Contacts of the strand formed by residues 177 - 184 (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 VAL 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LEU* 4.4 21.3 - - + -
170A VAL 3.4 6.7 - - - +
171A LYS* 4.4 17.9 - - + +
175A GLY 3.7 0.2 + - - -
176A ALA* 1.3 72.8 - - - +
178A VAL* 1.3 66.9 + - - +
179A GLY 3.9 8.7 - - - +
195A ALA 4.6 1.2 - - - +
198A THR* 3.8 28.5 - - - +
229A ALA* 5.5 0.2 - - + -
231A VAL* 5.3 1.8 - - + -
380A VAL* 4.2 11.9 - - + -
381A PRO 3.0 11.4 + - - +
382A GLY* 3.3 27.5 - - - +
383A LEU* 3.9 24.0 - - + -
429A LEU* 3.8 3.5 - - - +
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Residues in contact with VAL 178 (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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170A VAL* 2.8 20.4 + - + +
172A ASN* 4.0 20.4 - - + +
176A ALA 4.2 2.2 - - - +
177A VAL* 1.3 79.7 - - - +
179A GLY* 1.3 57.1 + - - +
192A TYR* 2.8 32.7 + - - +
194A LYS* 4.2 2.4 - - + +
195A ALA 3.2 29.4 + - - +
429A LEU* 3.9 24.0 - - + -
430A ARG 3.9 18.4 - - - +
431A ASP* 5.7 0.4 - - - -
432A ALA* 3.8 21.8 - - + +
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Residues in contact with GLY 179 (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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11A VAL* 5.7 1.3 - - - -
169A LEU* 3.6 4.3 - - - +
170A VAL* 2.9 24.4 + - - +
177A VAL* 3.7 4.0 - - - +
178A VAL* 1.3 78.4 - - - +
180A CYS* 1.3 62.7 + - - +
192A TYR* 4.1 0.9 - - - -
193A PHE 3.1 13.2 - - - -
195A ALA* 4.2 4.3 - - - -
198A THR* 3.2 26.1 + - - -
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Residues in contact with CYS 180 (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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11A VAL* 4.7 3.8 - - - +
13A ILE* 3.7 26.9 - - + -
36A LEU* 4.3 14.6 - - - -
166A ALA* 4.2 8.1 - - - -
168A ASP 3.3 20.2 - - - +
169A LEU* 4.1 3.8 - - + -
170A VAL* 3.8 7.0 - - - -
179A GLY* 1.3 75.7 - - - +
181A THR* 1.3 72.2 + - - +
192A TYR* 3.5 2.9 - - - -
193A PHE* 2.8 37.2 + - - +
198A THR* 5.0 0.7 - - + -
225A MET* 4.2 8.1 - - + -
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Residues in contact with THR 181 (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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3A LEU* 4.2 5.8 - - + -
166A ALA* 3.5 2.9 - - - -
167A LEU* 2.9 36.2 + - - +
168A ASP 3.2 7.1 + - - -
170A VAL* 4.3 4.0 - - + -
180A CYS* 1.3 80.3 - - - +
182A ALA* 1.3 63.1 + - - +
190A VAL* 4.7 0.4 - - - -
191A VAL 3.1 11.9 - - - +
192A TYR* 4.3 3.6 - - - -
437A VAL* 4.1 20.9 - - + -
440A SER* 3.3 32.4 - - - -
441A LEU* 3.9 22.5 - - + +
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Residues in contact with ALA 182 (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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36A LEU* 4.1 10.5 - - + -
164A TRP* 4.1 9.5 - - + -
165A TYR 3.0 17.3 - - - +
166A ALA* 4.0 3.4 - - - -
167A LEU* 4.1 5.4 - - - +
181A THR* 1.3 77.1 - - - +
183A LEU* 1.3 61.7 + - - +
184A CYS 4.1 0.4 + - - -
189A GLU 4.0 0.5 - - - +
190A VAL* 3.4 4.7 - - - +
191A VAL 3.0 31.5 + - - -
193A PHE* 3.7 28.9 - - + -
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Residues in contact with LEU 183 (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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164A TRP* 4.0 2.0 - - - -
165A TYR* 2.7 46.4 + - + +
167A LEU* 4.2 14.3 - - + +
182A ALA* 1.3 73.6 - - - +
184A CYS* 1.3 65.9 + - - +
185A ILE* 3.2 6.6 + - + -
188A GLY* 3.4 33.4 - - - +
189A GLU 3.7 1.6 - - - -
190A VAL* 3.8 12.6 - - + +
444A LEU* 5.2 4.0 - - + -
507A ASN 5.7 1.3 - - - +
510A ARG* 4.0 33.0 - - - +
511A VAL* 4.4 21.3 - - + -
514A LEU* 4.5 10.3 - - + -
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Residues in contact with CYS 184 (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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163A GLU 4.1 2.2 - - - -
164A TRP* 3.5 48.4 - - + -
183A LEU* 1.3 72.1 - - - +
185A ILE* 1.3 60.6 + - - +
186A GLU* 3.9 10.3 - - - -
187A THR* 3.2 36.1 - - - +
188A GLY* 2.8 31.9 + - - -
189A GLU* 2.8 17.2 + - + +
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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