Contacts of the strand formed by residues 176 - 183 (chain A) in PDB entry 4TR8
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 ARG 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.4 33.2 + - + -
145A ALA* 3.8 18.6 - - - +
146A MET 5.4 1.0 + - - -
172A THR* 2.7 28.1 + - - -
173A ASP* 2.8 33.0 + - - +
175A HIS* 1.3 77.9 - - - +
177A LEU* 1.3 59.3 + - - +
323A SER* 5.6 0.2 + - - -
324A TYR* 3.5 45.1 + - + +
327A ASP* 2.8 33.3 + - - +
361A VAL* 3.3 15.3 - - - +
362A VAL* 4.4 12.1 - - + -
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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
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144A PHE* 5.4 1.9 - - - -
145A ALA* 4.2 3.1 - - - -
170A VAL* 3.8 19.3 - - + -
171A ALA 3.3 11.0 - - - +
172A THR* 3.9 16.4 - - + +
176A ARG* 1.3 76.8 - - - +
178A ALA* 1.3 76.9 + - - +
179A MET* 4.1 12.6 - - + -
245A TYR* 3.8 21.8 - - + -
248A VAL* 4.6 15.5 - - + -
249A LEU* 4.0 22.9 - - + -
328A VAL* 5.7 1.0 - - - +
359A ALA 4.5 1.1 - - - +
360A TYR* 3.3 5.7 - - - +
361A VAL* 2.9 46.6 + - + +
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Residues in contact with ALA 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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142A THR* 3.7 32.1 - - - +
144A PHE* 3.9 4.3 - - + -
145A ALA* 3.8 7.8 - - + +
170A VAL* 3.4 4.2 - - - +
171A ALA 2.9 31.8 + - - +
177A LEU* 1.3 76.5 - - - +
179A MET* 1.3 60.2 + - - +
359A ALA 3.6 6.1 - - - -
360A TYR* 3.5 25.1 - - + -
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Residues in contact with MET 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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142A THR* 3.6 5.0 - - - +
168A ARG* 3.4 45.3 - - - +
169A SER 3.1 12.8 - - - +
170A VAL* 4.0 7.9 - - + -
177A LEU* 4.1 6.3 - - + -
178A ALA* 1.3 77.2 - - - +
180A CYS* 1.3 61.1 + - - +
181A SER* 4.4 4.5 - - - +
245A TYR* 4.2 8.7 - - + -
249A LEU* 3.7 38.1 - - + -
357A ASP 4.6 1.1 - - - +
358A SER* 3.4 4.3 - - - -
359A ALA* 2.9 56.1 + - + +
360A TYR* 4.7 1.7 - - - -
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Residues in contact with CYS 180 (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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137A ARG* 4.7 7.6 - - - -
138A LEU* 3.4 20.5 - - + +
141A ARG* 4.1 20.9 - - + -
142A THR* 3.7 8.3 - - + +
168A ARG* 3.2 3.5 - - - +
169A SER* 2.8 44.1 + - - +
179A MET* 1.3 75.9 - - - +
181A SER* 1.3 68.9 + - - +
182A LEU* 4.9 4.3 - - - -
357A ASP* 3.4 10.1 - - - -
358A SER* 3.5 20.4 - - - +
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Residues in contact with SER 181 (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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138A LEU* 4.2 0.2 - - - -
166A THR* 4.0 16.8 - - - -
167A LEU 3.5 4.5 - - - -
168A ARG* 2.8 35.7 + - - +
179A MET* 4.4 4.3 - - - +
180A CYS* 1.3 75.0 - - - +
182A LEU* 1.3 74.8 + - - +
357A ASP* 2.9 32.3 + - - +
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Residues in contact with LEU 182 (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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130A ILE* 5.7 2.2 - - + -
134A LYS* 3.4 49.1 - - + +
137A ARG* 4.6 14.8 - - + +
138A LEU* 3.8 19.1 - - + -
166A THR* 3.3 5.0 - - - +
167A LEU* 2.9 37.3 + - + +
180A CYS* 4.9 4.9 - - - -
181A SER* 1.3 82.6 - - - +
183A ASP* 1.3 63.7 + - - +
184A ALA* 3.0 6.3 + - + +
357A ASP* 5.0 11.7 - - + +
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Residues in contact with ASP 183 (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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165A GLY 5.7 0.7 - - - -
166A THR* 4.4 13.9 - - - +
182A LEU* 1.3 71.4 - - - +
184A ALA* 1.3 59.2 + - - +
185A GLN* 3.5 4.3 - - - +
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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