Contacts of the helix formed by residues 173 - 188 (chain H) in PDB entry 2PGW
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 GLY 173 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171H GLY 3.2 6.3 + - - -
172H ARG* 1.3 78.1 - - - +
174H GLU* 1.3 66.1 + - - -
175H LYS 3.5 2.2 - - - -
176H LEU 4.3 1.6 - - - -
177H ASP* 3.0 27.9 + - - -
201H TRP* 5.7 1.1 - - - +
209H MSE 5.1 0.4 - - - -
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Residues in contact with GLU 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ASP 5.6 1.6 - - - +
192F ARG* 5.8 4.5 - - - +
173H GLY* 1.3 71.3 - - - +
175H LYS* 1.3 64.7 - - - +
177H ASP* 3.6 0.9 - - - +
178H LEU* 3.1 38.3 + - + +
208H ASN* 5.8 1.4 - - - +
209H MSE 3.6 29.5 - - - +
212H LYS* 2.9 41.2 + - + +
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Residues in contact with LYS 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H GLY 3.5 0.4 - - - -
174H GLU* 1.3 79.4 - - - +
176H LEU* 1.3 66.5 + - - +
178H LEU* 3.4 5.2 + - - +
179H GLU* 3.0 59.1 + - + +
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Residues in contact with LEU 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H GLU 4.5 15.3 - - - +
147H THR* 5.4 0.7 - - - -
148H ALA* 5.0 5.8 - - + +
172H ARG* 3.8 44.4 - - + +
173H GLY 3.7 1.6 + - - -
174H GLU 3.4 0.2 - - - -
175H LYS* 1.3 80.7 - - - +
177H ASP* 1.3 64.0 + - - +
179H GLU* 3.6 17.5 - - + +
180H ILE* 2.9 50.4 + - + +
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Residues in contact with ASP 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H VAL* 3.4 18.5 - - + +
171H GLY* 2.7 31.0 + - - -
172H ARG* 2.9 23.8 + - - +
173H GLY 3.0 24.8 + - - +
176H LEU* 1.3 78.3 - - - +
178H LEU* 1.3 58.6 + - - +
180H ILE* 3.2 5.8 - - - +
181H THR* 2.8 35.8 + - - -
201H TRP* 3.8 4.3 + - - -
209H MSE 3.6 27.2 - - + +
213H LEU* 4.8 1.8 - - + -
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Residues in contact with LEU 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H GLU* 3.1 40.3 + - + +
175H LYS* 3.9 4.9 - - - +
177H ASP* 1.3 76.2 - - - +
179H GLU* 1.3 57.9 + - + +
181H THR* 4.1 2.9 - - - -
182H ALA* 3.0 31.7 + - - +
209H MSE 4.5 4.5 - - + -
212H LYS* 3.6 37.0 - - + +
213H LEU* 3.6 26.0 - - + -
216H TYR* 3.9 15.6 + - + +
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Residues in contact with GLU 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H ALA* 4.2 9.9 - - + +
175H LYS* 3.0 50.3 + - + +
176H LEU* 3.2 24.5 + - + +
178H LEU* 1.3 79.0 - - + +
180H ILE* 1.3 58.1 + - - +
182H ALA* 3.4 5.1 + - - +
183H ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H GLU 5.2 1.1 - - - +
147H THR* 4.4 1.1 - - - -
148H ALA* 3.8 26.9 - - + +
151H LEU* 3.9 18.6 - - + -
168H LEU* 4.2 8.1 - - + -
169H LYS 3.7 11.4 - - - +
170H VAL* 4.4 3.1 - - + -
172H ARG* 3.4 38.8 - - - +
176H LEU* 2.9 43.4 + - + +
177H ASP* 3.2 14.8 - - - +
179H GLU* 1.3 72.4 - - - +
181H THR* 1.3 67.0 + - - +
183H ALA* 3.7 1.6 - - - +
184H VAL* 2.9 35.5 + - - +
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Residues in contact with THR 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H LEU* 3.8 11.1 - - - +
