Contacts of the helix formed by residues 145 - 151 (chain F) 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 HIS 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C LEU 3.2 16.9 + - - -
144C THR* 4.6 1.5 + - - -
145C HIS* 3.1 34.1 + + - -
113F VAL* 3.5 28.1 + - + +
142F ASP* 3.0 21.9 + - - -
143F LEU 3.4 9.2 + - - -
144F THR* 1.3 78.3 + - - +
146F GLN* 1.3 63.8 + - - +
148F SER* 3.4 2.2 + - - -
149F LYS* 2.9 45.4 + - - +
154F TYR* 3.2 39.7 + + + -
159F GLY 3.9 6.5 + - - -
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Residues in contact with GLN 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LYS* 5.8 1.8 - - - +
142F ASP* 3.3 2.2 + - - +
144F THR* 3.1 20.3 + - - +
145F HIS* 1.3 78.1 - - - +
147F ILE* 1.3 68.7 + - + +
149F LYS* 3.8 6.6 - - - +
150F ASP* 3.0 47.2 + - - +
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Residues in contact with ILE 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F TYR 6.1 0.2 - - - -
51F TRP* 3.8 31.4 - - + -
52F GLU 3.8 22.9 - - - +
53F GLY* 5.1 0.2 - - - -
76F PHE* 4.0 10.5 - - + -
78F PHE* 3.9 20.6 - - + -
111F CYS* 4.6 1.6 - - - -
140F LEU* 4.1 19.5 - - + -
141F SER 4.5 7.6 - - - +
142F ASP* 3.0 23.6 + - + +
146F GLN* 1.3 82.0 - - + +
148F SER* 1.3 64.0 + - - +
150F ASP* 3.1 8.3 + - - +
151F TYR* 3.0 33.9 + - + -
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Residues in contact with SER 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F PHE* 3.7 17.0 - - - -
113F VAL* 4.0 5.0 + - - +
142F ASP* 2.6 27.5 + - - +
145F HIS* 3.8 4.5 - - - -
147F ILE* 1.3 76.5 - - - +
149F LYS* 1.3 57.1 + - - +
151F TYR 3.3 1.0 + - - -
152F GLY 3.0 8.0 + - - -
153F VAL* 3.0 28.5 + - - +
154F TYR* 3.9 17.3 - - - -
161F THR* 3.1 34.0 - - - +
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Residues in contact with LYS 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LYS* 5.4 8.1 - - - +
39F LEU 4.6 1.7 - - - +
40F SER* 4.1 8.5 - - - -
144F THR 4.8 3.6 + - - -
145F HIS* 2.9 35.5 + - + +
146F GLN* 3.8 5.6 - - - +
148F SER* 1.3 74.8 - - - +
150F ASP* 1.3 67.9 + - - +
152F GLY* 3.0 14.5 + - - +
154F TYR* 3.7 39.7 - - + -
156F GLU* 3.7 16.6 + - - +
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Residues in contact with ASP 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LYS* 2.8 67.3 + - + +
42F ALA 3.4 6.4 + - - -
49F PRO* 3.8 12.0 - - + +
50F TYR 4.3 12.5 - - - +
146F GLN* 3.0 41.4 + - - +
147F ILE* 3.1 8.7 + - - +
149F LYS* 1.3 78.4 - - - +
151F TYR* 1.3 66.3 + - + +
152F GLY 3.3 0.4 - - - -
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Residues in contact with TYR 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F SER* 3.7 7.6 + - - -
42F ALA* 4.1 7.4 - - + +
48F ALA* 3.6 15.5 - - + +
49F PRO* 2.8 48.6 + - + -
50F TYR 5.0 0.2 - - - -
51F TRP* 3.4 24.8 + + + -
66F LEU* 4.0 0.3 - - - +
76F PHE* 3.7 17.5 - + - -
78F PHE* 3.6 28.9 - + + -
147F ILE* 3.0 20.7 + - + +
148F SER 4.0 2.5 - - - +
150F ASP* 1.3 81.4 - - + +
152F GLY* 1.3 63.2 + - - +
153F VAL* 3.3 2.0 + - + +
166F PHE* 3.3 57.5 - + + -
168F ILE* 4.0 7.3 - - + +
174F LEU* 5.4 1.3 - - + -
179F LEU* 5.5 0.2 - - - +
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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