Contacts of the strand formed by residues 176 - 180 (chain A) in PDB entry 1P3W
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 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 4.5 3.6 - - + -
90A TYR* 4.1 32.8 - - + +
93A LYS* 5.1 6.7 - - - +
146A ILE 3.1 19.9 + - - +
147A LEU* 3.3 19.4 - - + +
148A VAL* 3.0 25.5 + - - +
174A GLY 5.5 2.0 - - - +
175A ILE* 1.3 74.4 - - - +
177A TYR* 1.3 62.3 + - - +
198A ASP* 3.4 13.5 - - + +
199A LEU* 3.7 23.3 - - + -
224A VAL* 3.9 29.2 - - + -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 3.4 17.5 - - + -
150A ILE* 3.0 27.6 + - + -
163A ILE* 3.4 28.4 - - - +
166A ILE* 3.6 33.9 - - + +
167A GLY* 3.5 20.6 - - - -
170A CYS* 3.8 18.8 - - + -
176A ILE* 1.3 76.0 - - - +
178A HIS* 1.3 78.6 + - - +
179A VAL* 3.4 20.9 - - + +
196A LYS 4.0 5.4 - - - +
197A VAL* 3.7 17.0 - - + +
198A ASP* 2.8 36.7 + - - +
199A LEU 3.1 8.6 + - - +
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP* 3.4 27.4 - - - -
82A ALA* 3.5 26.6 - - + +
83A ILE* 4.1 7.9 - - + +
107A VAL* 4.5 3.6 - - + -
147A LEU* 4.2 12.1 - - + -
148A VAL 2.8 15.1 + - - +
149A SER* 2.8 29.0 + - - +
150A ILE 3.1 24.9 + - - -
176A ILE 4.1 0.6 + - - -
177A TYR* 1.3 77.6 - - - +
179A VAL* 1.3 80.5 + - - +
180A ASP* 4.0 4.0 - - + -
199A LEU* 3.3 27.4 - - + -
200A MET 4.1 0.9 - - - -
201A SER* 2.8 22.0 + - - -
216A LEU* 4.6 0.2 - - + -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE 3.7 4.5 - - - +
152A HIS* 3.6 33.0 - - + +
163A ILE* 4.2 7.0 - - + -
177A TYR* 3.4 40.4 - - + +
178A HIS* 1.3 78.2 + - - +
180A ASP* 1.3 66.4 + - - +
181A ALA 3.3 1.1 + - - +
197A VAL* 3.6 20.6 - - + -
199A LEU 2.8 9.5 + - - -
200A MET* 3.1 27.8 - - + +
201A SER 2.9 23.9 + - - -
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP* 2.9 29.6 - - - +
103A GLU* 4.4 7.4 - - - +
104A HIS* 4.0 7.3 - - - +
107A VAL* 4.3 2.6 - - + +
149A SER* 5.2 0.4 + - - -
150A ILE 4.6 0.4 - - - -
151A MET* 3.5 20.5 - - + +
152A HIS* 3.1 19.9 + - - +
153A VAL 4.5 3.8 + - - +
178A HIS* 4.0 7.7 + - + -
179A VAL* 1.3 71.5 - - - +
181A ALA* 1.3 57.5 + - - +
182A THR* 2.7 28.9 + - - -
183A GLN 5.1 0.2 + - - -
201A SER* 4.2 8.4 - - - -
764A PLP 2.8 32.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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