Contacts of the helix formed by residues 157 - 175 (chain A) in PDB entry 3TNF
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 ASN 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LYS* 6.1 0.8 - - - +
148A MET* 3.6 22.1 - - + +
149A GLU* 3.0 27.1 + - - +
150A THR* 3.7 4.3 - - + +
155A ASN 3.9 2.6 + - - -
156A ILE* 1.3 81.6 - - - +
158A VAL* 1.3 57.6 + - - +
159A GLU 3.7 0.2 - - - -
160A ASN* 3.3 29.4 + - - +
161A ALA* 2.9 29.1 + - - +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.9 21.5 - - + +
27A ARG* 4.1 7.6 - - + -
28A PHE* 3.8 32.3 - - + +
150A THR* 4.4 8.5 - - + -
151A SER 3.5 29.2 - - - +
152A ALA* 4.3 8.1 - - - -
155A ASN* 3.9 14.1 - - - +
156A ILE 3.2 4.4 - - - +
157A ASN* 1.3 74.6 - - - +
159A GLU* 1.3 68.4 + - + +
161A ALA* 3.4 3.8 + - - +
162A PHE* 3.3 32.0 + - + -
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.8 8.4 - - + -
48A ARG* 2.8 44.8 + - - +
155A ASN* 4.7 15.4 - - - +
158A VAL* 1.3 77.1 - - + +
160A ASN* 1.3 65.9 + - - +
162A PHE* 3.2 1.7 + - - -
163A PHE* 2.9 45.0 + - + -
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Residues in contact with ASN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 3.6 20.1 - - - +
157A ASN* 3.3 35.8 + - - +
159A GLU* 1.3 78.2 - - - +
161A ALA* 1.3 63.0 + - - +
163A PHE* 3.8 4.6 - - - +
164A THR* 2.8 34.9 + - - -
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.4 13.8 - - + +
117A MET* 3.1 15.7 - - - +
119A LEU* 3.5 34.5 - - + -
148A MET* 3.5 12.0 - - - -
150A THR* 4.5 1.1 - - + -
157A ASN 2.9 17.2 + - - +
158A VAL* 3.7 5.8 - - - +
159A GLU 3.4 0.4 - - - -
160A ASN* 1.3 76.9 - - - +
162A PHE* 1.3 58.9 + - + +
165A LEU 3.0 21.8 + - - -
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Residues in contact with PHE 162 (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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11A LEU* 3.6 31.1 - - + +
13A LEU* 4.0 23.3 - - + -
24A VAL* 3.9 25.8 - - + -
25A LEU* 5.1 1.8 - - - -
28A PHE* 3.6 56.3 - + + -
59A LEU* 4.7 4.9 - - + +
61A ILE* 4.0 21.1 - - + -
85A MET* 3.7 22.4 - - + -
119A LEU* 5.8 0.7 - - + -
158A VAL* 3.3 22.5 + - + +
159A GLU 3.2 2.6 + - - +
161A ALA* 1.3 78.4 - - + +
163A PHE* 1.3 60.0 + - - +
165A LEU* 3.3 1.6 + - - +
166A ALA* 2.9 31.4 + - - +
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Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 4.3 4.3 - + - -
48A ARG* 4.4 3.6 - - - -
50A ILE* 3.5 43.3 - - + -
51A GLU 4.2 13.7 - - - -
52A LEU* 3.9 19.0 - - + +
159A GLU* 2.9 54.5 + - + +
160A ASN* 3.8 4.3 - - - +
162A PHE* 1.3 76.1 - - - +
164A THR* 1.3 56.3 + - - +
166A ALA* 3.3 7.1 + - - +
167A ARG* 2.8 40.3 + - - +
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Residues in contact with THR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MET* 3.6 20.4 - - + -
146A LYS* 4.0 20.9 - - + +
148A MET* 4.2 7.5 - - + +
160A ASN* 2.8 34.3 + - - -
161A ALA* 4.3 0.7 - - - -
163A PHE* 1.3 74.9 - - - +
165A LEU* 1.3 64.2 + - - +
167A ARG* 3.1 8.8 + - + +
168A ASP* 2.9 41.9 + - - +
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Residues in contact with LEU 165 (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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11A LEU* 4.2 20.9 - - + -
83A GLY* 4.2 1.6 - - - -
84A ILE 4.2 14.8 - - - +
85A MET* 3.9 33.9 - - + +
115A GLU* 3.6 46.0 - - + +
116A LYS 4.3 2.2 - - - +
117A MET* 3.6 19.1 - - + +
161A ALA 3.0 18.8 + - - +
162A PHE 3.9 3.4 - - - +
163A PHE 3.3 0.2 - - - -
164A THR* 1.3 76.4 - - - +
166A ALA* 1.3 63.9 + - - +
168A ASP* 3.3 5.8 + - - +
169A ILE* 3.3 31.6 + - + +
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Residues in contact with ALA 166 (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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9A PHE* 3.7 14.3 - - + -
