Contacts of the helix formed by residues 372 - 378 (chain A) in PDB entry 2WJP
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 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A GLY 3.0 13.0 + - - +
346A ASP* 4.0 2.4 - - - +
347A GLY* 2.7 35.7 + - - +
348A LYS 4.2 0.9 + - - -
349A SER* 5.1 2.1 + - - -
352A PHE* 4.3 16.8 - - + -
369A PHE 4.3 0.2 - - - -
370A GLY 3.2 0.2 - - - -
371A ARG* 1.3 96.8 + - - +
373A GLY* 1.3 64.0 + - - +
374A ALA 3.2 3.1 - - - -
375A GLN* 3.1 28.4 + - - +
376A LEU* 3.2 18.4 + - + +
413A CYS* 5.0 0.2 - - - -
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Residues in contact with GLY 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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368A CYS* 3.3 12.8 - - - +
369A PHE* 3.4 30.0 + - - -
370A GLY 3.1 11.9 + - - -
371A ARG 3.4 1.0 + - - -
372A ASP* 1.3 77.8 - - - +
374A ALA* 1.3 57.9 + - - +
376A LEU* 3.3 3.7 + - - -
377A ALA* 3.0 25.3 + - - +
386A GLN* 4.0 10.2 - - - +
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Residues in contact with ALA 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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371A ARG 5.0 1.4 + - - +
372A ASP 3.2 1.2 - - - -
373A GLY* 1.3 76.4 - - - +
375A GLN* 1.3 61.8 + - - +
377A ALA* 3.4 4.7 + - - +
378A ALA* 3.1 23.0 + - - +
386A GLN* 3.5 29.0 - - - +
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Residues in contact with GLN 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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349A SER* 6.0 1.6 - - - -
350A ALA 3.9 13.0 + - - +
351A ASP* 5.4 1.6 - - - +
352A PHE* 3.8 35.0 - - + +
372A ASP* 3.1 24.7 + - + +
374A ALA* 1.3 77.2 - - - +
376A LEU* 1.3 62.1 + - - +
378A ALA* 3.4 18.9 + - + +
379A LEU* 3.8 7.8 + - - +
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Residues in contact with LEU 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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343A LEU* 3.8 17.4 - - + +
344A GLY* 3.4 38.6 - - - +
352A PHE* 3.6 42.4 - - + -
355A LEU* 4.8 4.3 - - + -
366A LEU* 4.3 3.6 - - - +
368A CYS* 3.8 16.1 - - - -
372A ASP 3.2 17.2 + - - +
373A GLY* 3.7 6.5 - - - +
375A GLN* 1.3 74.9 - - - +
377A ALA* 1.3 65.3 + - - +
378A ALA 3.1 1.3 - - - -
379A LEU* 3.1 33.1 + - + +
411A PRO 4.9 2.0 - - - +
412A ALA* 5.1 0.2 - - + -
413A CYS* 4.0 12.3 - - - -
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Residues in contact with ALA 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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366A LEU* 4.8 0.2 - - - +
368A CYS* 3.5 16.2 - - + -
373A GLY 3.0 15.8 + - - +
374A ALA* 3.4 7.8 + - - +
376A LEU* 1.3 76.6 - - - +
378A ALA* 1.3 59.0 + - - +
379A LEU 3.0 5.9 + - - -
380A ARG 3.1 14.2 + - - -
381A PRO* 3.3 15.1 - - + +
384A ALA* 3.7 20.3 - - + +
385A GLU 5.0 1.3 - - - +
386A GLN* 4.8 13.0 - - + +
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Residues in contact with ALA 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 ALA 3.1 13.3 + - - +
375A GLN* 3.5 15.7 - - + +
376A LEU 3.1 1.2 - - - -
377A ALA* 1.3 76.1 - - - +
379A LEU* 1.3 62.7 + - - +
380A ARG 3.2 0.7 + - - -
381A PRO* 3.5 20.1 - - + +
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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