Contacts of the strand formed by residues 180 - 184 (chain C) in PDB entry 2HU4
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 ALA 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C PHE* 4.7 3.8 - - + -
134C LEU* 3.9 10.7 - - + +
158C LEU* 3.6 37.2 - - + -
177C ALA* 4.5 0.2 - - + -
179C SER* 1.3 76.4 + - - +
181C SER* 1.3 62.0 + - - +
192C ILE 3.0 15.3 - - - +
193C GLY* 4.4 1.3 - - - -
225C THR* 3.2 10.7 - - - +
227C GLU* 2.9 36.9 + - - -
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.9 7.4 - - - -
158C LEU* 4.3 4.5 - - - +
180C ALA* 1.3 77.4 - - - +
182C ALA* 1.3 74.0 + - - +
191C THR* 3.8 0.5 - - - -
192C ILE* 3.0 38.5 + - - +
225C THR* 4.1 13.2 - - - -
226C GLN* 3.4 22.1 + - - -
228C SER 3.3 19.6 + - - -
230C CYS* 3.7 11.2 - - - +
239C THR* 4.0 0.9 + - - -
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.9 18.6 - - + -
123C SER* 3.6 4.4 + - - -
132C PHE* 4.1 18.8 - - + -
158C LEU* 5.3 0.7 - - + -
181C SER* 1.3 83.2 + - - +
183C CYS* 1.3 61.8 + - - +
189C TRP* 4.8 0.7 - - + -
190C LEU* 3.2 15.7 - - - +
191C THR* 4.1 13.7 - - + -
228C SER 3.9 0.8 + - - -
229C GLU* 3.0 29.1 - - - +
230C CYS* 3.0 6.5 + - - -
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Residues in contact with CYS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C SER* 3.7 11.4 - - - +
182C ALA* 1.3 72.6 - - - +
184C HIS* 1.3 59.2 + - - +
185C ASP 4.2 0.5 + - - -
189C TRP* 3.5 7.5 - - - -
190C LEU* 2.9 34.8 + - - +
229C GLU* 5.4 0.7 - - - +
230C CYS* 2.0 62.1 - - - +
232C CYS* 3.3 29.3 - - - +
237C CYS* 3.8 10.3 - - - -
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Residues in contact with HIS 184 (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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85C LEU* 3.3 19.6 - - + +
124C CYS 3.8 5.7 + - - +
125C SER* 3.4 34.8 - - - -
126C HIS* 3.6 13.9 + + - -
183C CYS* 1.3 75.2 - - - +
185C ASP* 1.3 59.1 + - - +
186C GLY* 3.0 46.3 - - - -
187C THR 3.5 12.0 + - - -
188C SER* 3.7 18.7 - - - -
189C TRP* 3.4 45.1 + + + -
232C CYS* 3.7 8.4 - - - +
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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