Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 2WP9
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 TRP 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG* 5.0 9.0 - - - -
36A LEU* 4.4 16.3 - - + +
37A SER 3.0 9.6 + - - +
38A LYS* 3.3 17.0 + - - +
161A PHE* 3.5 44.9 - + + +
162A SER 3.4 16.8 + - - +
163A GLU* 1.3 81.1 - - - +
165A TYR* 1.3 61.9 + - - +
166A ALA 3.8 1.9 + - - -
182A ALA* 4.1 9.0 - - + -
183A LEU 3.4 6.1 - - - -
184A CYS* 3.5 46.9 - - + -
185A ILE* 4.7 0.4 - - - -
189A GLU* 4.2 12.8 - - - -
191A VAL* 3.9 27.4 - - + -
193A PHE* 3.7 31.6 - + - -
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 3.8 24.5 - - + -
164A TRP* 1.3 71.8 - - - +
166A ALA* 1.3 80.1 + - - +
167A LEU* 3.3 15.1 + - + -
182A ALA* 3.0 3.5 - - - -
183A LEU* 2.7 49.3 + - + +
185A ILE* 4.3 13.4 - - + +
221A ASP* 3.1 38.3 + - - -
443A ARG* 4.5 3.1 - - - -
511A VAL* 3.8 16.4 - - + -
514A LEU* 3.7 30.4 - - + -
515A GLU* 3.6 22.5 + - + +
518A ASN* 3.3 10.7 + - - -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.7 35.9 - - + -
36A LEU* 4.5 6.9 - - + +
38A LYS* 5.7 0.2 - - - +
164A TRP 3.8 3.4 + - - -
165A TYR* 1.3 91.7 - - - +
167A LEU* 1.3 62.0 + - - +
180A CYS* 4.2 5.8 - - - -
181A THR 3.5 9.4 - - - +
182A ALA* 4.0 3.1 - - - +
221A ASP* 5.2 2.8 - - - +
225A MET* 3.9 22.9 - - + +
443A ARG* 4.7 0.2 + - - -
518A ASN* 5.7 0.5 + - - -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TYR* 3.8 15.9 - - + +
166A ALA* 1.3 71.5 - - - +
168A ASP* 1.3 67.4 + - - +
181A THR* 2.9 18.9 + - - +
182A ALA 4.1 18.2 - - - +
183A LEU* 4.2 7.2 - - + +
190A VAL* 4.2 3.4 - - + -
225A MET* 3.6 9.6 - - - +
440A SER 4.5 7.0 - - - +
441A LEU* 3.9 18.6 - - + -
443A ARG* 2.8 25.8 + - - +
444A LEU* 3.9 31.6 - - + -
514A LEU* 3.6 38.1 - - + -
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 1.3 85.3 - - - +
169A LEU* 1.3 70.8 + - - +
180A CYS* 3.3 1.6 - - - +
181A THR* 3.2 25.7 + - - -
225A MET* 3.6 18.2 - - - +
228A ARG* 2.8 38.5 + - - +
440A SER* 3.6 28.9 + - - +
443A ARG* 2.9 29.5 + - - +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.6 2.0 - - + -
168A ASP* 1.3 78.2 + - - +
170A VAL* 1.3 62.9 + - - +
171A LYS* 4.2 3.3 + - + +
177A VAL* 4.4 14.6 - - + -
179A GLY 3.6 5.6 - - - +
180A CYS* 4.3 1.3 - - + -
198A THR* 4.1 26.2 - - + -
200A LEU* 4.5 10.3 - - + -
225A MET* 3.6 37.6 + - + +
226A ALA* 4.5 2.5 - - - -
229A ALA* 4.0 29.2 - - + +
231A VAL* 5.3 0.2 - - + -
383A LEU* 4.0 30.1 - - + -
440A SER* 3.0 13.9 + - - -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 1.3 75.2 - - - +
171A LYS* 1.3 63.5 + - - +
177A VAL* 3.4 5.4 - - - +
178A VAL* 2.8 30.7 + - + -
179A GLY 2.9 12.9 + - - +
180A CYS* 3.8 21.3 - - - -
181A THR* 4.1 4.3 - - + +
192A TYR* 3.9 18.6 - - + -
432A ALA* 3.8 29.4 - - + -
436A ASP 4.0 18.4 - - - +
437A VAL* 4.2 7.9 - - + -
440A SER* 3.1 22.2 - - - +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 4.2 2.8 + - + +
170A VAL* 1.3 77.8 - - - +
172A ASN* 1.3 66.0 + - - +
175A GLY* 3.3 29.8 + - - +
176A ALA 3.0 10.1 - - - +
177A VAL* 4.4 14.8 - - + -
178A VAL* 4.2 3.5 - - - +
229A ALA* 3.1 41.1 + - + +
230A GLY* 5.2 3.6 - - - -
231A VAL* 5.1 6.3 - - - +
380A VAL* 5.3 3.9 - - - +
436A ASP* 3.2 30.6 + - - +
562A GLU* 5.8 2.0 + - - -
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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