11A LEU* 5.7 1.7 - - + +
50A ILE* 3.9 23.8 - - + -
52A LEU* 3.9 7.9 - - + -
57A ILE* 5.0 0.9 - - + -
59A LEU* 4.4 16.6 - - + -
162A PHE 2.9 17.7 + - - +
163A PHE 3.5 4.3 - - - +
165A LEU* 1.3 73.3 - - - +
167A ARG* 1.3 66.5 + - - +
169A ILE* 2.9 7.5 + - - +
170A LYS* 2.9 23.7 + - - +
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.5 39.8 - - + +
53A ASP* 3.7 26.7 + - - +
163A PHE* 2.8 28.0 + - - +
164A THR* 3.1 14.4 - - + +
166A ALA* 1.3 72.8 - - - +
168A ASP* 1.3 57.5 + - - +
169A ILE 3.1 0.3 + - - -
170A LYS* 3.3 3.2 + - - +
171A ALA* 2.7 36.7 + - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 3.6 40.0 - - + +
117A MET* 5.0 1.4 - - - +
146A LYS* 3.0 40.1 - - - +
164A THR* 2.9 22.6 + - - +
165A LEU* 3.8 5.1 - - - +
166A ALA 3.2 0.4 - - - -
167A ARG* 1.3 80.5 - - - +
169A ILE* 1.3 59.0 + - - +
171A ALA* 3.7 8.8 - - - +
172A LYS* 3.5 17.8 + - - +
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Residues in contact with ILE 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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9A PHE* 3.6 34.8 - - + -
11A LEU* 4.0 18.8 - - + -
82A MET* 4.0 17.9 - - + +
83A GLY* 3.9 26.5 - - - +
115A GLU* 3.9 17.9 - - + +
165A LEU* 3.3 20.9 - - + +
166A ALA* 2.9 6.6 + - - +
168A ASP* 1.3 76.4 - - - +
170A LYS* 1.3 61.5 + - - +
171A ALA 3.1 0.7 - - - -
172A LYS* 3.3 4.6 + - - +
173A MET* 2.8 39.8 + - + +
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Residues in contact with LYS 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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7A TYR* 3.5 23.3 - - + -
9A PHE* 3.7 17.4 - - + -
52A LEU* 2.9 36.4 + - + -
53A ASP* 3.7 24.1 - - - +
55A LYS* 3.1 29.9 - - - +
57A ILE* 3.8 14.3 - - + +
166A ALA 2.9 15.9 + - - +
167A ARG* 3.7 6.5 - - - +
169A ILE* 1.3 72.7 - - - +
171A ALA* 1.3 61.5 + - - +
173A MET* 4.2 2.5 - - - -
174A ASP* 2.8 56.9 + - - +
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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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167A ARG 2.7 21.4 + - - +
168A ASP* 3.7 11.7 - - - +
170A LYS* 1.3 77.4 - - - +
172A LYS* 1.3 64.0 + - - +
173A MET 2.9 0.3 + - - -
174A ASP* 3.1 12.5 + - - +
175A LYS* 3.0 31.8 - - - +
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Residues in contact with LYS 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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113A ASP* 3.4 37.8 + - - +
114A VAL 5.2 1.0 + - - -
115A GLU* 3.0 29.6 + - - +
168A ASP 3.5 10.9 + - - +
169A ILE* 3.3 6.3 + - - +
171A ALA* 1.3 78.2 - - - +
173A MET* 1.3 59.5 + - + +
175A LYS* 3.7 25.9 + - + +
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Residues in contact with MET 173 (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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7A TYR* 3.7 41.7 - - + -
9A PHE* 3.6 20.6 - - + -
82A MET* 4.1 16.2 - - + -
169A ILE* 2.8 22.8 + - + +
170A LYS* 3.8 2.7 - - - +
172A LYS* 1.3 75.6 - - + +
174A ASP* 1.3 62.0 + - - +
175A LYS* 3.0 9.2 + - - +
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Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 2.8 32.8 + - - -
53A ASP* 4.6 3.6 - - - +
55A LYS* 5.0 0.2 + - - -
170A LYS* 2.8 48.7 + - - +
171A ALA* 3.5 7.3 + - - +
173A MET* 1.3 72.4 - - - +
175A LYS* 1.3 60.9 + - + +
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Residues in contact with LYS 175 (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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171A ALA* 3.0 36.5 - - - +
172A LYS* 3.7 20.4 - - + +
173A MET 3.0 4.9 - - - +
174A ASP* 1.3 84.1 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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