Contacts of the helix formed by residues 166 - 177 (chain A) in PDB entry 2ERR
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 SER 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A SER* 4.3 21.0 + - - -
142A LYS* 5.2 8.3 - - - -
165A ASN* 1.3 79.5 - - - +
167A ALA* 1.3 60.1 + - - +
168A ASP* 4.1 11.0 - - - -
169A ALA* 3.1 10.1 + - - +
170A ASP* 3.0 24.5 + - - +
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Residues in contact with ALA 167 (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 SER* 1.3 72.9 - - - +
168A ASP* 1.3 57.4 + - - +
170A ASP* 3.5 9.8 - - - +
171A ARG* 2.9 30.4 + - - +
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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
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140A PHE* 4.3 15.1 - - - +
142A LYS* 2.7 39.2 + - - +
166A SER* 3.3 5.5 - - - -
167A ALA* 1.3 76.6 - - - +
169A ALA* 1.3 56.8 + - - +
171A ARG* 2.7 45.5 + - - +
172A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 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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142A LYS* 4.5 13.2 - - + +
163A PHE* 3.3 44.2 - - + +
164A GLU* 4.0 7.6 - - + +
165A ASN 3.8 13.0 - - - +
166A SER* 3.1 13.2 + - - +
168A ASP* 1.3 75.9 + - - +
170A ASP* 1.3 58.3 + - - +
172A ALA* 3.5 1.4 + - - +
173A ARG* 2.9 29.3 + - - +
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Residues in contact with ASP 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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164A GLU* 5.5 1.4 - - - +
165A ASN 5.7 0.7 - - - +
166A SER 3.0 12.3 + - - +
167A ALA* 3.5 13.6 - - - +
169A ALA* 1.3 74.6 - - - +
171A ARG* 1.3 58.9 + - - +
173A ARG* 2.8 45.9 + - - +
174A GLU* 2.9 41.3 + - - +
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Residues in contact with ARG 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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140A PHE* 3.8 23.5 - - - -
167A ALA 2.9 20.9 + - - +
168A ASP* 2.7 32.6 + - - +
170A ASP* 1.3 72.2 + - - +
172A ALA* 1.3 58.1 + - - +
174A GLU* 3.3 9.1 + - - +
175A LYS* 2.9 32.4 + - - +
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Residues in contact with ALA 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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140A PHE* 3.3 42.2 - - + -
142A LYS* 6.4 0.2 - - + -
163A PHE* 3.8 17.7 - - + -
168A ASP* 2.9 22.7 + - - +
169A ALA* 3.6 5.4 - - - +
170A ASP 3.3 0.2 - - - -
171A ARG* 1.3 69.7 - - - +
173A ARG* 1.3 64.5 + - - +
175A LYS* 3.1 3.3 + - - +
176A LEU* 3.0 29.9 + - + +
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LEU* 4.2 10.1 - - + -
137A PHE* 5.3 2.2 - - - -
163A PHE* 4.8 1.8 - - - -
164A GLU* 2.8 33.4 + - + +
169A ALA 2.9 16.3 + - - +
170A ASP* 2.8 50.4 + - - +
172A ALA* 1.3 69.1 - - - +
174A GLU* 1.3 86.9 + - - +
176A LEU* 3.1 2.5 + - - -
177A HIS* 2.8 35.2 + - + +
188A VAL* 3.1 43.8 - - + +
190A ASN* 4.1 17.7 - - - +
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Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ASP* 2.9 36.4 + - - +
171A ARG* 3.5 11.2 - - - +
173A ARG* 1.3 94.4 + - - +
175A LYS* 1.3 58.3 + - - +
177A HIS* 3.7 22.4 - - - +
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A GLN* 5.3 4.5 - - - +
140A PHE* 3.6 29.2 - - + -
171A ARG* 2.9 18.8 + - - +
172A ALA 3.4 3.4 - - - +
174A GLU* 1.3 76.6 - - - +
176A LEU* 1.3 67.4 + - + +
177A HIS 3.5 2.4 + - - +
178A GLY 4.5 0.9 - - - -
179A THR* 3.2 22.3 + - - +
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Residues in contact with LEU 176 (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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136A MET* 4.2 12.6 - - + +
137A PHE* 3.5 52.9 - - + -
139A GLN* 3.6 28.9 - - - +
140A PHE* 4.3 8.5 - - + -
172A ALA 3.0 22.6 + - - +
173A ARG 4.2 1.3 - - - +
175A LYS* 1.3 80.6 - - + +
177A HIS* 1.3 58.5 + - - +
178A GLY 3.0 1.8 + - - -
179A THR* 3.0 41.1 + - + +
186A ILE* 3.4 15.7 - - + +
188A VAL* 4.2 13.9 - - + -
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Residues in contact with HIS 177 (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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173A ARG* 2.8 24.3 + - + +
174A GLU* 3.7 23.0 - - - +
175A LYS 3.4 2.0 - - - +
176A LEU* 1.3 71.2 - - - +
178A GLY* 1.3 57.6 + - - +
179A THR 3.7 0.2 - - - -
186A ILE 3.6 3.1 - - - -
187A GLU* 3.4 26.5 - - + +
188A VAL* 2.9 41.6 + - + +
189A ASN* 3.1 25.0 + - - -
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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