Contacts of the helix formed by residues 173 - 186 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLY 3.3 5.3 + - - -
172A ARG* 1.3 79.6 - - - +
174A GLU* 1.3 66.6 + - - -
175A LYS 3.4 2.4 + - - -
176A LEU 3.5 2.2 + - - -
177A ASP* 2.9 28.0 + - - -
201A TRP* 5.5 1.7 - - - +
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Residues in contact with GLU 174 (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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173A GLY* 1.3 70.5 - - - +
175A LYS* 1.3 65.7 + - - +
177A ASP* 3.3 0.9 + - - +
178A LEU* 3.1 40.0 + - + +
208A ASN* 5.8 1.7 - - - +
209A MSE 3.6 31.1 - - - +
212A LYS* 2.7 42.6 + - - +
190E ASP 5.5 2.4 - - - +
192E ARG* 6.0 2.3 - - - +
217E ASP* 5.0 0.2 - - - +
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Residues in contact with LYS 175 (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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173A GLY 3.4 0.6 - - - -
174A GLU* 1.3 82.3 - - - +
176A LEU* 1.3 62.8 + - - +
178A LEU* 4.0 5.2 - - - +
179A GLU* 2.9 60.8 + - + +
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Residues in contact with LEU 176 (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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146A GLU 4.6 14.4 - - - +
147A THR* 5.3 1.1 - - - -
148A ALA* 4.9 7.6 - - + +
172A ARG* 3.8 44.0 - - + +
173A GLY 3.5 1.8 + - - -
174A GLU 3.4 0.2 - - - -
175A LYS* 1.3 77.5 - - - +
177A ASP* 1.3 61.0 + - - +
179A GLU* 3.3 15.9 + - + +
180A ILE* 2.9 55.8 + - + +
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Residues in contact with ASP 177 (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 VAL* 3.4 16.3 - - + +
171A GLY* 2.8 32.1 + - - -
172A ARG* 2.8 25.4 + - - +
173A GLY 2.9 26.1 + - - +
174A GLU 3.7 3.1 - - - +
176A LEU* 1.3 76.3 - - - +
178A LEU* 1.3 59.0 + - - +
180A ILE* 3.2 7.4 - - - +
181A THR* 2.8 35.5 + - - -
201A TRP* 3.7 13.0 + - - -
209A MSE 3.8 15.3 - - + +
213A LEU* 4.7 2.7 - - + -
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Residues in contact with LEU 178 (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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174A GLU* 3.1 36.6 + - + +
175A LYS* 4.0 4.9 - - - +
177A ASP* 1.3 76.0 - - - +
179A GLU* 1.3 58.3 + - + +
181A THR* 3.8 3.8 - - - -
182A ALA* 2.8 33.7 + - - +
209A MSE 4.4 4.5 - - + -
212A LYS* 3.4 41.3 - - + +
213A LEU* 3.6 20.6 - - + -
216A TYR* 4.0 18.1 + - + +
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Residues in contact with GLU 179 (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* 4.3 11.1 - - + +
175A LYS* 2.9 55.5 + - + +
176A LEU* 3.7 19.2 - - + +
177A ASP 3.3 0.2 - - - -
178A LEU* 1.3 78.0 - - + +
180A ILE* 1.3 58.6 + - - +
182A ALA* 3.7 5.3 - - - +
183A ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 180 (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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147A THR* 4.4 0.9 - - - -
148A ALA* 3.9 15.5 - - + +
151A LEU* 3.7 25.6 - - + -
168A LEU* 4.2 8.5 - - + -
169A LYS 3.6 13.0 - - - +
170A VAL* 4.6 1.8 - - + -
172A ARG* 3.5 37.7 - - - +
176A LEU* 2.9 38.9 + - + +
177A ASP* 3.2 18.6 - - - +
179A GLU* 1.3 73.2 - - - +
181A THR* 1.3 66.1 + - - +
183A ALA* 3.4 7.3 - - - +
184A VAL* 2.9 33.6 + - - +
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Residues in contact with THR 181 (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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168A LEU* 3.7 17.5 - - - +
170A VAL* 4.0 8.8 - - - +
177A ASP 2.8 22.1 + - - -
178A LEU 3.8 3.1 - - - -
180A ILE* 1.3 73.3 - - - +
182A ALA* 1.3 67.1 + - - +
184A VAL* 3.3 1.6 + - - +
185A ARG* 2.9 23.4 + - - +
193A LEU* 4.1 15.6 - - + +
195A LEU* 4.2 2.7 - - + +
213A LEU* 3.7 17.3 - - + +
216A TYR* 3.5 34.3 - - + -
218A ILE* 4.1 8.3 - - + -
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Residues in contact with ALA 182 (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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178A LEU 2.8 19.5 + - - +
179A GLU* 3.7 6.1 - - - +
181A THR* 1.3 77.4 - - - +
183A ALA* 1.3 65.3 + - - +
185A ARG* 3.3 2.4 + - - +
186A GLY* 3.0 20.6 + - - -
216A TYR* 3.5 31.6 - - + +
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Residues in contact with ALA 183 (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* 3.7 30.7 - - + +
152A ALA* 4.0 10.9 - - + +
179A GLU 2.9 19.9 + - - +
180A ILE* 3.4 8.5 - - - +
182A ALA* 1.3 78.9 - - - +
184A VAL* 1.3 61.4 + - - +
186A GLY* 3.5 7.6 + - - -
187A GLU* 3.7 17.3 + - - +
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Residues in contact with VAL 184 (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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143A LEU* 3.9 17.9 - - + -
151A LEU* 4.1 23.3 - - + +
152A ALA* 4.8 0.9 - - - +
155A ALA* 3.8 19.1 - - + -
166A PHE* 4.9 1.1 - - + -
168A LEU* 3.9 26.9 - - + -
180A ILE 2.9 22.0 + - - +
181A THR 3.9 2.7 - - - +
183A ALA* 1.3 73.5 - - - +
185A ARG* 1.3 68.2 + - - +
187A GLU* 3.0 12.8 + - - +
188A ILE* 3.3 20.0 + - + +
193A LEU* 3.9 18.8 - - + -
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Residues in contact with ARG 185 (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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181A THR 2.9 17.9 + - - +
182A ALA* 3.7 7.2 - - - +
184A VAL* 1.3 76.1 - - - +
186A GLY* 1.3 63.0 + - - +
187A GLU 3.2 1.2 + - - -
188A ILE* 3.4 28.6 + - - +
189A GLY* 2.9 32.3 + - - +
190A ASP* 3.6 7.8 - - - +
191A ALA 2.8 31.3 + - - +
192A ARG* 4.9 0.2 - - - +
193A LEU* 3.5 16.4 - - + +
216A TYR* 2.9 33.7 + - + +
217A ASP* 2.8 40.7 + - - +
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Residues in contact with GLY 186 (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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182A ALA 3.0 14.6 + - - -
183A ALA 3.5 3.1 + - - -
184A VAL 3.1 0.8 - - - -
185A ARG* 1.3 78.8 - - - +
187A GLU* 1.3 66.1 + - - +
189A GLY* 4.7 2.8 + - - -
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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