Contacts of the strand formed by residues 173 - 179 (chain A) in PDB entry 1HJV
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 LEU 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A HIS* 4.1 29.6 - - + +
91A LYS* 4.2 16.6 - - + -
93A LEU* 4.0 20.2 - - + -
133A ASP* 2.6 23.3 + - + +
134A GLY* 2.9 1.0 - - - -
135A LEU 2.6 34.2 + - - -
161A PHE* 3.4 3.9 - - - -
171A GLN* 4.5 7.6 - - + +
172A LEU* 1.3 74.5 - - - +
174A LEU* 1.3 55.9 + - - +
199A ASP* 3.2 26.0 - - + +
200A PHE* 5.4 4.3 - - + -
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Residues in contact with LEU 174 (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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135A LEU* 3.5 16.6 - - + -
137A LEU* 4.5 10.1 - - + -
154A ILE* 3.6 26.5 - - + +
157A MET* 3.9 21.3 - - + -
158A LYS* 3.9 18.8 - - + +
161A PHE* 3.8 16.2 - - + -
172A LEU 3.9 0.2 + - - -
173A LEU* 1.3 74.3 - - - +
175A SER* 1.3 69.3 + - - +
197A HIS 3.9 18.8 - - - +
198A LEU* 3.6 16.2 - - + -
199A ASP* 2.7 46.4 + - - +
200A PHE* 5.8 0.2 - - - -
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Residues in contact with SER 175 (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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55A ILE* 4.3 0.2 - - - +
93A LEU* 3.6 7.4 - - - +
135A LEU 3.1 7.0 + - - -
136A ASP* 2.4 35.3 + - - +
137A LEU* 2.7 29.8 + - - +
174A LEU* 1.3 79.6 - - - +
176A ALA* 1.3 57.9 + - - +
198A LEU* 4.3 4.4 - - - +
200A PHE* 3.4 45.9 - - - -
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Residues in contact with ALA 176 (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 ASP* 3.6 4.5 - - - -
137A LEU* 3.2 20.2 - - + +
150A PHE* 4.7 8.5 - - + -
154A ILE* 4.7 0.4 - - + -
175A SER* 1.3 77.6 - - - +
177A ALA* 1.3 62.2 + - - +
178A LEU* 3.8 16.0 + - + -
198A LEU* 3.6 26.2 - - + +
200A PHE 3.8 4.0 + - - -
201A ILE* 3.8 4.9 - - - +
202A SER* 3.1 23.4 + - - +
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Residues in contact with ALA 177 (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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27A TYR* 3.7 21.5 - - + +
136A ASP* 3.9 3.2 + - - +
137A LEU 2.9 14.7 + - - +
138A ALA* 4.7 3.9 - - + -
139A TRP 5.1 1.9 + - - +
140A LEU* 4.2 14.4 - - + +
176A ALA* 1.3 71.3 - - - +
178A LEU* 1.3 65.5 + - - +
189A TYR* 4.5 1.2 + - - -
202A SER* 3.3 12.1 - - - +
204A MET* 3.8 21.1 - - + -
3F NAG 4.0 13.2 - - + +
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Residues in contact with LEU 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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141A TYR* 5.2 0.4 - - - -
150A PHE* 4.3 15.5 - - + -
176A ALA* 4.3 10.1 - - + +
177A ALA* 1.3 81.0 - - - +
179A SER* 1.3 61.8 + - - +
189A TYR* 3.3 35.7 - - + +
191A ILE* 3.8 28.5 - - + -
194A ILE* 4.1 7.0 - - + -
198A LEU* 5.4 0.2 - - + -
201A ILE* 3.5 36.8 - - + -
202A SER 2.7 13.3 + - - +
203A ILE* 3.8 1.2 - - - -
204A MET* 2.9 34.8 + - - +
244A MET* 4.0 13.2 - - + -
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Residues in contact with SER 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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141A TYR* 3.4 32.4 + - - -
178A LEU* 1.3 75.6 - - - +
180A ALA* 1.3 61.4 + - - +
181A GLY* 3.0 13.6 + - - -
184A THR* 3.5 29.1 + - - +
185A ILE* 3.3 20.1 - - - +
189A TYR* 3.0 14.5 + - - -
203A ILE* 4.1 1.4 - - - +
204A MET* 4.8 0.2 - - - -
244A MET* 3.5 8.1 - - - +
1F NAG 4.5 5.5 + - - -
2F NAG 4.7 5.2 - - - -
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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