Contacts of the helix formed by residues 187 - 198 (chain A) in PDB entry 2EX4
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A MET* 4.5 0.4 - - - -
171A ALA* 3.4 20.6 - - - +
172A GLN 4.0 3.4 - - - +
173A GLU* 3.7 9.0 - - - +
174A GLY* 2.8 38.9 + - - +
186A ARG* 1.3 76.7 - - - +
188A LEU* 1.3 64.0 + - - +
189A ASP* 3.0 16.1 + - - +
190A VAL* 2.8 30.3 + - - +
191A VAL* 3.0 20.8 + - - +
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Residues in contact with LEU 188 (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 MET* 3.6 23.3 - - + +
171A ALA 4.4 2.6 + - - +
187A ASP* 1.3 73.1 - - - +
189A ASP* 1.3 60.8 + - - +
191A VAL* 3.8 1.2 - - - +
192A ARG* 2.9 61.4 + - - +
219A TYR* 3.4 60.6 - - + +
221A PHE* 3.9 15.0 - - + -
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Residues in contact with ASP 189 (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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187A ASP* 3.0 12.6 + - - +
188A LEU* 1.3 81.2 - - - +
190A VAL* 1.3 58.2 + - + +
192A ARG* 3.8 15.5 + - - +
193A ARG* 2.9 32.4 + - - +
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Residues in contact with VAL 190 (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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0A GLY* 4.1 13.0 - - - +
144A ASP* 5.0 1.6 - - - +
174A GLY* 4.3 6.3 - - - +
175A VAL* 4.1 17.9 - - + -
186A ARG* 3.8 28.7 - - + +
187A ASP* 2.8 32.4 + - - +
189A ASP* 1.3 76.5 - - + +
191A VAL* 1.3 62.9 + - - +
193A ARG* 3.2 30.8 + - - +
194A ILE* 3.0 30.3 + - + +
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Residues in contact with VAL 191 (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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139A ILE* 4.4 18.4 - - + -
147A LEU* 6.0 2.5 - - + -
166A ILE* 5.2 4.0 - - + -
170A MET* 3.7 22.7 - - + -
186A ARG* 3.8 24.0 - - + +
187A ASP 3.0 15.7 + - - +
188A LEU 3.9 3.8 - - - +
190A VAL* 1.3 76.2 - - - +
192A ARG* 1.3 63.1 + - - +
194A ILE* 3.1 9.7 + - + +
195A ILE* 3.0 41.4 + - + +
221A PHE* 4.1 21.1 - - + -
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Residues in contact with ARG 192 (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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188A LEU* 2.9 54.6 + - - +
189A ASP* 3.8 15.0 + - - +
191A VAL* 1.3 72.3 - - - +
193A ARG* 1.3 57.6 + - - +
195A ILE* 3.5 9.7 + - + +
196A CYS* 2.9 30.2 + - - +
202A LEU* 4.7 13.1 - - + +
205A GLU* 2.9 44.6 + - - +
219A TYR* 5.2 0.2 - - - -
221A PHE* 4.4 11.0 - - + -
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Residues in contact with ARG 193 (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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0A GLY 3.6 19.6 + - - -
1A SER* 5.3 2.8 - - - -
144A ASP* 4.9 6.7 + - - -
189A ASP* 2.9 20.7 + - - +
190A VAL* 3.6 37.9 + - - +
191A VAL 3.2 0.2 - - - -
192A ARG* 1.3 75.0 - - - +
194A ILE* 1.3 66.5 + - - +
196A CYS* 3.7 5.1 - - + +
197A SER* 2.8 43.1 + - - +
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Residues in contact with ILE 194 (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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144A ASP* 3.5 37.7 - - + +
147A LEU* 3.9 30.1 - - + -
148A ALA* 4.1 22.8 - - + +
151A LEU* 4.7 4.3 - - + -
186A ARG* 3.5 23.1 - - - +
190A VAL* 3.0 18.4 + - + +
191A VAL* 3.1 8.0 + - + +
193A ARG* 1.3 83.9 - - - +
195A ILE* 1.3 63.9 + - + +
197A SER* 3.2 7.4 + - - -
198A ALA* 3.0 22.2 + - - +
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Residues in contact with ILE 195 (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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151A LEU* 4.5 7.6 - - + -
166A ILE* 4.3 12.1 - - + -
191A VAL* 3.0 38.4 + - + +
192A ARG* 3.7 8.7 - - + +
194A ILE* 1.3 76.6 - - + +
196A CYS* 1.3 64.2 + - - +
198A ALA* 3.1 16.0 + - - +
200A LEU* 3.4 33.4 + - + +
202A LEU* 5.1 8.5 - - + -
221A PHE* 4.2 20.4 - - + -
223A LEU* 3.6 44.9 - - + -
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Residues in contact with CYS 196 (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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192A ARG 2.9 19.0 + - - +
193A ARG* 3.7 7.0 - - + +
195A ILE* 1.3 76.1 - - - +
197A SER* 1.3 58.9 + - - +
199A GLY* 2.9 23.2 + - - -
200A LEU 4.4 8.1 - - - -
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Residues in contact with SER 197 (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 ALA* 5.5 5.8 - - - +
152A ARG* 2.8 27.0 + - - -
193A ARG* 2.8 27.5 + - - +
194A ILE* 3.8 6.1 - - - -
196A CYS* 1.3 77.1 - - - +
198A ALA* 1.3 50.2 + - - +
199A GLY 3.2 0.7 - - - -
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Residues in contact with ALA 198 (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 ALA* 3.9 26.2 - - - +
151A LEU* 4.1 16.8 - - + -
152A ARG* 3.3 33.9 + - + +
155A LYS* 4.9 4.3 - - - +
194A ILE 3.0 12.2 + - - +
195A ILE* 3.1 12.1 + - - +
197A SER* 1.3 76.2 - - - +
199A GLY* 1.3 61.4 + - - +
200A LEU* 3.3 10.9 + - + +
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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