Contacts of the strand formed by residues 174 - 180 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H ALA* 3.8 12.8 - - + -
43H LYS 3.7 28.5 - - - +
44H ILE* 3.5 7.2 - - + -
45H SER* 2.7 32.2 + - - -
46H LYS 2.9 17.8 + - - +
48H ALA* 4.0 10.7 - - + +
49H PRO* 5.3 3.4 - - + -
151H TYR* 5.5 0.7 - - + -
166H PHE* 3.8 21.8 - - + -
167H ILE 3.5 17.3 - - - +
168H ILE* 4.0 10.5 - - + +
172H GLY 3.8 2.2 + - - -
173H ILE* 1.3 71.5 - - - +
175H ARG* 1.3 60.8 + - - +
176H GLN 3.7 14.6 - - - +
177H ILE* 3.7 27.6 - - + -
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Residues in contact with ARG 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ASP* 3.0 59.0 + - - +
183B PRO* 3.8 14.6 - - - +
44H ILE* 4.1 4.5 - - - -
73H TYR* 3.5 13.1 + - + +
167H ILE* 2.8 15.9 + - + +
169H ASP* 3.1 36.9 + - + +
173H ILE* 3.4 20.9 - - - +
174H LEU* 1.3 78.4 - - - +
176H GLN* 1.3 60.6 + - + +
198H PHE* 3.3 44.1 - - + -
201H THR* 4.8 0.8 + - - -
202H ASP* 3.0 27.3 + - - -
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Residues in contact with GLN 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B THR* 3.6 11.1 - - - +
179B LEU 3.3 7.2 + - - +
180B ASN* 3.1 28.6 + - - +
44H ILE* 4.2 1.9 - - - +
165H LEU* 4.2 3.5 - - - +
166H PHE* 3.5 5.5 - - - -
167H ILE* 3.0 52.2 + - + +
174H LEU* 3.7 3.4 - - - +
175H ARG* 1.3 81.5 - - - +
177H ILE* 1.3 83.5 + - - +
178H THR* 2.7 30.4 + - - -
194H LEU* 3.8 22.0 - - + +
198H PHE* 3.9 13.5 - - + -
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Residues in contact with ILE 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ILE 3.9 0.5 - - - +
178B THR* 3.7 1.6 - - - -
179B LEU* 2.9 59.5 + - + -
42H ALA* 4.1 14.1 - - + +
43H LYS* 5.2 0.2 - - - -
44H ILE* 3.9 15.5 - - + +
165H LEU 3.5 2.9 - - - -
166H PHE* 3.8 19.1 - - + -
174H LEU* 3.7 28.9 - - + -
176H GLN* 1.3 82.8 + - - +
178H THR* 1.3 63.6 + - - +
179H LEU* 3.8 33.4 - - + -
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Residues in contact with THR 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B GLN* 3.6 18.4 - - - +
177B ILE 3.6 2.7 - - - -
178B THR* 4.7 4.7 - - + +
190B GLU* 6.2 0.4 - - - +
194B LEU* 6.0 1.8 - - + -
163H ARG 3.4 2.3 - - - +
164H GLY* 3.3 1.9 - - - -
165H LEU* 2.7 53.7 + - + +
176H GLN* 2.7 31.9 + - - -
177H ILE* 1.3 72.7 - - - +
179H LEU* 1.3 62.7 + - - +
180H ASN* 3.8 8.5 - - - +
186H ARG* 4.6 13.5 - - + -
194H LEU* 4.8 4.3 - - - +
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Residues in contact with LEU 179 (chain H).
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* 3.3 17.4 - - + +
176B GLN* 3.2 6.1 + - - -
177B ILE* 2.8 64.6 + - + +
179B LEU* 5.9 0.9 - - + -
38H HIS* 6.0 5.8 - - + +
151H TYR 5.7 0.2 - - - +
152H GLY 5.3 7.4 - - - +
153H VAL* 3.9 17.7 - - + -
162H LEU* 4.1 12.1 - - + -
163H ARG 3.5 2.0 - - - -
164H GLY* 3.6 22.7 - - - -
166H PHE* 4.3 3.1 - - + -
177H ILE* 3.8 24.5 - - + -
178H THR* 1.3 75.3 - - - +
180H ASN* 1.3 63.4 + - - +
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Residues in contact with ASN 180 (chain H).
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* 4.3 4.0 - - - -
175B ARG 4.1 2.7 - - - -
176B GLN* 3.0 29.8 + - + +
194B LEU* 3.7 16.6 - - - +
198B PHE* 4.8 2.0 - - + -
162H LEU* 3.7 5.0 - - - +
163H ARG* 2.9 36.4 + - + -
178H THR* 3.8 8.7 - - - +
179H LEU* 1.3 73.9 - - - +
181H ASP* 1.3 65.0 + - - +
184H VAL* 3.0 30.6 + - - +
185H GLY 3.4 19.2 + - - -
186H ARG* 3.8 13.1 - - - +
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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