Contacts of the strand formed by residues 177 - 183 (chain A) in PDB entry 3T2D
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 LYS 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL 3.8 0.2 - - - +
171A LEU* 3.7 3.0 - - - +
172A ASP* 2.8 34.1 + - + +
175A GLU* 2.7 44.2 + - + +
176A HIS* 1.3 80.0 - - - +
178A VAL* 1.3 63.8 + - - +
179A TYR* 3.8 29.7 + - + +
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Residues in contact with VAL 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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169A GLU* 3.7 29.6 - - + -
170A VAL 3.3 6.1 - - - +
171A LEU* 3.9 12.6 - - + -
176A HIS 5.6 0.7 - - - +
177A LYS* 1.3 78.2 - - - +
179A TYR* 1.3 76.6 + - - +
180A LEU* 5.0 6.3 - - + -
203A ARG* 3.5 23.6 - - - +
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Residues in contact with TYR 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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168A PHE 3.4 2.4 - - - +
169A GLU* 3.5 2.8 - - - -
170A VAL* 2.8 41.5 + - + +
172A ASP* 4.1 5.6 + - + -
175A GLU* 5.2 0.7 + - - -
177A LYS* 3.8 42.8 + - + +
178A VAL* 1.3 78.5 - - - +
180A LEU* 1.3 63.1 + - - +
181A LEU* 3.6 20.2 - - + -
193A LEU* 4.2 18.6 - - + -
200A TYR* 4.0 28.9 + + - -
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Residues in contact with LEU 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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167A ILE* 4.1 20.0 - - + -
168A PHE 3.4 2.7 - - - +
169A GLU* 3.9 35.4 - - + +
178A VAL* 5.0 5.2 - - + -
179A TYR* 1.3 73.5 - - - +
181A LEU* 1.3 64.0 + - - +
182A LYS* 4.5 7.0 + - + +
186A ASP* 4.5 3.1 - - - +
206A PHE* 5.6 4.0 - - + -
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Residues in contact with LEU 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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166A PHE 3.9 0.3 - - - +
167A ILE* 3.5 2.9 - - - +
168A PHE* 2.8 40.8 + - + +
170A VAL* 4.0 20.4 - - + -
179A TYR* 3.6 28.7 - - + -
180A LEU* 1.3 76.6 - - - +
182A LYS* 1.3 63.9 + - - +
186A ASP* 3.6 15.3 - - + +
189A SER* 4.0 15.9 - - - +
190A LEU* 3.7 44.2 - - + +
193A LEU* 4.1 13.5 - - + -
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Residues in contact with LYS 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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166A PHE 3.4 4.7 - - - +
167A ILE* 4.3 20.4 - - + -
180A LEU* 4.8 6.7 - - + +
181A LEU* 1.3 78.0 - - - +
183A THR* 1.3 60.8 + - - +
185A GLU* 3.5 20.1 + - - +
186A ASP* 2.8 47.7 + - - +
208A ARG* 3.7 29.8 - - - +
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Residues in contact with THR 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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147A PHE 4.1 2.4 + - - -
148A ALA* 3.8 21.2 - - + +
165A GLY* 3.4 3.7 - - - -
166A PHE* 3.0 28.7 + - - +
168A PHE* 3.4 32.2 - - + -
182A LYS* 1.3 77.2 - - - +
184A PRO* 1.3 66.9 - - - +
185A GLU 3.6 0.9 - - - -
186A ASP 4.7 0.2 - - - -
187A ALA* 4.1 19.5 - - + +
190A LEU* 3.7 18.6 - - + -
208A ARG* 3.0 13.3 + - - -
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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