Contacts of the strand formed by residues 174 - 180 (chain B) in PDB entry 3TKR
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 LEU 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ALA* 3.9 13.0 - - + -
43B LYS 3.8 26.5 - - - +
44B ILE* 3.5 8.5 - - + +
45B SER* 2.8 31.2 + - - -
46B LYS 2.9 16.3 + - - +
48B ALA* 4.0 11.3 - - + +
49B PRO* 5.3 3.6 - - + -
151B TYR* 5.5 1.1 - - + -
166B PHE* 3.7 21.8 - - + -
167B ILE 3.5 17.9 - - - +
168B ILE* 4.0 10.5 - - + +
172B GLY 3.8 2.4 + - - -
173B ILE* 1.3 71.5 - - - +
175B ARG* 1.3 59.1 + - - +
176B GLN 3.6 16.2 - - - +
177B ILE* 3.8 26.0 - - + -
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 4.2 4.7 - - - -
73B TYR* 3.4 16.4 + - + +
167B ILE* 2.8 15.1 + - + +
169B ASP* 3.2 37.7 + - + +
173B ILE* 3.4 21.7 - - - +
174B LEU* 1.3 77.5 - - - +
176B GLN* 1.3 60.4 + - + +
198B PHE* 3.2 45.8 - - + -
201B THR* 4.7 1.4 - - - +
202B ASP* 2.9 27.9 + - - -
181H ASP* 3.0 58.5 + - - -
183H PRO* 3.8 14.5 - - - +
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Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 4.1 2.1 - - - +
165B LEU* 4.2 4.7 - - - +
166B PHE* 3.4 5.2 - - - -
167B ILE* 3.0 46.6 + - + +
174B LEU* 3.6 3.4 - - - +
175B ARG* 1.3 82.4 - - - +
177B ILE* 1.3 82.8 + - - +
178B THR* 2.7 30.8 + - - -
194B LEU* 3.9 24.1 - - + +
198B PHE* 4.0 11.7 - - + -
178H THR* 3.6 11.7 - - - +
179H LEU 3.2 6.5 + - - +
180H ASN* 3.0 34.0 + - - +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 4.2 13.7 - - + +
44B ILE* 3.9 15.7 - - + +
165B LEU 3.5 2.9 - - - +
166B PHE* 3.7 26.0 - - + -
174B LEU* 3.8 22.0 - - + -
176B GLN* 1.3 81.9 + - - +
178B THR* 1.3 64.0 + - - +
179B LEU* 3.7 34.8 - - + -
38H HIS* 6.3 1.3 - - + -
177H ILE* 3.9 0.9 - - + +
178H THR* 3.6 1.4 - - - -
179H LEU* 2.8 61.6 + - + +
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Residues in contact with THR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ARG 3.4 2.3 - - - +
164B GLY* 3.3 2.3 - - - -
165B LEU* 2.7 52.3 + - - +
176B GLN* 2.7 31.6 + - - -
177B ILE* 1.3 70.6 - - - +
179B LEU* 1.3 61.1 + - - +
180B ASN* 3.8 9.0 - - - +
186B ARG* 4.7 13.2 - - + -
194B LEU* 4.8 4.2 - - - +
176H GLN* 3.6 18.8 - - - +
177H ILE 3.7 2.7 - - - -
178H THR* 4.7 5.1 - - + +
190H GLU* 6.2 0.2 - - - +
194H LEU* 6.0 2.0 - - + -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLY 5.3 7.6 - - - +
153B VAL* 3.9 18.2 - - + -
162B LEU* 4.1 10.3 - - + -
163B ARG 3.5 2.5 - - - -
164B GLY* 3.6 16.8 - - - -
166B PHE* 4.3 2.5 - - + -
177B ILE* 3.7 25.8 - - + -
178B THR* 1.3 80.4 - - - +
180B ASN* 1.3 63.5 + - - +
44H ILE* 3.3 19.2 - - + +
176H GLN* 3.3 5.4 + - - -
177H ILE* 2.9 65.8 + - + +
179H LEU* 5.9 1.1 - - + -
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LEU* 3.7 5.7 - - - +
163B ARG* 2.9 38.0 + - + -
178B THR* 3.8 7.5 - - - +
179B LEU* 1.3 74.2 - - - +
181B ASP* 1.3 66.1 + - - +
184B VAL* 3.0 29.6 + - - +
185B GLY 3.4 19.2 + - - -
186B ARG* 3.7 13.3 - - - +
44H ILE* 4.2 3.1 - - - -
175H ARG 4.2 2.5 - - - -
176H GLN* 3.1 31.1 + - - +
194H LEU* 3.7 17.1 - - - +
198H PHE* 4.9 2.5 - - + -
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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