Contacts of the strand formed by residues 173 - 179 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C LYS* 6.4 2.0 - - - -
53C HIS* 4.6 8.5 - - + +
91C LYS* 4.4 26.9 - - + +
93C LEU* 4.2 28.0 - - + -
133C ASP* 3.1 20.2 + - + +
135C LEU 2.8 25.8 + - - -
161C PHE* 3.1 8.7 - - - -
170C LYS* 6.5 1.1 - - - -
171C GLN 4.8 4.7 - - - +
172C LEU* 1.3 71.9 - - - +
174C LEU* 1.3 60.7 + - - +
199C ASP* 3.2 33.9 - - + +
200C PHE* 5.8 4.7 - - + -
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 3.5 44.0 - - + +
137C LEU* 4.4 6.7 - - + -
154C ILE* 3.8 32.1 - - + +
157C MET* 3.7 25.6 - - + -
158C LYS* 4.0 16.6 - - + +
161C PHE* 4.3 8.7 - - + -
172C LEU 5.0 0.2 - - - +
173C LEU* 1.3 76.5 - - - +
175C SER* 1.3 65.0 + - - +
197C HIS 4.7 5.8 - - - +
198C LEU* 3.3 10.4 - - + +
199C ASP* 2.9 36.3 + - - +
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Residues in contact with SER 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ILE* 4.1 0.9 - - - +
93C LEU* 3.5 12.3 - - - +
135C LEU 3.1 5.9 + - - -
136C ASP* 2.8 21.5 + - - -
137C LEU* 2.9 21.8 + - - +
174C LEU* 1.3 80.5 - - - +
176C ALA* 1.3 64.1 + - - +
198C LEU* 4.4 1.7 - - - +
200C PHE* 3.0 55.3 - - - +
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Residues in contact with ALA 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ASP* 3.9 5.2 - - - -
137C LEU* 3.7 17.9 - - + +
150C PHE* 4.8 0.7 - - + -
154C ILE* 4.7 4.9 - - + -
175C SER* 1.3 78.3 - - - +
177C ALA* 1.3 60.5 + - - +
178C LEU* 3.7 18.4 + - + +
198C LEU* 3.5 28.5 - - + -
200C PHE 3.5 5.3 + - - -
201C ILE* 3.6 4.2 - - - -
202C SER* 3.0 25.8 + - - +
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Residues in contact with ALA 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR* 3.4 23.6 - - + +
136C ASP* 3.9 3.4 + - - +
137C LEU 3.2 17.4 + - - +
138C ALA* 4.6 6.7 - - + -
139C TRP 4.9 2.3 + - - +
140C LEU* 4.6 7.8 - - - +
176C ALA* 1.3 71.7 - - - +
178C LEU* 1.3 67.2 + - - +
189C TYR* 4.4 1.0 + - - -
202C SER* 3.4 9.6 - - - -
204C MET* 3.8 22.6 - - + +
3J NAG 4.3 12.3 - - + +
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LEU 5.0 0.2 - - - +
140C LEU* 5.7 0.2 - - - -
150C PHE* 3.9 13.9 - - + -
176C ALA* 3.8 23.8 - - + +
177C ALA* 1.3 91.6 - - - +
179C SER* 1.3 66.2 + - - +
189C TYR* 3.3 35.4 - - + +
191C ILE* 4.7 8.7 - - + -
194C ILE* 4.1 14.8 - - + -
198C LEU* 4.8 1.1 - - + -
201C ILE* 3.4 40.2 - - + -
202C SER 2.9 7.9 + - - +
203C ILE* 3.7 2.8 - - - -
204C MET* 2.9 33.5 + - - +
244C MET* 4.9 5.6 - - + -
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TYR* 3.6 25.9 + - - -
178C LEU* 1.3 74.7 - - - +
180C ALA* 1.3 57.0 + - - +
181C GLY* 3.0 17.5 + - - -
184C THR* 3.4 38.7 + - - -
185C ILE* 3.3 19.8 - - - +
189C TYR* 2.9 12.9 + - - -
203C ILE* 4.2 1.3 - - - +
204C MET* 4.6 4.5 - - - -
244C MET* 4.1 6.9 - - - +
1J NAG 3.7 7.4 + - - -
2J NAG 4.8 0.6 + - - -
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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