Contacts of the strand formed by residues 176 - 179 (chain A) in PDB entry 1HXD
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 ASP 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ARG* 2.8 21.5 + - - -
154A GLY* 5.8 0.7 - - - -
171A VAL* 3.8 1.2 - - - +
172A LYS* 3.0 53.3 + - + +
175A ASN* 1.3 96.1 - - - +
177A LEU* 1.3 69.0 + - - +
178A TYR* 3.7 20.4 + - + -
183A LYS* 3.3 29.6 + - + +
185A ALA 3.6 8.1 - - - +
186A GLY* 3.6 8.7 - - - -
187A ILE* 4.2 7.1 - - - +
313A GLU* 5.5 0.3 - - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLY* 3.9 28.3 - - - +
157A MET* 3.8 18.6 - - + -
158A ALA* 4.4 5.2 - - + -
161A LEU* 3.3 33.9 - - + -
169A VAL* 4.2 7.6 - - + -
170A ARG 3.3 11.7 - - - +
171A VAL* 4.0 8.3 - - + -
176A ASP* 1.3 76.8 - - - +
178A TYR* 1.3 67.2 + - - +
183A LYS* 3.5 1.2 - - - -
184A LEU* 2.7 33.0 + - + -
185A ALA* 3.0 37.6 + - + +
187A ILE* 5.0 4.7 - - + -
207A ILE* 5.4 0.9 - - + -
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Residues in contact with TYR 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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168A LYS 4.3 0.5 - - - +
169A VAL* 3.4 5.0 - - - +
170A ARG* 2.7 41.4 + - - +
172A LYS* 3.6 43.8 + - + +
176A ASP* 3.7 18.3 + - + -
177A LEU* 1.3 83.0 - - - +
179A LEU* 1.3 63.3 + - - +
181A ASP* 3.5 26.5 - - - -
182A ARG 3.3 13.9 - - - -
183A LYS* 3.6 27.8 - - + +
184A LEU* 4.3 2.2 - - - +
222A GLY 5.3 0.9 - - - -
270A ASN* 4.1 27.4 - - + +
271A PHE* 4.4 10.9 - + - -
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Residues in contact with LEU 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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166A ALA* 5.9 0.2 - - + -
168A LYS* 3.8 39.9 - - + +
169A VAL* 4.0 17.7 - - + +
178A TYR* 1.3 78.0 - - - +
180A GLN* 1.3 78.3 + - + +
181A ASP 2.8 3.6 - - - +
182A ARG* 2.6 28.6 + - - -
184A LEU* 4.4 19.5 - - + -
224A ILE* 3.2 22.3 - - + +
225A THR 5.0 0.9 - - - +
226A LEU* 4.8 6.3 - - + -
229A ALA* 3.8 25.4 - - + -
231A ILE* 4.5 13.9 - - + -
270A ASN* 5.9 0.2 - - - -
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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