Contacts of the strand formed by residues 353 - 358 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B MET 4.2 4.3 - - - +
169B GLN* 4.3 6.8 - - - +
170B MET 4.5 1.2 + - - +
311B ILE* 3.5 24.2 - - + -
312B THR 3.4 33.0 - - - -
313B ILE* 4.1 13.7 - - + -
349B VAL* 3.2 29.8 - - + -
350B MET* 2.9 15.4 + - - +
351B GLU 3.5 0.5 - - - -
352B GLY* 1.3 88.0 - - - +
354B TYR* 1.3 63.7 + - - +
355B VAL* 3.8 6.2 + - + +
366B PHE* 4.4 18.8 - + + -
367B ALA 3.3 25.4 - - - +
368B ALA* 4.5 2.7 - - - -
369B SER* 3.5 12.3 + - - -
380B SER* 3.9 4.3 - - - -
381B GLU 3.3 21.5 - - - -
382B ILE* 4.2 4.3 - - + -
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Residues in contact with TYR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B SER* 2.7 37.3 + - - -
168B MET 3.3 21.5 - - - -
169B GLN* 3.7 12.6 - - + +
186B SER 5.5 0.2 - - - -
188B VAL* 3.9 1.8 - - + +
192B ILE* 3.7 11.6 - - + -
193B GLU* 2.8 29.4 + - - +
196B LEU* 3.7 29.9 - - + +
197B TYR* 3.6 42.8 - + + -
353B PHE* 1.3 70.5 - - - +
355B VAL* 1.3 62.6 + - - +
356B ILE* 3.8 8.5 + - + +
365B GLY 3.6 1.0 - - - +
366B PHE* 3.5 4.7 - - - -
367B ALA* 2.8 39.6 + - + +
369B SER* 4.7 2.2 - - - -
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B SER* 3.2 3.8 - - - -
168B MET 2.7 42.1 + - - +
240B VAL* 4.2 5.2 - - + -
350B MET* 4.0 33.2 - - + -
353B PHE* 4.5 8.1 - - + +
354B TYR* 1.3 75.5 - - - +
356B ILE* 1.3 63.5 + - - +
357B PHE* 3.3 35.3 - - + -
364B VAL* 4.0 20.4 - - + -
365B GLY 3.4 3.4 - - - +
366B PHE* 4.2 21.3 - - + -
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B VAL* 4.5 7.2 - - + -
166B PHE 4.7 0.7 - - - +
167B SER* 3.9 13.5 - - - -
192B ILE* 3.1 54.1 - - + -
197B TYR* 5.8 0.2 - - + -
201B ILE* 3.2 26.0 - - + -
203B TYR* 4.0 12.3 - - + +
354B TYR* 4.5 13.2 - - + +
355B VAL* 1.3 76.1 - - - +
357B PHE* 1.3 63.7 + - - +
358B ASP* 3.3 13.3 + - + +
364B VAL* 3.3 8.5 - - - +
365B GLY* 2.7 40.4 + - - +
367B ALA* 6.2 0.4 - - + -
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Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 3.7 20.2 - - + -
165B VAL* 3.7 1.9 - - - -
166B PHE* 2.8 72.3 + + + +
167B SER* 4.6 0.4 - - - -
168B MET* 4.3 11.0 - - + -
206B ILE* 5.9 0.2 - - - -
212B TYR* 3.6 48.5 - + + -
240B VAL* 3.8 25.4 - - + -
350B MET* 4.5 4.7 - - + -
355B VAL* 3.3 36.3 - - + -
356B ILE* 1.3 71.6 - - - +
358B ASP* 1.3 59.8 + - - +
359B ARG* 3.1 10.9 + - - +
363B ARG 4.4 1.8 - - - -
364B VAL* 4.8 7.2 - - + +
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Residues in contact with ASP 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B VAL* 3.6 26.3 - - - +
192B ILE* 5.5 1.9 - - - +
203B TYR* 4.1 6.4 + - + -
206B ILE* 4.8 1.1 - - - -
356B ILE* 3.3 11.5 + - + +
357B PHE* 1.3 68.1 - - - +
359B ARG* 1.3 65.1 + - - +
360B ALA* 3.6 1.2 + - - +
361B GLN* 3.1 28.7 + - - +
362B LYS 3.1 15.2 + - - -
363B ARG* 3.0 63.9 + - + +
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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
------------------------------------------------------------
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