Contacts of the helix formed by residues 163 - 174 (chain A) in PDB entry 2DGS
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 ASP 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASN* 4.1 3.4 - - - +
161A PHE* 4.2 1.2 - - - +
162A GLU* 1.3 104.6 - - - +
164A GLU* 1.3 69.2 + - - +
165A GLN* 2.6 20.1 + - + +
166A SER* 2.8 26.4 + - - +
167A VAL 4.1 0.2 + - - -
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Residues in contact with GLU 164 (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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111A LYS* 4.5 26.8 - - + +
112A SER 4.6 11.2 - - - +
113A ASN* 3.6 29.1 - - - +
163A ASP* 1.3 68.8 - - - +
165A GLN* 1.3 70.8 + - - +
167A VAL* 2.9 33.7 + - + +
168A ASP* 4.2 10.7 + - - +
187A ARG* 5.2 5.0 - - - +
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Residues in contact with GLN 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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163A ASP* 2.6 19.7 + - + +
164A GLU* 1.3 79.1 + - - +
166A SER* 1.3 66.9 + - - +
168A ASP* 2.7 20.8 + - - +
169A GLN* 3.1 26.3 + - + +
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Residues in contact with SER 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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136A PHE* 4.1 18.8 + - - +
137A GLY* 3.9 13.3 - - - -
138A VAL 4.2 1.0 + - - -
161A PHE* 2.9 46.9 - - - +
163A ASP* 2.8 20.0 + - - +
165A GLN* 1.3 72.8 - - - +
167A VAL* 1.3 65.5 + - - +
169A GLN* 3.0 9.9 + - - +
170A ALA* 3.0 20.1 + - - +
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Residues in contact with VAL 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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112A SER 4.4 2.2 - - - +
113A ASN* 3.3 46.2 - - + +
114A LYS 3.9 5.6 - - - +
115A ILE* 3.4 27.6 - - + -
161A PHE* 4.4 2.6 - - + -
164A GLU* 2.9 26.8 + - - +
166A SER* 1.3 74.6 - - - +
168A ASP* 1.3 65.0 + - - +
170A ALA* 3.0 3.0 + - - +
171A VAL* 2.8 27.7 + - + +
187A ARG* 3.9 29.2 - - + -
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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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164A GLU* 3.5 12.6 + - - +
165A GLN* 2.7 16.3 + - - +
167A VAL* 1.3 75.6 - - - +
169A GLN* 1.3 73.3 + - - +
171A VAL* 3.0 10.1 + - - +
172A ASN* 2.9 34.7 + - - +
187A ARG* 6.2 0.7 - - - -
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Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.0 54.2 + - + +
165A GLN* 3.1 22.9 + - + +
166A SER* 3.0 14.6 + - - +
168A ASP* 1.3 86.3 - - - +
170A ALA* 1.3 64.6 + - - +
172A ASN* 3.7 6.1 + - - +
173A MET* 3.5 16.3 + - - +
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Residues in contact with ALA 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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115A ILE* 4.2 14.4 - - + -
133A PHE* 4.8 1.6 - - + -
136A PHE* 4.3 11.4 - - + -
161A PHE* 4.9 2.5 - - + -
166A SER 3.0 10.3 + - - +
167A VAL* 3.5 7.4 - - - +
169A GLN* 1.3 76.6 - - - +
171A VAL* 1.3 67.2 + - - +
173A MET* 3.0 6.9 + - - +
174A HIS* 2.9 18.4 + - - -
176A HIS* 3.8 21.9 + - + +
185A VAL* 3.7 21.7 - - + +
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Residues in contact with VAL 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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115A ILE* 5.1 0.4 - - + -
167A VAL* 2.8 29.3 + - + +
168A ASP* 3.4 11.4 - - - +
170A ALA* 1.3 71.9 - - - +
172A ASN* 1.3 69.0 + - - +
174A HIS* 2.7 22.7 + - - +
185A VAL* 4.0 10.8 - - + +
186A LYS* 3.8 10.1 - - + +
187A ARG* 3.3 48.2 - - + +
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Residues in contact with ASN 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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168A ASP* 2.9 28.4 + - - +
169A GLN* 3.8 6.7 - - - +
171A VAL* 1.3 76.8 - - - +
173A MET* 1.3 64.2 + - - +
174A HIS* 4.0 3.6 - - - +
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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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132A TYR* 5.3 5.8 - - - +
136A PHE* 4.9 12.1 - - + -
169A GLN 3.5 8.3 + - - +
170A ALA 3.0 10.2 + - - +
172A ASN* 1.3 79.8 + - - +
174A HIS* 1.3 67.8 + - - +
175A PHE* 2.8 46.9 + - + +
176A HIS* 3.9 14.6 - - + +
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Residues in contact with HIS 174 (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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170A ALA 2.9 6.2 + - - -
171A VAL 2.7 23.6 + - - +
172A ASN 4.0 3.6 - - - +
173A MET* 1.3 71.9 - - - +
175A PHE* 1.3 88.7 + + + +
184A GLU* 2.8 42.2 + - + +
185A VAL 3.1 27.6 - - - +
186A LYS* 3.6 24.1 + - + +
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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