Contacts of the strand formed by residues 165 - 168 (chain A) in PDB entry 3EWS
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 CYS 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A MET* 3.5 54.1 - - + -
155A GLN* 4.8 0.9 - - - -
156A VAL* 4.1 18.6 - - - -
163A PRO* 5.0 0.3 - - - +
164A GLN* 1.3 87.8 + - - +
166A LEU* 1.3 62.3 + - - +
212A GLN 3.2 3.7 + - - +
213A ILE* 3.6 15.4 - - + -
214A VAL* 3.0 28.2 + - - +
236A ILE* 4.6 2.6 - - - +
237A LYS* 5.5 0.2 - - - -
238A VAL* 3.4 16.6 - - - +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 3.5 3.8 - - - +
165A CYS* 1.3 75.4 - - - +
167A CYS* 1.3 62.2 + - - +
168A LEU* 4.3 5.4 - - + -
214A VAL* 3.4 35.2 - - + +
221A VAL* 3.9 33.9 - - + -
225A CYS* 4.5 11.2 - - - -
231A ILE* 4.9 5.2 - - + -
236A ILE* 4.1 24.2 - - + -
238A VAL 2.8 12.6 + - - +
239A PHE* 3.3 23.9 - - + -
240A VAL 2.8 25.3 + - - +
260A ILE* 4.2 11.2 - - + -
264A LEU* 4.8 4.3 - - + -
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Residues in contact with CYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 4.1 23.3 - - - -
152A MET* 3.3 22.0 - - + -
166A LEU* 1.3 73.4 - - - +
168A LEU* 1.3 74.4 + - - +
169A SER* 4.7 2.0 - - - -
178A THR* 4.3 8.1 - - + -
214A VAL 2.9 10.5 + - - +
215A ILE* 3.3 26.8 - - + +
216A GLY 3.1 25.6 + - - +
240A VAL* 3.4 12.1 - - + -
242A ASP* 4.4 7.2 - - - -
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 4.5 5.8 - - + -
167A CYS* 1.3 76.6 - - - +
169A SER* 1.3 59.8 + - - +
216A GLY 3.3 3.6 - - - +
218A PRO* 4.5 8.3 - - + -
221A VAL* 3.6 42.6 - - + -
239A PHE* 3.8 32.8 - - + -
240A VAL 2.8 13.7 + - - +
241A LEU* 4.7 4.7 - - + -
242A ASP* 3.1 27.0 + - - +
247A MET* 3.6 15.3 - - - +
257A SER* 3.6 24.7 - - - +
260A ILE* 3.9 16.8 - - + -
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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