* 4.9 2.1 - - - +
375A ARG* 2.9 35.2 - - - +
376A LYS* 3.5 18.1 + - - +
378A LEU* 1.3 75.2 - - - +
380A THR* 1.3 56.7 + - - +
381A PHE 3.7 2.5 - - - -
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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