Contacts of the strand formed by residues 346 - 349 (chain W) in PDB entry 3EXG
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 346 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339W ILE* 4.2 12.1 - - + -
340W TYR* 3.8 41.3 - + + -
343W ASP* 5.7 2.7 - - + -
344W PRO 3.8 9.6 - - - +
345W PRO* 1.3 76.0 - - - +
347W GLU* 1.3 81.4 + - - +
348W VAL* 4.3 7.0 - - + -
358W LYS* 3.6 4.6 - - - +
359W SER* 2.6 73.3 + - - +
360W VAL* 5.9 0.4 - - - -
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Residues in contact with GLU 347 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346W PHE* 1.3 94.8 - - - +
348W VAL* 1.3 63.6 + - - +
356W LYS* 3.4 42.7 - - + +
357W PHE 3.3 11.4 - - - +
358W LYS* 4.7 6.1 - - + -
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Residues in contact with VAL 348 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298V ALA* 6.0 0.2 - - + -
299V ASP* 3.2 37.9 - - + +
300V VAL* 3.9 9.6 - - + -
335W LEU* 6.3 0.2 - - + -
336W GLY* 4.3 7.6 - - - +
339W ILE* 3.6 13.7 - - + -
346W PHE* 4.3 4.0 - - + -
347W GLU* 1.3 81.2 - - - +
349W ARG* 1.3 68.0 + - - +
356W LYS* 3.7 3.4 - - - -
357W PHE* 2.6 46.8 + - + +
359W SER* 3.5 29.4 - - - +
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Residues in contact with ARG 349 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267V PRO* 4.3 15.4 - - + +
294V ARG* 3.3 37.8 + - - +
296V THR* 4.2 12.1 + - - +
298V ALA* 3.2 3.8 - - - +
299V ASP* 2.9 42.3 + - + +
348W VAL* 1.3 79.0 - - - +
350W GLY* 1.3 73.1 + - - +
352W ASN* 4.4 6.5 - - - +
353W GLN* 3.7 27.6 - - - +
355W ILE 3.9 5.2 - - - +
356W LYS* 5.1 0.4 - - - +
357W PHE* 5.0 0.8 - - - -
278X ARG* 5.7 3.6 - - - +
281X GLU* 2.9 42.4 + - - -
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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