Contacts of the helix formed by residues 173 - 186 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B GLY 3.3 5.3 + - - -
172B ARG* 1.3 77.9 - - - +
174B GLU* 1.3 66.9 + - - -
175B LYS 3.5 2.2 - - - -
176B LEU 3.5 2.3 + - - -
177B ASP* 2.9 27.9 + - - +
201B TRP* 5.6 1.7 - - - +
209B MSE 5.4 0.2 - - - -
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B GLY* 1.3 71.4 - - - +
175B LYS* 1.3 65.9 + - - +
177B ASP* 3.6 0.5 - - - +
178B LEU* 2.9 45.0 + - + +
209B MSE 3.6 22.0 - - - -
212B LYS* 2.7 40.1 + - - +
2200B GOL 2.6 38.5 + - - +
190C ASP* 5.2 7.6 - - - +
192C ARG* 5.7 1.0 - - - +
217C ASP* 4.8 0.5 - - - +
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B GLY 3.5 0.6 - - - -
174B GLU* 1.3 79.7 - - - +
176B LEU* 1.3 58.2 + - - +
178B LEU* 3.4 5.9 + - - +
179B GLU* 2.8 64.9 + - + +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLU 4.6 13.2 - - - +
147B THR* 5.2 1.1 - - - -
148B ALA* 4.9 7.9 - - + +
172B ARG* 3.9 42.6 - - + +
173B GLY 3.5 1.6 + - - -
174B GLU 3.4 0.4 - - - -
175B LYS* 1.3 76.7 - - - +
177B ASP* 1.3 66.1 + - - +
179B GLU* 3.7 17.9 - - + +
180B ILE* 2.9 49.9 + - + +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.4 19.1 - - + +
171B GLY* 2.7 30.0 + - - -
172B ARG* 2.8 25.6 + - - +
173B GLY 2.9 23.3 + - - +
174B GLU 3.6 2.9 - - - +
176B LEU* 1.3 75.1 - - - +
178B LEU* 1.3 63.5 + - - +
180B ILE* 3.2 6.4 - - - +
181B THR* 2.9 31.0 + - - -
201B TRP* 3.7 12.8 + - - -
209B MSE 3.7 16.1 - - + +
213B LEU* 4.7 2.2 - - + -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLU* 2.9 44.2 + - + +
175B LYS* 3.8 5.6 - - - +
177B ASP* 1.3 75.9 - - - +
179B GLU* 1.3 63.1 + - + +
181B THR* 4.0 2.7 - - - -
182B ALA* 3.0 26.9 + - - +
209B MSE 4.3 4.3 - - + -
212B LYS* 3.8 33.9 - - + +
213B LEU* 3.7 24.2 - - + -
216B TYR* 3.9 16.9 + - + +
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ALA* 4.4 11.8 - - + +
175B LYS* 2.8 62.1 + - + +
176B LEU* 3.6 21.7 - - + +
178B LEU* 1.3 79.1 - - + +
180B ILE* 1.3 58.3 + - - +
182B ALA* 3.4 4.9 + - - +
183B ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLU 5.6 0.2 - - - +
147B THR 4.3 0.9 - - - -
148B ALA* 3.8 16.6 - - - +
151B LEU* 3.6 26.7 - - + -
168B LEU* 4.2 11.4 - - + -
169B LYS 3.7 11.7 - - - +
170B VAL* 4.5 1.8 - - + -
172B ARG* 3.5 36.8 - - - +
176B LEU* 2.9 44.1 + - + +
177B ASP* 3.2 14.4 - - - +
179B GLU* 1.3 70.3 - - - +
181B THR* 1.3 65.1 + - - +
183B ALA* 3.3 7.9 + - - +
184B VAL* 2.9 34.7 + - - +
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 3.7 17.2 - - - +
170B VAL* 3.9 8.8 - - - +
177B ASP 2.9 22.4 + - - -
178B LEU 4.0 2.7 - - - -
180B ILE* 1.3 76.1 - - - +
182B ALA* 1.3 58.1 + - - +
184B VAL* 3.4 1.2 + - - +
185B ARG* 2.9 29.0 + - - +
193B LEU* 4.2 8.4 - - + +
195B LEU* 4.1 3.5 - - + +
213B LEU* 3.7 17.6 - - + +
216B TYR* 3.6 33.0 - - + -
218B ILE* 4.1 15.7 - - + -
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LEU 3.0 19.7 + - - +
179B GLU* 3.7 4.7 - - - +
181B THR* 1.3 76.8 - - - +
183B ALA* 1.3 64.1 + - - +
185B ARG* 3.4 1.7 + - - +
186B GLY* 3.0 21.1 + - - -
216B TYR* 3.4 32.5 - - + +
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ALA* 3.9 29.2 - - + +
151B LEU* 5.8 0.2 - - + -
152B ALA* 4.1 10.0 - - + +
179B GLU 3.0 16.2 + - - +
180B ILE* 3.4 8.7 - - - +
181B THR 3.2 0.2 - - - -
182B ALA* 1.3 78.9 - - - +
184B VAL* 1.3 62.7 + - - +
186B GLY* 3.4 5.4 + - - -
187B GLU* 3.4 21.3 + - - +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.9 26.5 - - + -
151B LEU* 4.1 28.5 - - + +
152B ALA* 4.9 0.7 - - - +
155B ALA* 4.0 14.6 - - + -
166B PHE* 5.0 0.4 - - + -
168B LEU* 3.9 17.5 - - + -
180B ILE 2.9 21.6 + - - +
181B THR 3.9 2.9 - - - +
183B ALA* 1.3 73.0 - - - +
185B ARG* 1.3 67.8 + - - +
187B GLU* 2.9 13.6 + - - +
188B ILE* 3.3 21.3 + - + +
193B LEU* 4.0 20.6 - - + -
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Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B THR 2.9 18.8 + - - +
182B ALA* 3.8 6.1 - - - +
184B VAL* 1.3 77.6 - - - +
186B GLY* 1.3 62.4 + - - +
187B GLU 3.1 1.6 + - - -
188B ILE* 3.4 28.2 + - - +
189B GLY* 2.8 37.8 + - - +
190B ASP* 3.4 8.7 + - - +
191B ALA 2.7 29.7 + - - -
192B ARG* 4.8 0.4 - - - +
193B LEU* 3.6 17.1 - - + +
216B TYR* 3.1 32.4 + - + +
217B ASP* 2.9 39.6 + - - +
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ALA 3.0 16.9 + - - -
183B ALA 3.4 2.7 + - - -
184B VAL 3.1 0.8 - - - -
185B ARG* 1.3 77.7 - - - +
187B GLU* 1.3 68.0 + - - +
189B GLY 4.8 2.0 + - - -
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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