Contacts of the helix formed by residues 367 - 373 (chain A) in PDB entry 5IG0
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 367 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ALA* 2.9 13.6 + - - +
365A SER* 3.2 18.5 - - - +
366A GLY* 1.3 73.1 - - - +
368A TRP* 1.3 62.3 + - - +
369A ASP* 3.4 10.4 + - - +
370A ALA* 3.1 34.1 + - + +
371A TYR* 3.1 17.7 + - - +
401A PHE* 3.8 2.5 - - - -
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Residues in contact with TRP 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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366A GLY 3.1 8.6 + - - +
367A ASP* 1.3 69.4 + - - +
369A ASP* 1.3 76.9 + - - +
371A TYR* 3.0 40.4 + + - +
372A THR* 3.1 35.8 + - + +
394A LEU* 3.4 39.5 - - + -
398A LYS* 3.5 62.9 - - + +
401A PHE* 3.4 38.6 - + + -
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Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASP* 3.3 7.6 + - - +
368A TRP* 1.3 87.4 - - - +
370A ALA* 1.3 62.6 + - - +
372A THR* 2.7 24.5 + - - -
373A THR* 3.3 13.7 + - - +
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Residues in contact with ALA 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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358A GLU* 5.9 2.7 - - + +
362A ALA* 3.7 14.6 - - + -
367A ASP* 3.1 33.2 + - - +
369A ASP* 1.3 72.9 - - - +
371A TYR* 1.3 66.1 + - - +
373A THR* 2.6 30.0 + - - +
374A MET* 3.3 15.3 - - + +
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Residues in contact with TYR 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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359A LEU* 3.5 26.9 - - + -
362A ALA* 4.2 2.6 - - + +
363A VAL* 3.6 29.6 - - + -
367A ASP 3.1 12.3 + - - +
368A TRP* 3.0 37.8 + + + +
370A ALA* 1.3 75.2 - - - +
372A THR* 1.3 57.7 + - - +
374A MET* 3.1 3.6 + - - -
375A VAL* 3.1 53.0 + - + +
394A LEU* 3.9 18.4 - - + -
397A HIS* 3.5 30.4 + + + -
401A PHE* 3.7 16.2 - + + -
466A LEU* 5.2 0.5 - - - +
469A PHE* 4.4 2.8 - - - -
501A SO4 3.3 24.1 + - - -
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Residues in contact with THR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TRP* 3.1 48.9 + - + +
369A ASP* 2.7 23.2 + - - -
371A TYR* 1.3 76.4 - - + +
373A THR* 1.3 61.4 + - - +
374A MET 3.2 2.1 + - - -
375A VAL 4.0 14.9 - - - +
394A LEU* 4.5 13.9 - - + +
460A PHE* 4.4 6.1 - - - -
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Residues in contact with THR 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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369A ASP* 3.3 16.2 - - + +
370A ALA* 2.6 25.5 + - - +
372A THR* 1.3 79.4 - - - +
374A MET* 1.3 66.4 + - - +
460A PHE* 3.5 17.5 - - - +
461A LYS* 3.9 43.9 + - + +
462A PHE* 4.1 9.7 + - - -
464A TRP 4.6 1.2 - - - +
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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