Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 2EWY
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 PHE 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A MET 4.2 4.0 - - - +
169A GLN* 4.3 6.8 - - - +
170A MET 4.5 1.0 + - - +
311A ILE* 3.5 24.9 - - + -
312A THR 3.4 33.4 - - - -
313A ILE* 4.1 14.4 - - + -
349A VAL* 3.2 29.2 - - + -
350A MET* 2.9 16.0 + - - +
351A GLU 3.5 0.7 - - - -
352A GLY* 1.3 87.9 - - - +
354A TYR* 1.3 63.8 + - - +
355A VAL* 3.8 5.3 + - + +
366A PHE* 4.4 20.2 - + + -
367A ALA 3.3 24.9 - - - +
368A ALA* 4.5 3.1 - - - -
369A SER* 3.5 12.7 + - - -
380A SER* 3.9 5.2 - - - -
381A GLU 3.3 20.9 - - - -
382A ILE* 4.2 4.3 - - + -
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Residues in contact with TYR 354 (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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167A SER* 2.7 36.0 + - - -
168A MET* 3.3 22.0 - - - -
169A GLN* 3.7 12.6 - - + +
186A SER 5.5 0.2 - - - -
188A VAL* 3.9 1.7 - - + +
192A ILE* 3.7 12.7 - - + -
193A GLU* 2.8 28.9 + - - +
196A LEU* 3.7 31.7 - - + +
197A TYR* 3.6 43.3 - + + -
353A PHE* 1.3 71.6 - - - +
355A VAL* 1.3 60.9 + - - +
356A ILE* 3.8 8.4 + - + +
365A GLY 3.6 0.9 - - - +
366A PHE* 3.5 4.7 - - - -
367A ALA* 2.8 39.5 + - + +
369A SER* 4.7 2.0 - - - -
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Residues in contact with VAL 355 (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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167A SER* 3.2 3.5 - - - -
168A MET 2.7 43.2 + - - +
240A VAL* 4.2 5.2 - - + -
350A MET* 4.0 33.0 - - + -
353A PHE* 3.8 8.7 - - + +
354A TYR* 1.3 74.2 - - - +
356A ILE* 1.3 64.2 + - - +
357A PHE* 3.3 35.0 - - + -
364A VAL* 4.0 20.6 - - + -
365A GLY 3.4 3.4 - - - +
366A PHE* 4.2 22.0 - - + -
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Residues in contact with ILE 356 (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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165A VAL* 4.5 7.4 - - + -
166A PHE 4.7 0.7 - - - +
167A SER* 3.9 13.2 - - - -
192A ILE* 3.1 52.7 - - + -
197A TYR* 5.8 0.4 - - + -
201A ILE* 3.2 25.6 - - + -
203A TYR* 4.0 11.9 - - + +
354A TYR* 4.5 14.4 - - + +
355A VAL* 1.3 77.3 - - - +
357A PHE* 1.3 63.3 + - - +
358A ASP* 3.3 12.7 + - + +
364A VAL* 3.3 8.1 - - - +
365A GLY* 2.7 41.9 + - - +
367A ALA* 6.2 0.9 - - + -
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Residues in contact with PHE 357 (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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49A THR* 3.7 20.6 - - + -
165A VAL* 3.7 1.9 - - - -
166A PHE* 2.8 72.7 + + + +
167A SER* 4.6 0.4 - - - -
168A MET* 4.3 11.2 - - + -
212A TYR* 3.6 47.8 - + + -
240A VAL* 3.8 25.4 - - + -
350A MET* 4.5 4.9 - - + -
355A VAL* 3.3 36.3 - - + -
356A ILE* 1.3 71.2 - - - +
358A ASP* 1.3 60.0 + - - +
359A ARG* 3.1 10.6 + - - +
363A ARG 4.4 1.6 - - - -
364A VAL* 4.8 7.4 - - + +
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Residues in contact with ASP 358 (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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165A VAL* 3.6 25.7 - - - +
192A ILE* 5.5 2.3 - - - +
203A TYR* 4.1 7.2 + - + -
206A ILE* 4.8 0.9 - - - -
356A ILE* 3.3 10.8 + - + +
357A PHE* 1.3 69.1 - - - +
359A ARG* 1.3 65.4 + - - +
360A ALA* 3.1 1.8 + - - +
361A GLN* 3.1 27.0 + - - +
362A LYS 3.1 14.7 + - - -
363A ARG* 3.0 64.9 + - + +
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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