Contacts of the strand formed by residues 353 - 358 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D MET 4.2 3.6 - - - +
169D GLN* 4.3 7.1 - - - +
170D MET 4.5 1.0 + - - +
311D ILE* 3.5 24.7 - - + -
312D THR 3.4 32.1 - - - -
313D ILE* 4.1 13.9 - - + -
349D VAL* 3.2 29.2 - - + -
350D MET* 2.9 15.3 + - - +
351D GLU 3.5 0.5 - - - -
352D GLY* 1.3 87.4 - - - +
354D TYR* 1.3 64.2 + - - +
355D VAL* 3.8 6.2 + - + +
366D PHE* 4.4 18.8 - + + -
367D ALA 3.3 25.4 - - - +
368D ALA* 4.5 3.1 - - - -
369D SER* 3.5 13.0 + - - -
380D SER* 3.9 5.2 - - - -
381D GLU 3.3 22.2 - - - -
382D ILE* 4.2 4.5 - - + -
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Residues in contact with TYR 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D SER* 2.7 37.7 + - - -
168D MET 3.3 20.9 - - - -
169D GLN* 3.7 13.9 - - + +
186D SER 5.5 0.2 - - - -
188D VAL* 3.9 1.1 - - + +
192D ILE* 3.7 13.0 - - + -
193D GLU* 2.8 29.7 + - - +
196D LEU* 3.7 30.8 - - + +
197D TYR* 3.6 43.1 - + + -
353D PHE* 1.3 71.4 - - - +
355D VAL* 1.3 62.6 + - - +
356D ILE* 3.8 9.5 + - + +
365D GLY 3.6 0.7 - - - +
366D PHE* 3.5 5.0 - - - -
367D ALA* 2.8 38.2 + - + +
369D SER* 4.7 2.2 - - - -
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Residues in contact with VAL 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D SER* 3.2 3.6 - - - -
168D MET 2.7 42.3 + - - +
240D VAL* 4.2 5.4 - - + -
350D MET* 4.0 32.5 - - + -
353D PHE* 4.5 9.0 - - + +
354D TYR* 1.3 75.0 - - - +
356D ILE* 1.3 63.1 + - - +
357D PHE* 3.3 35.2 - - + -
364D VAL* 4.0 20.6 - - + -
365D GLY 3.4 3.4 - - - +
366D PHE* 4.2 20.9 - - + -
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Residues in contact with ILE 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D VAL* 4.5 7.2 - - + -
166D PHE 4.7 0.4 - - - +
167D SER* 3.9 13.7 - - - -
192D ILE* 3.1 52.7 - - + -
197D TYR* 5.8 0.4 - - + -
201D ILE* 3.2 25.6 - - + -
203D TYR* 4.0 12.6 - - + +
354D TYR* 4.5 13.0 - - + +
355D VAL* 1.3 75.2 - - - +
357D PHE* 1.3 61.6 + - - +
358D ASP* 3.3 13.0 + - + +
364D VAL* 3.3 8.3 - - - +
365D GLY* 2.7 42.6 + - - +
366D PHE 6.2 0.4 - - - -
367D ALA* 6.2 0.2 - - + -
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Residues in contact with PHE 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D THR* 3.7 20.9 - - + -
165D VAL* 3.7 1.6 - - - -
166D PHE* 2.8 72.7 + + + +
167D SER* 4.6 0.7 - - - -
168D MET* 4.3 11.0 - - + -
206D ILE* 5.8 0.2 - - - -
212D TYR* 3.6 48.5 - + + -
240D VAL* 3.8 26.2 - - + -
350D MET* 4.5 4.7 - - + -
355D VAL* 3.3 36.8 - - + -
356D ILE* 1.3 70.6 - - - +
358D ASP* 1.3 59.5 + - - +
359D ARG* 3.1 11.4 + - - +
363D ARG 4.4 1.6 - - - -
364D VAL* 4.8 7.6 - - + +
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Residues in contact with ASP 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D VAL* 3.6 25.5 - - - +
192D ILE* 5.5 1.9 - - - +
203D TYR* 4.1 6.4 + - + -
206D ILE* 4.8 1.1 - - - +
356D ILE* 3.3 11.4 + - + +
357D PHE* 1.3 69.6 - - - +
359D ARG* 1.3 65.3 + - - +
360D ALA* 3.6 1.4 + - - +
361D GLN* 3.1 28.2 + - - +
362D LYS 3.1 15.9 + - - -
363D ARG* 3.0 64.5 + - + +
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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