Contacts of the helix formed by residues 369 - 375 (chain I) in PDB entry 4PHZ
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 369 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298I ARG* 3.0 21.0 + - - +
326I PHE* 3.7 23.5 - - + -
344I ALA* 3.1 28.2 - - + +
345I ASP 4.0 5.5 + - - -
346I ARG* 4.4 7.3 + - - +
368I GLN* 1.3 79.3 - - - +
370I ALA* 1.3 79.1 + - - +
371I ARG* 3.0 35.9 + - - +
372I TRP* 3.2 18.2 + - - +
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Residues in contact with ALA 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298I ARG* 3.5 26.1 + - - +
369I ASP* 1.3 78.5 + - - +
371I ARG* 1.3 58.3 + - + +
373I ASP* 3.0 10.0 + - - +
374I ILE* 2.9 43.7 + - + +
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Residues in contact with ARG 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324I LEU* 3.6 13.8 - - + +
326I PHE* 5.3 0.2 - - + -
340I ASP* 2.9 47.3 + - - -
341I TYR* 3.3 24.8 + - - +
342I LEU 4.1 2.2 - - - -
343I LEU* 3.0 32.3 + - - +
344I ALA* 4.1 5.7 - - + +
345I ASP 5.3 0.2 - - - +
369I ASP* 3.0 32.1 + - + +
370I ALA* 1.3 75.7 - - + +
372I TRP* 1.3 59.8 + - - +
373I ASP 3.2 0.2 - - - -
374I ILE* 3.7 15.5 - - + -
375I GLU* 2.8 34.7 + - + +
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Residues in contact with TRP 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I MET* 4.6 8.5 - - - -
293I TYR* 4.3 25.2 - + + +
294I LYS 5.2 1.2 + - - -
297I GLY 3.8 17.6 + - - -
298I ARG 3.9 16.8 - - - +
299I GLU 4.1 11.5 + - - +
300I LEU* 4.0 19.7 - - + -
319I TYR* 5.2 8.7 - + - -
321I ALA* 5.5 0.7 - - + -
324I LEU* 4.1 4.9 - - - +
326I PHE* 4.2 25.8 - + + -
367I ILE* 5.0 6.7 - - + -
369I ASP 3.2 14.1 + - - +
371I ARG* 1.3 77.6 - - - +
373I ASP* 1.3 59.6 + - - +
377I LEU* 3.0 79.4 + - + +
378I SER* 3.4 16.8 + - - +
380I LEU* 4.9 1.3 - - + -
388I ILE* 3.7 28.9 - - + -
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Residues in contact with ASP 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296I PRO* 5.4 2.8 - - - +
297I GLY 2.9 30.5 + - - +
298I ARG* 3.6 24.0 + - - +
369I ASP 4.0 0.4 + - - -
370I ALA 3.0 10.0 + - - +
372I TRP* 1.3 79.3 - - - +
374I ILE* 1.3 59.4 + - - +
376I ARG* 2.7 28.8 + - - +
378I SER* 3.0 21.6 + - - -
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Residues in contact with ILE 374 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LYS* 3.8 16.0 - - + +
298I ARG* 5.4 2.0 - - - +
341I TYR* 5.8 1.3 - - + +
370I ALA* 2.9 40.6 + - + +
371I ARG* 3.4 13.4 + - + +
373I ASP* 1.3 77.8 - - + +
375I GLU* 1.3 71.4 + - - +
376I ARG* 3.3 7.6 + - - +
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Residues in contact with GLU 375 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLU* 4.3 11.3 - - - +
32I LYS* 3.6 23.9 + - - +
39I ARG* 2.9 26.4 + - - +
324I LEU* 3.7 33.0 - - + -
341I TYR* 4.0 40.9 - - - +
342I LEU* 4.8 2.9 - - + +
371I ARG* 2.8 25.0 + - + +
372I TRP 4.0 0.9 - - - +
374I ILE* 1.3 87.3 - - - +
376I ARG* 1.3 62.5 + - - +
377I LEU* 2.8 12.3 + - + +
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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