Contacts of the strand formed by residues 353 - 358 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C MET 4.2 4.7 - - - +
169C GLN* 4.3 6.8 - - - +
170C MET 4.5 0.9 + - - -
311C ILE* 3.5 24.9 - - + -
312C THR 3.4 33.0 - - - -
313C ILE* 4.1 14.1 - - + -
349C VAL* 3.2 29.2 - - + -
350C MET* 2.9 16.7 + - - +
351C GLU 3.5 0.7 - - - -
352C GLY* 1.3 85.6 - - - +
354C TYR* 1.3 64.3 + - - +
355C VAL* 3.8 5.8 + - + +
366C PHE* 4.4 18.2 - + + -
367C ALA 3.3 27.1 - - - +
368C ALA* 4.5 2.7 - - - -
369C SER* 3.5 13.2 + - - -
380C SER* 3.9 4.5 - - - -
381C GLU 3.3 21.3 - - - -
382C ILE* 4.2 4.5 - - + -
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Residues in contact with TYR 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C SER* 2.7 36.9 + - - -
168C MET 3.3 20.4 - - - -
169C GLN* 3.7 13.7 - - + +
186C SER 5.5 0.2 - - - -
188C VAL* 3.9 1.4 - - + +
192C ILE* 3.7 12.0 - - + -
193C GLU* 2.8 29.3 + - - +
196C LEU* 3.7 31.3 - - + +
197C TYR* 3.6 42.4 - + + -
353C PHE* 1.3 71.9 - - - +
355C VAL* 1.3 61.7 + - - +
356C ILE* 3.8 9.1 + - + +
365C GLY 3.6 0.9 - - - +
366C PHE* 3.5 4.9 - - - -
367C ALA* 2.8 38.9 + - + +
369C SER* 4.7 2.0 - - - -
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Residues in contact with VAL 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C SER* 3.2 3.3 - - - -
168C MET 2.7 41.7 + - - +
240C VAL* 4.2 5.8 - - + -
350C MET* 4.0 32.5 - - + -
353C PHE* 4.5 8.7 - - + +
354C TYR* 1.3 75.6 - - - +
356C ILE* 1.3 62.5 + - - +
357C PHE* 3.3 34.4 - - + -
364C VAL* 4.0 20.6 - - + -
365C GLY 3.4 2.9 - - - +
366C PHE* 4.2 20.9 - - + -
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Residues in contact with ILE 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 4.5 7.4 - - + -
166C PHE 4.7 0.9 - - - +
167C SER* 3.9 13.0 - - - -
192C ILE* 3.1 53.2 - - + -
197C TYR* 5.8 0.4 - - + -
201C ILE* 3.2 25.8 - - + -
203C TYR* 4.0 12.1 - - + +
354C TYR* 4.5 13.7 - - + +
355C VAL* 1.3 76.5 - - - +
357C PHE* 1.3 64.0 + - - +
358C ASP* 3.3 12.5 + - + +
364C VAL* 3.3 8.3 - - - +
365C GLY* 2.7 39.5 + - - +
366C PHE 6.2 0.2 - - - -
367C ALA* 6.2 0.2 - - + -
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Residues in contact with PHE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C THR* 3.7 21.1 - - + -
165C VAL* 3.7 2.1 - - - -
166C PHE* 2.8 73.2 + + + +
167C SER* 4.6 0.4 - - - -
168C MET* 4.3 10.5 - - + -
212C TYR* 3.6 46.7 - + + -
240C VAL* 3.8 25.1 - - + -
350C MET* 4.5 4.7 - - + -
355C VAL* 3.3 37.5 - - + -
356C ILE* 1.3 71.4 - - - +
358C ASP* 1.3 59.2 + - - +
359C ARG* 3.1 11.0 + - - +
363C ARG 4.4 1.6 - - - -
364C VAL* 4.8 7.4 - - + +
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Residues in contact with ASP 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 3.6 25.6 - - - +
192C ILE* 5.5 1.9 - - - +
203C TYR* 4.1 7.1 + - + -
206C ILE* 4.8 1.3 - - - -
356C ILE* 3.3 11.4 + - + +
357C PHE* 1.3 68.3 - - - +
359C ARG* 1.3 63.1 + - - +
360C ALA* 3.6 1.6 + - - +
361C GLN* 3.1 28.2 + - - +
362C LYS 3.1 15.4 + - - -
363C ARG* 3.0 64.4 + - + +
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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