170H VAL* 3.8 16.8 - - - +
177H ASP 2.8 21.9 + - - -
178H LEU 4.1 2.5 - - - -
180H ILE* 1.3 76.9 - - - +
182H ALA* 1.3 63.4 + - - +
184H VAL* 3.9 1.2 - - - +
185H ARG* 3.0 24.1 + - - +
193H LEU* 4.2 7.7 - - + +
195H LEU* 4.2 4.1 - - + +
213H LEU* 3.7 20.3 - - + +
216H TYR* 3.7 32.5 - - + -
218H ILE* 4.1 14.1 - - + -
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Residues in contact with ALA 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178H LEU 3.0 19.9 + - - +
179H GLU* 3.7 5.8 - - - +
181H THR* 1.3 78.6 - - - +
183H ALA* 1.3 55.9 + - - +
185H ARG* 3.4 1.9 + - - +
186H GLY* 3.0 26.3 + - - -
216H TYR* 3.4 32.9 - - + +
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Residues in contact with ALA 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H ALA* 3.9 31.6 - - + +
152H ALA* 3.9 8.0 - - + +
179H GLU 2.9 17.9 + - - +
180H ILE 3.7 4.5 - - - +
182H ALA* 1.3 77.4 - - - +
184H VAL* 1.3 62.8 + - + +
186H GLY* 3.3 9.6 + - - -
187H GLU* 3.4 20.3 + - - +
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Residues in contact with VAL 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H LEU* 3.8 27.1 - - + -
151H LEU* 4.1 30.3 - - + +
152H ALA* 4.6 2.2 - - - +
155H ALA* 3.9 14.1 - - + -
166H PHE* 5.0 0.4 - - + -
168H LEU* 3.9 16.8 - - + -
180H ILE 2.9 20.7 + - - +
181H THR 3.9 3.1 - - - +
183H ALA* 1.3 73.0 - - - +
185H ARG* 1.3 68.0 + - - +
187H GLU* 2.9 12.3 + - - +
188H ILE* 3.3 21.1 + - + +
193H LEU* 3.9 20.4 - - + -
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Residues in contact with ARG 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H THR 3.0 18.3 + - - +
182H ALA 3.8 4.0 - - - +
184H VAL* 1.3 76.0 - - - +
186H GLY* 1.3 63.6 + - - +
187H GLU 3.1 1.2 + - - -
188H ILE* 3.3 28.5 + - - +
189H GLY* 2.8 32.4 + - - +
190H ASP* 3.4 8.2 - - - +
191H ALA 2.7 30.9 + - - +
192H ARG* 4.8 0.4 - - - +
193H LEU* 3.5 18.9 - - + +
216H TYR* 3.0 36.7 + - + +
217H ASP* 2.9 38.2 + - - +
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Residues in contact with GLY 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H ALA 3.0 14.8 + - - -
183H ALA* 3.3 5.1 + - - -
184H VAL 3.1 0.6 - - - -
185H ARG* 1.3 79.4 - - - +
187H GLU* 1.3 69.9 + - - +
188H ILE 3.6 0.2 - - - -
189H GLY* 4.9 1.8 + - - -
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Residues in contact with GLU 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H ALA* 3.4 36.2 - - + +
155H ALA* 4.4 2.2 - - + -
156H ALA* 4.1 23.1 - - - +
159H HIS* 4.0 13.5 + - - +
183H ALA 3.5 13.6 - - - +
184H VAL 2.9 8.3 + - - +
186H GLY* 1.3 86.5 - - - +
188H ILE* 1.3 63.5 + - - +
189H GLY 3.6 2.0 - - - -
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Residues in contact with ILE 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H ALA* 3.7 24.0 - - + +
159H HIS* 3.3 27.6 + - + -
166H PHE* 3.8 38.6 - - + -
184H VAL* 3.3 30.1 - - + +
185H ARG* 3.3 31.8 + - - +
187H GLU* 1.3 82.3 - - - +
189H GLY* 1.3 66.2 + - - +
190H ASP 3.1 0.2 + - - -
191H ALA 3.0 22.7 + - - +
193H LEU* 4.1 11.4 - - + -
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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