Contacts of the strand formed by residues 179 - 184 (chain A) in PDB entry 2AQ5
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 ILE 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TRP* 6.1 1.2 - - - -
136A ILE* 3.5 15.9 - - + +
150A ALA* 4.1 10.5 - - + -
151A GLY 4.5 5.4 + - - +
154A ASN* 3.8 33.0 + - - +
155A VAL 4.3 0.4 - - - +
156A ILE* 3.8 26.7 - - + -
175A HIS* 3.7 27.6 - - + +
177A ASP 4.0 1.8 - - - +
178A THR* 1.3 81.8 - - - +
180A TYR* 1.3 60.1 + - - +
181A SER 3.6 11.2 - - - +
182A VAL* 3.6 29.8 - - + -
193A THR* 4.8 6.5 - - - -
194A SER 3.7 6.1 - - - +
195A CYS* 4.5 1.1 - - - +
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Residues in contact with TYR 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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36A ASP* 6.0 0.2 - - - +
136A ILE* 3.9 8.4 - - - +
178A THR* 3.5 14.8 + - + -
179A ILE* 1.3 73.1 - - - +
181A SER* 1.3 60.1 + - - +
194A SER* 2.8 14.8 + - - +
195A CYS 3.6 17.0 - - - -
196A ARG* 3.3 49.8 + - + +
198A LYS* 6.0 1.7 - - + +
221A THR 4.7 5.5 + - - -
222A ARG 4.5 3.7 + - - -
223A PRO* 3.6 35.3 - - + +
224A VAL* 3.2 42.0 - - + +
225A HIS* 3.4 22.7 + - - +
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Residues in contact with SER 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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136A ILE* 4.0 5.4 - - - -
179A ILE* 3.5 4.1 - - - +
180A TYR* 1.3 79.5 - - - +
182A VAL* 1.3 68.4 + - - +
192A CYS 4.4 0.4 + - - -
193A THR* 3.3 3.9 - - - -
194A SER* 3.0 36.2 + - - -
225A HIS* 3.6 20.0 - - - -
226A ALA* 3.1 33.0 + - - +
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Residues in contact with VAL 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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136A ILE* 4.3 15.1 - - + +
138A ALA* 4.7 12.3 - - + +
148A LEU* 3.8 36.3 - - + -
150A ALA* 4.2 13.5 - - + -
156A ILE* 4.1 9.4 - - + -
179A ILE* 3.6 19.3 - - + -
181A SER* 1.3 83.0 - - - +
183A ASP* 1.3 65.2 + - - +
184A TRP* 5.2 0.7 - - - +
191A ILE* 4.2 11.2 - - + -
192A CYS 3.3 8.7 - - - +
193A THR* 4.1 16.2 - - + -
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Residues in contact with ASP 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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182A VAL* 1.3 78.6 - - - +
184A TRP* 1.3 76.2 + - - +
191A ILE* 3.2 6.5 - - - -
192A CYS* 2.8 34.5 + - + +
226A ALA 3.9 17.0 - - - +
227A VAL* 3.5 18.2 - - + +
228A PHE* 2.8 34.5 + - + +
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Residues in contact with TRP 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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138A ALA* 3.1 33.1 + - + +
139A TRP 3.2 22.2 + - - -
140A HIS* 3.4 33.4 - + + -
141A PRO* 3.6 21.8 - - + -
146A VAL* 4.6 6.7 - - + -
148A LEU* 3.8 32.0 - - + +
158A VAL* 4.7 7.0 - - + -
182A VAL* 6.0 0.9 - - + -
183A ASP* 1.3 90.8 + - - +
185A SER* 1.3 63.5 + - - +
188A GLY* 3.5 17.9 - - - -
190A LEU 3.6 12.1 - - - -
191A ILE* 3.4 24.9 - - + -
205A PRO* 3.9 9.2 - - + -
228A PHE* 3.6 2.7 - - - +
379A TRP* 3.8 20.0 - + - -
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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