Contacts of the helix formed by residues 163 - 173 (chain C) in PDB entry 2GRA
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 GLU 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C ALA* 4.7 1.8 - - - -
162C VAL* 1.3 77.4 - - - +
164C GLU* 1.3 57.5 + - - +
165C ASP* 2.8 31.4 - - - +
166C LEU* 2.9 31.8 + - + +
167C ILE* 3.5 3.3 + - - +
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Residues in contact with GLU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C THR* 3.0 15.8 - - - +
101C ILE* 2.7 52.6 + - + +
119C ARG* 3.1 49.1 + - - +
136C ALA* 4.0 9.4 - - + +
162C VAL 3.8 1.4 + - - -
163C GLU* 1.3 68.5 - - - +
165C ASP* 1.3 58.0 + - - +
166C LEU 3.0 6.4 + - - -
167C ILE* 3.5 20.6 + - + +
168C ASP* 3.3 14.2 - - - +
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Residues in contact with ASP 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLU* 2.8 37.4 - - - +
164C GLU* 1.3 74.5 - - - +
166C LEU* 1.3 79.0 + - + +
168C ASP* 3.9 12.8 + - - +
169C ALA* 4.9 1.0 + - - +
266C ARG* 4.6 12.5 + - - -
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C VAL* 4.0 29.2 - - + -
163C GLU* 3.3 10.5 - - + +
165C ASP* 1.3 101.0 + - - +
167C ILE* 1.3 55.9 + - - +
168C ASP 2.9 3.4 - - - -
169C ALA* 2.6 34.4 + - + +
170C VAL* 2.9 18.5 + - + +
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Residues in contact with ILE 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ALA* 6.0 1.1 - - - -
119C ARG* 3.6 43.5 - - + +
120C CYS* 4.6 6.3 - - - +
121C MET* 4.1 24.3 - - + +
134C VAL* 5.1 5.8 - - + +
135C TYR 4.8 1.3 - - - -
136C ALA* 3.8 24.9 - - + +
162C VAL* 4.6 10.1 - - + -
163C GLU 3.5 3.3 + - - +
164C GLU* 3.5 33.8 + - + +
166C LEU* 1.3 79.3 - - - +
168C ASP* 1.3 53.9 + - - +
170C VAL* 3.6 9.8 + - - +
171C THR* 2.6 35.4 + - - +
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Residues in contact with ASP 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ARG* 3.2 12.3 + - - -
164C GLU 3.3 18.4 - - - +
165C ASP* 3.9 10.8 - - - +
166C LEU 2.9 0.4 + - - -
167C ILE* 1.3 78.5 - - - +
169C ALA* 1.3 61.5 + - - +
171C THR* 3.4 16.3 - - - -
262C CYS* 3.4 19.6 - - - +
265C THR* 3.8 13.2 + - + +
266C ARG* 3.8 29.7 + - + +
269C GLN* 2.6 43.0 + - - +
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Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ASP 4.9 1.3 + - - +
166C LEU* 2.6 26.6 + - + +
168C ASP* 1.3 70.2 - - - +
170C VAL* 1.3 56.9 + - + +
171C THR 2.9 1.3 - - - -
172C GLY* 2.5 29.1 + - - -
173C LEU* 3.1 9.5 + - - +
258C VAL* 5.3 1.4 - - - +
262C CYS* 4.2 14.7 - - - +
266C ARG* 5.1 5.6 - - - +
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C MET* 4.4 15.9 - - + +
132C ALA 6.1 0.2 - - - +
134C VAL* 4.0 40.4 - - + -
162C VAL* 5.1 4.5 - - + -
166C LEU* 2.9 21.7 + - + +
167C ILE* 3.7 10.5 - - - +
169C ALA* 1.3 71.5 - - + +
171C THR* 1.3 65.3 + - - +
173C LEU* 2.9 21.1 + - + -
174C SER* 2.9 33.2 + - - +
175C GLY 3.0 3.3 + - - +
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Residues in contact with THR 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ALA* 4.5 10.9 - - + +
121C MET* 3.6 25.2 - - + +
167C ILE* 2.6 22.4 + - - +
168C ASP* 3.4 13.1 + - - -
169C ALA 2.7 3.6 + - - -
170C VAL* 1.3 76.0 - - - +
172C GLY* 1.3 56.8 + - - -
175C GLY* 2.7 14.1 - - - -
176C SER* 2.7 35.4 + - - +
261C SER* 3.7 5.5 + - - +
265C THR* 3.4 26.6 - - + +
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Residues in contact with GLY 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ASP 3.7 2.2 + - - -
169C ALA 2.5 16.1 + - - -
171C THR* 1.3 75.3 - - - +
173C LEU* 1.3 60.5 + - - +
176C SER* 4.0 0.2 - - - -
180C TYR* 2.7 24.3 + - - -
258C VAL* 3.0 19.5 - - - +
261C SER* 2.9 25.5 + - - -
262C CYS* 3.8 7.6 - - - +
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ALA 3.1 8.2 + - - +
170C VAL* 2.9 13.6 + - + +
172C GLY* 1.3 78.0 - - - +
174C SER* 1.3 60.1 + - - +
175C GLY 3.1 0.4 + - - -
177C GLY* 2.7 35.9 + - - -
180C TYR* 4.1 0.9 - - - -
258C VAL* 3.6 25.9 - - + +
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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