Contacts of the helix formed by residues 160 - 168 (chain A) in PDB entry 2E7G
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 ALA 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU 3.2 1.1 + - - -
157A GLN* 3.0 16.2 + - - +
159A SER* 1.3 75.8 - - - +
161A ALA* 1.3 70.1 + - - +
162A HIS 3.2 1.3 - - - -
163A MET* 2.8 9.3 + - - +
164A ARG* 2.8 23.8 + - - +
179A ILE* 4.5 21.5 - - + +
181A PHE* 3.8 25.8 - - + -
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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
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157A GLN 4.3 2.0 + - - -
158A ARG 4.4 6.7 + - - +
160A ALA* 1.3 79.3 - - - +
162A HIS* 1.3 64.7 + - - +
164A ARG* 3.1 38.2 + - - +
165A HIS* 3.3 6.2 + - - +
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Residues in contact with HIS 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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113A VAL* 3.4 32.5 - - + +
158A ARG 5.0 2.8 + - - +
159A SER* 4.6 9.2 - - - +
160A ALA 3.2 1.0 - - - +
161A ALA* 1.3 77.7 - - - +
163A MET* 1.3 64.2 + - - +
165A HIS* 3.1 16.8 + + + +
166A LEU* 3.0 33.7 + - + +
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Residues in contact with MET 163 (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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104A LEU* 4.4 20.6 - - + -
107A LEU* 3.8 25.7 - - + +
108A LEU* 3.6 19.3 - - + -
113A VAL* 5.7 3.8 - - + -
114A SER* 5.2 6.5 - - - -
117A LEU* 3.4 31.2 - - + -
156A LEU* 3.8 16.8 - - + -
159A SER* 3.1 28.0 + - - +
160A ALA* 2.8 16.8 + - - +
162A HIS* 1.3 75.0 - - + +
164A ARG* 1.3 61.8 + - - +
166A LEU* 3.1 11.5 + - + +
167A LEU* 3.1 27.9 + - - +
179A ILE* 5.5 1.6 - - + -
181A PHE* 4.4 7.6 - - + -
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Residues in contact with ARG 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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160A ALA 2.8 12.6 + - - +
161A ALA* 3.1 31.0 + - - +
163A MET* 1.3 73.4 - - - +
165A HIS* 1.3 66.5 + - - +
167A LEU* 3.3 9.5 + - - +
168A MET* 3.1 42.5 + - + +
176A VAL* 4.0 26.0 + - + +
177A PRO 3.9 17.0 - - - +
178A PRO* 4.2 14.1 - - - -
179A ILE* 4.5 17.6 - - + +
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Residues in contact with HIS 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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161A ALA 3.3 6.1 + - - +
162A HIS* 3.1 19.3 + + + +
164A ARG* 1.3 81.1 + - - +
166A LEU* 1.3 70.4 + - + +
168A MET* 3.0 43.9 + - + +
169A SER* 3.6 3.6 + - - -
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Residues in contact with LEU 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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107A LEU* 3.6 33.7 - - + -
113A VAL* 3.3 36.6 - - + -
162A HIS* 3.0 29.3 + - + +
163A MET* 3.1 11.2 + - + +
165A HIS* 1.3 80.7 - - + +
167A LEU* 1.3 62.7 + - - +
169A SER* 3.5 17.4 - - - -
170A GLN* 5.8 0.3 - - - +
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Residues in contact with LEU 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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100A LEU* 3.6 31.0 - - + -
103A ALA* 3.4 33.9 - - + +
104A LEU* 4.1 21.3 - - + -
107A LEU* 3.4 26.5 - - + -
163A MET 3.1 12.7 + - - +
164A ARG* 3.6 7.2 - - - +
166A LEU* 1.3 75.0 - - - +
168A MET* 1.3 66.5 + - - +
169A SER 3.0 2.0 - - - -
170A GLN* 2.9 31.6 + - - +
173A LEU* 5.5 4.5 - - + +
176A VAL* 5.2 8.3 - - + -
179A ILE* 4.4 6.3 - - + -
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Residues in contact with MET 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 ARG* 3.1 39.6 + - - +
165A HIS* 3.0 41.2 + - + +
167A LEU* 1.3 75.8 - - - +
169A SER* 1.3 64.0 + - - +
170A GLN 2.8 11.8 + - - +
171A GLN* 3.8 2.8 + - - +
176A VAL* 4.8 29.1 - - + +
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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