Contacts of the helix formed by residues 166 - 173 (chain A) in PDB entry 2W3C
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 MET 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A SER 3.6 0.2 + - - -
165A PRO* 1.3 79.4 - - + +
167A GLY* 1.3 62.9 + - - +
168A VAL 3.5 1.8 - - - -
169A SER* 4.0 21.1 - - - -
170A ARG* 3.1 39.9 + - + +
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Residues in contact with GLY 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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128A LEU* 4.5 4.3 - - - +
161A ILE* 3.9 17.5 - - - -
164A SER* 3.1 16.4 + - - -
165A PRO 3.0 5.1 - - - -
166A MET* 1.3 78.5 - - - +
168A VAL* 1.3 61.4 + - - +
170A ARG* 3.8 17.9 + - - +
171A LEU* 3.3 25.6 + - - +
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Residues in contact with VAL 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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161A ILE* 4.1 16.1 + - + -
162A LEU* 4.8 8.3 - - - -
167A GLY* 1.3 72.7 - - - +
169A SER* 1.3 64.1 + - - +
170A ARG 3.2 0.4 - - - -
171A LEU* 3.2 8.9 + - - +
172A MET* 3.1 25.6 + - + +
193A LEU* 4.2 11.2 - - + -
200A ILE* 4.1 23.1 - - + -
203A ILE* 4.0 33.7 - - + -
204A VAL* 3.8 29.8 - - + +
207A GLU* 5.4 0.2 - - + -
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Residues in contact with SER 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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166A MET* 3.7 28.0 + - - -
167A GLY 3.5 0.2 - - - -
168A VAL* 1.3 76.2 - - - +
170A ARG* 1.3 64.1 + - - +
172A MET* 3.1 18.7 - - - +
173A ASP* 3.3 12.4 + - - +
203A ILE* 5.3 3.1 - - - +
207A GLU* 3.3 37.3 + - - +
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Residues in contact with ARG 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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125A THR* 5.0 3.2 + - - +
128A LEU* 3.6 25.8 - - + +
129A SER* 3.9 18.4 - - - +
131A LEU 5.8 0.2 - - - +
132A GLU* 2.8 51.5 + - + +
164A SER* 3.4 24.0 + - - -
165A PRO 3.7 13.0 + - - -
166A MET* 3.1 28.0 + - + +
167A GLY* 3.8 6.7 + - - +
169A SER* 1.3 82.7 - - - +
171A LEU* 1.3 62.8 + - + +
173A ASP* 3.1 31.8 + - - +
174A LEU* 4.1 5.2 + - - +
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Residues in contact with LEU 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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128A LEU* 3.9 14.6 - - + -
131A LEU* 4.0 16.4 - - + -
146A LEU* 3.8 24.2 - - + -
161A ILE* 3.8 21.1 - - + -
167A GLY 3.3 17.2 + - - +
168A VAL 3.2 7.3 + - - +
170A ARG* 1.3 80.5 - - + +
172A MET* 1.3 60.8 + - - +
174A LEU* 3.1 32.0 + - + +
175A LEU 4.4 0.7 + - - -
189A LEU* 4.1 14.1 - - + -
190A LEU* 4.3 19.5 - - + +
193A LEU* 3.8 28.5 - - + -
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Residues in contact with MET 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 VAL* 3.1 22.1 + - + +
169A SER* 3.1 13.2 - - - +
170A ARG 3.1 0.4 - - - -
171A LEU* 1.3 72.2 - - - +
173A ASP* 1.3 57.2 + - - +
174A LEU 2.9 10.5 + - - -
175A LEU* 3.0 26.5 + - + +
190A LEU* 3.9 24.7 - - + -
204A VAL* 3.8 30.5 - - - +
207A GLU* 3.3 43.5 - - + +
209A ALA* 3.8 17.5 - - + -
212A ARG* 3.1 28.7 + - - +
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Residues in contact with ASP 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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134A PHE* 6.5 0.4 - - + -
139A ARG* 4.6 13.5 + - - +
169A SER 3.7 8.4 - - - +
170A ARG* 3.1 26.3 + - - +
172A MET* 1.3 76.3 - - - +
174A LEU* 1.3 57.6 + - + +
175A LEU 3.2 0.2 - - - -
176A ALA* 3.1 29.5 + - + +
177A ASP* 3.5 4.3 + - - -
212A ARG* 4.3 3.4 + - - +
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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