Contacts of the strand formed by residues 166 - 172 (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 THR 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A GLU 3.6 0.3 - - - +
162A VAL* 3.4 9.0 - - - +
163A ASN* 3.2 36.4 + - - -
164A GLY* 5.3 0.2 - - - -
165A GLY* 1.4 79.6 + - - +
167A LEU* 1.3 71.9 + - - +
168A ARG* 4.2 8.1 - - + +
181A SER* 4.0 20.2 - - - +
182A LEU 3.3 17.4 + - - +
183A ASP* 4.5 8.8 - - - +
184A ALA 4.3 1.1 - - - +
186A ILE* 4.4 0.7 - - - -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 4.0 22.9 - - + -
130A ILE* 3.7 20.9 - - + -
135A LEU* 4.3 15.0 - - + -
138A LEU* 3.6 28.4 - - + +
160A LEU* 4.6 13.2 - - + -
161A GLU 3.4 22.2 - - - +
162A VAL* 4.0 18.6 - - + -
165A GLY 4.0 0.8 + - - -
166A THR* 1.3 73.4 - - - +
168A ARG* 1.3 63.2 - - - +
181A SER* 3.5 0.9 - - - -
182A LEU* 2.9 33.6 + - + +
184A ALA* 4.1 8.3 - - + +
186A ILE* 3.9 9.9 - - + -
219A LEU* 6.0 1.3 - - + -
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Residues in contact with ARG 168 (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* 4.8 3.8 - - - -
159A LEU* 3.6 0.7 - - - +
160A LEU* 3.4 5.5 - - - +
161A GLU* 2.8 55.0 + - + +
163A ASN* 5.8 2.3 - - + +
166A THR* 4.9 7.9 - - + +
167A LEU* 1.3 75.1 - - - +
169A SER* 1.3 69.9 + - - +
170A VAL* 3.8 8.7 - - + -
179A MET* 3.4 22.9 - - + +
180A CYS 3.2 13.0 - - - +
181A SER* 2.8 26.1 + - - +
245A TYR* 2.8 41.3 + - - -
246A GLU* 3.6 22.0 + - - -
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Residues in contact with SER 169 (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* 2.8 36.8 + - - +
142A THR* 3.4 14.8 - - - +
158A MET* 3.9 14.4 - - - -
159A LEU 3.2 5.6 - - - -
160A LEU* 3.9 9.4 - - - -
168A ARG* 1.3 71.6 - - - +
170A VAL* 1.3 67.2 + - - +
179A MET* 3.1 5.8 - - - +
180A CYS* 2.8 33.7 + - - +
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Residues in contact with VAL 170 (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* 5.1 0.4 - - - -
158A MET* 3.7 3.6 - - - +
159A LEU* 2.8 45.1 + - + +
168A ARG* 3.8 24.0 - - + -
169A SER* 1.3 80.5 - - - +
171A ALA* 1.3 65.7 + - - +
177A LEU* 3.8 26.5 - - + -
178A ALA 3.4 10.5 - - - +
179A MET* 4.0 6.3 - - + -
242A PHE* 3.6 27.8 - - + -
245A TYR* 3.9 22.2 - - + -
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Residues in contact with ALA 171 (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* 3.4 30.7 - - - +
145A ALA* 3.4 3.4 - - - +
146A MET* 3.6 29.2 - - + +
157A GLY 4.5 3.6 - - - +
158A MET* 4.6 3.4 - - + -
170A VAL* 1.3 76.2 - - - +
172A THR* 1.3 60.3 + - - +
177A LEU* 3.3 4.5 - - - +
178A ALA 2.9 34.4 + - - +
242A PHE* 4.3 2.9 - - - -
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Residues in contact with THR 172 (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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145A ALA 3.1 10.2 + - - -
146A MET* 4.4 0.4 - - - +
147A ALA 3.5 10.7 + - - -
155A LEU* 3.5 36.6 - - + +
157A GLY 5.2 0.6 + - - -
171A ALA* 1.3 76.2 - - - +
173A ASP* 1.3 57.5 + - - +
174A GLY* 3.2 13.6 + - - +
176A ARG 2.7 21.8 + - - -
177A LEU* 3.9 18.9 - - + +
242A PHE* 3.9 21.0 - - + -
243A PRO* 4.6 7.4 - - + -
245A TYR* 6.0 0.4 - - + -
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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