Contacts of the helix formed by residues 166 - 176 (chain A) in PDB entry 1G8I
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 LEU 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ARG* 4.5 23.6 - - + -
105A PHE* 3.4 52.9 - - + -
114A GLY 4.2 2.7 + - - +
165A THR* 1.3 72.6 - - - +
167A GLN* 1.3 58.6 + - - +
169A PHE* 3.3 3.2 + - + +
170A GLN* 2.9 62.5 + - + +
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Residues in contact with GLN 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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165A THR* 3.2 10.0 + - - +
166A LEU* 1.3 80.1 - - + +
168A GLU* 1.3 58.1 + - + +
170A GLN* 3.4 15.1 + - - +
171A GLU* 3.0 53.1 + - - +
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Residues in contact with GLU 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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156A MET* 3.4 23.5 - - - +
157A ASP* 3.9 1.3 - - - -
158A LYS* 3.0 30.8 + - + +
159A ASN* 3.1 13.7 + - - +
163A LYS 3.0 9.7 - - - +
164A LEU* 3.3 5.1 - - + -
165A THR* 3.1 35.2 + - - +
167A GLN* 1.3 76.5 - - + +
169A PHE* 1.3 57.8 + - - +
171A GLU* 4.8 4.3 - - - -
172A GLY* 2.8 28.6 + - - -
1599A CA 2.3 31.3 - - - -
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Residues in contact with PHE 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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101A LEU* 3.4 38.6 - - + -
104A ALA* 3.9 13.2 - - + -
105A PHE* 3.8 29.8 - + + -
108A TYR* 4.3 7.9 - + - -
116A ILE* 3.6 22.9 - - + -
121A MET* 4.8 1.3 - - + -
156A MET* 3.9 9.5 - - - +
164A LEU* 4.3 15.4 - - + +
165A THR 3.0 15.8 + - - +
166A LEU* 3.6 6.5 - - + +
167A GLN 3.3 0.2 - - - -
168A GLU* 1.3 77.9 - - - +
170A GLN* 1.3 58.3 + - - +
173A SER* 2.7 38.5 + - - -
951A 1PE 3.5 44.6 - - - -
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Residues in contact with GLN 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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98A ASP* 5.3 2.2 - - - +
101A LEU* 4.2 27.3 - - + +
102A ARG* 3.7 24.1 + - - +
166A LEU* 2.9 50.9 + - + +
167A GLN* 3.5 21.9 + - - +
169A PHE* 1.3 76.6 - - + +
171A GLU* 1.3 61.5 + - + +
173A SER* 3.4 2.1 + - - -
174A LYS* 3.0 40.9 + - - +
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Residues in contact with GLU 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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158A LYS* 5.8 5.5 + - - +
167A GLN* 3.0 38.4 + - + +
168A GLU* 4.2 3.9 - - - +
170A GLN* 1.3 77.0 - - + +
172A GLY* 1.3 65.4 + - - +
174A LYS* 3.4 8.5 + - + +
175A ALA* 3.1 24.8 + - - +
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Residues in contact with GLY 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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155A MET* 4.8 7.5 - - - +
156A MET* 3.5 31.4 - - - +
158A LYS* 6.5 0.4 - - - -
168A GLU 2.8 20.5 + - - -
171A GLU* 1.3 79.3 - - - +
173A SER* 1.3 62.0 + - - +
175A ALA* 3.5 13.5 + - - +
176A ASP* 3.6 10.9 + - - +
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Residues in contact with SER 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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101A LEU* 3.5 26.6 - - - +
156A MET* 3.7 9.0 - - - +
169A PHE* 2.7 24.1 + - - -
170A GLN 3.7 1.6 - - - -
172A GLY* 1.3 77.9 - - - +
174A LYS* 1.3 61.3 + - - +
176A ASP 3.2 20.1 + - - +
179A ILE* 3.6 20.4 - - - +
180A VAL* 3.7 3.8 - - - +
951A 1PE 3.3 24.1 - - - -
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Residues in contact with LYS 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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97A LEU* 4.3 20.7 - - + +
98A ASP* 2.7 34.1 + - - -
101A LEU* 4.1 19.1 - - + -
170A GLN* 3.0 27.4 + - + +
171A GLU* 3.4 7.8 + - + +
173A SER* 1.3 75.6 - - - +
175A ALA* 1.3 60.4 + - - +
176A ASP 3.3 0.4 - - - -
180A VAL* 3.4 20.2 - - + +
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Residues in contact with ALA 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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155A MET* 5.8 3.1 - - + +
171A GLU 3.1 16.5 + - - +
172A GLY* 3.7 9.0 - - - +
173A SER 3.2 0.6 - - - -
174A LYS* 1.3 77.1 - - - +
176A ASP* 1.3 57.7 + - - +
177A PRO* 3.4 3.8 - - - +
1596A NA 2.5 25.2 - - - -
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Residues in contact with ASP 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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148A ARG* 5.2 6.9 + - - -
152A ILE* 5.3 0.2 - - - +
155A MET* 3.3 31.2 - - + +
172A GLY 3.6 6.5 + - - +
173A SER 3.2 6.9 + - - +
174A LYS 4.6 0.2 - - - -
175A ALA* 1.3 78.8 - - - +
177A PRO* 1.3 70.1 - - - +
178A SER* 2.7 30.6 + - - -
179A ILE* 3.2 29.2 + - + +
180A VAL* 3.0 21.4 + - - +
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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