Contacts of the helix formed by residues 173 - 186 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171F GLY 3.3 4.4 + - - -
172F ARG* 1.3 79.9 - - - +
174F GLU* 1.3 60.0 + - - -
175F LYS 3.4 2.5 - - - -
176F LEU 3.5 1.6 + - - -
177F ASP* 2.8 34.2 + - - +
201F TRP* 5.6 1.7 - - - +
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Residues in contact with GLU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASP* 5.5 3.1 - - - +
192A ARG* 5.9 0.9 - - - +
217A ASP* 4.7 0.7 - - - +
173F GLY* 1.3 70.2 - - - +
175F LYS* 1.3 65.2 + - - +
177F ASP* 3.8 0.2 - - - +
178F LEU* 3.0 40.4 + - + +
209F MSE 3.7 22.3 - - - -
212F LYS* 2.7 40.7 + - + +
2600F GOL 2.7 38.5 + - - +
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Residues in contact with LYS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F GLY 3.4 0.4 - - - -
174F GLU* 1.3 79.9 - - - +
176F LEU* 1.3 62.3 + - - +
178F LEU* 4.1 4.9 - - - +
179F GLU* 3.0 55.0 + - - +
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Residues in contact with LEU 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F GLU 4.5 15.7 - - - +
147F THR* 5.3 1.1 - - - -
148F ALA* 5.0 6.7 - - + +
172F ARG* 3.8 42.0 - - + +
173F GLY 3.5 2.0 + - - -
175F LYS* 1.3 77.3 - - - +
177F ASP* 1.3 60.6 + - - +
179F GLU* 3.2 16.4 + - + +
180F ILE* 2.8 54.5 + - + +
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Residues in contact with ASP 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F VAL* 3.4 19.5 - - + +
171F GLY* 2.7 29.8 + - - -
172F ARG* 2.8 25.7 + - - +
173F GLY 2.8 26.9 + - - +
176F LEU* 1.3 72.5 - - - +
178F LEU* 1.3 57.7 + - - +
180F ILE* 3.1 7.4 - - - +
181F THR* 2.8 35.1 + - - +
201F TRP* 3.6 13.0 + - - -
209F MSE 3.6 19.3 - - + +
213F LEU* 4.8 1.3 - - + -
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Residues in contact with LEU 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F GLU* 3.0 43.0 + - + +
175F LYS* 4.1 3.8 - - - +
177F ASP* 1.3 76.7 - - - +
179F GLU* 1.3 58.5 + - + +
181F THR* 3.9 3.0 - - - -
182F ALA* 3.0 31.4 + - - +
209F MSE 4.6 4.5 - - + -
212F LYS* 3.5 42.4 - - + +
213F LEU* 3.7 21.5 - - + -
215F LYS* 6.2 0.2 - - - -
216F TYR* 3.9 16.6 + - + +
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Residues in contact with GLU 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ALA* 4.0 10.5 - - + +
175F LYS* 3.0 54.3 + - + +
176F LEU* 3.2 21.1 + - + +
178F LEU* 1.3 80.2 - - + +
180F ILE* 1.3 57.9 + - - +
182F ALA* 3.8 4.9 - - - +
183F ALA* 3.1 27.5 + - - +
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Residues in contact with ILE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F GLU 5.5 0.2 - - - +
147F THR* 4.4 1.1 - - - -
148F ALA* 4.0 18.6 - - - +
151F LEU* 3.7 26.5 - - + -
168F LEU* 4.2 12.8 - - + -
169F LYS 3.6 23.8 - - - +
170F VAL* 4.4 2.2 - - + -
172F ARG* 3.6 23.6 - - - +
176F LEU* 2.8 38.4 + - + +
177F ASP* 3.1 20.2 - - - +
179F GLU* 1.3 74.6 - - - +
181F THR* 1.3 64.2 + - - +
183F ALA* 3.4 1.7 + - - +
184F VAL* 3.0 35.6 + - - +
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Residues in contact with THR 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F LEU* 3.8 16.3 - - - +
170F VAL* 4.0 8.0 - - - +
177F ASP 2.8 22.3 + - - -
178F LEU 4.0 2.2 - - - -
180F ILE* 1.3 77.8 - - - +
182F ALA* 1.3 62.7 + - - +
184F VAL* 4.0 0.9 - - - +
185F ARG* 3.0 23.7 + - - +
193F LEU* 4.0 16.1 - - + +
195F LEU* 4.2 4.3 - - + +
213F LEU* 3.5 21.6 - - + +
216F TYR* 3.6 31.4 - - + -
218F ILE* 4.0 6.5 - - + -
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Residues in contact with ALA 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F LEU 3.0 20.3 + - - +
179F GLU* 3.8 5.8 - - - +
181F THR* 1.3 78.5 - - - +
183F ALA* 1.3 61.2 + - - +
185F ARG* 3.7 2.4 - - - +
186F GLY* 3.0 20.3 + - - -
216F TYR* 3.6 31.4 - - + +
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Residues in contact with ALA 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ALA* 3.9 30.5 - - + +
152F ALA* 4.0 9.8 - - + +
179F GLU 3.1 18.2 + - - +
180F ILE 3.8 3.4 - - - +
181F THR 3.3 0.2 - - - -
182F ALA* 1.3 77.4 - - - +
184F VAL* 1.3 61.9 + - - +
186F GLY* 3.3 9.6 + - - -
187F GLU* 3.5 18.7 + - - +
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Residues in contact with VAL 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F LEU* 3.8 26.9 - - + -
151F LEU* 4.0 30.5 - - + +
152F ALA* 4.6 0.7 - - - +
155F ALA* 4.1 13.2 - - + -
166F PHE* 5.0 0.4 - - + -
168F LEU* 4.0 15.9 - - + -
180F ILE 3.0 22.1 + - - +
181F THR 4.0 2.5 - - - +
183F ALA* 1.3 73.4 - - + +
185F ARG* 1.3 68.3 + - - +
187F GLU* 3.0 12.5 + - - +
188F ILE* 3.4 20.5 + - + +
193F LEU* 4.0 21.1 - - + -
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Residues in contact with ARG 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F THR 3.0 19.2 + - - +
182F ALA 3.7 4.7 - - - +
184F VAL* 1.3 77.2 - - - +
186F GLY* 1.3 62.9 + - - +
187F GLU 3.2 1.2 + - - -
188F ILE* 3.4 30.2 + - - +
189F GLY* 2.8 38.5 + - - +
190F ASP* 3.7 3.9 - - - +
191F ALA 2.8 31.9 + - - +
192F ARG* 4.9 0.2 - - - +
193F LEU* 3.6 19.3 - - + +
216F TYR* 3.0 34.7 + - + +
217F ASP* 2.8 39.5 + - - +
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Residues in contact with GLY 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F ALA 3.0 15.4 + - - -
183F ALA* 3.3 5.4 + - - -
184F VAL 3.1 0.8 - - - -
185F ARG* 1.3 79.1 - - - +
187F GLU* 1.3 66.6 + - - +
188F ILE 3.6 0.2 - - - -
189F GLY 4.8 2.5 + - - -
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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