Contacts of the helix formed by residues 173 - 186 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C GLY* 3.4 4.6 + - - -
172C ARG* 1.3 78.2 - - - +
174C GLU* 1.3 59.9 + - - -
175C LYS 3.5 2.2 - - - -
176C LEU 3.6 1.7 + - - -
177C ASP* 2.9 32.9 + - - +
201C TRP* 5.7 0.8 - - - +
209C MSE 5.3 0.4 - - - -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLY* 1.3 70.4 - - - -
175C LYS* 1.3 65.0 + - - +
177C ASP* 3.6 0.5 - - - +
178C LEU* 3.0 46.0 + - + +
208C ASN* 5.7 2.3 - - - +
209C MSE 3.7 28.9 - - - +
212C LYS* 2.7 42.8 + - - +
190D ASP 5.7 1.4 - - - +
192D ARG* 5.9 3.6 - - - +
217D ASP* 5.0 0.5 - - - +
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLY 3.5 0.8 - - - -
174C GLU* 1.3 78.6 - - - +
176C LEU* 1.3 58.0 + - - +
178C LEU* 3.5 5.8 + - - +
179C GLU* 2.7 65.1 + - + +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLU 4.6 13.7 - - - +
147C THR* 5.4 1.6 - - - -
148C ALA* 5.1 5.4 - - + +
172C ARG* 4.0 42.0 - - + +
173C GLY 3.6 1.8 + - - -
174C GLU 3.4 0.2 - - - -
175C LYS* 1.3 76.1 - - - +
177C ASP* 1.3 61.2 + - - +
179C GLU* 3.7 17.3 - - + +
180C ILE* 2.8 53.9 + - + +
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Residues in contact with ASP 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL* 3.5 14.1 - - + +
171C GLY* 2.6 29.9 + - - -
172C ARG* 2.7 30.1 + - - +
173C GLY 2.9 23.4 + - - +
174C GLU 3.6 3.6 - - - +
176C LEU* 1.3 77.4 - - - +
178C LEU* 1.3 55.9 + - - +
180C ILE* 3.2 7.6 - - - +
181C THR* 2.7 38.6 + - - -
201C TRP* 3.6 14.0 + - - -
209C MSE 3.7 15.6 - - + +
213C LEU* 4.8 1.1 - - + -
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLU* 3.0 46.6 + - + +
175C LYS* 3.9 4.7 - - - +
177C ASP* 1.3 75.3 - - - +
179C GLU* 1.3 58.7 + - + +
181C THR* 3.9 3.4 - - - -
182C ALA* 3.0 30.8 + - - +
209C MSE 4.2 4.5 - - + -
212C LYS* 3.8 36.8 - - + +
213C LEU* 3.7 26.0 - - + -
216C TYR* 4.1 15.0 + - + +
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Residues in contact with GLU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ALA* 4.1 8.5 - - + +
175C LYS* 2.7 64.2 + - + +
176C LEU* 3.1 23.5 + - + +
178C LEU* 1.3 76.4 - - + +
180C ILE* 1.3 65.4 + - - +
182C ALA* 3.9 4.0 - - - +
183C ALA* 3.0 24.3 + - - +
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Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLU 5.2 0.9 - - - +
147C THR* 4.3 1.3 - - - -
148C ALA* 3.8 21.8 - - - +
151C LEU* 3.7 25.1 - - + +
168C LEU* 4.2 9.2 - - + -
169C LYS 3.6 11.9 - - - +
170C VAL* 4.6 2.2 - - + -
172C ARG* 3.4 37.7 - - - +
176C LEU* 2.8 44.3 + - + +
177C ASP* 3.2 15.5 - - - +
179C GLU* 1.3 69.7 - - - +
181C THR* 1.3 70.0 + - - +
183C ALA* 3.4 1.4 + - - +
184C VAL* 2.9 29.1 + - - +
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Residues in contact with THR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C LEU* 3.8 17.5 - - - +
170C VAL* 4.0 8.3 - - - +
177C ASP 2.7 23.2 + - - -
178C LEU 3.9 2.9 - - - -
180C ILE* 1.3 76.7 - - - +
182C ALA* 1.3 63.2 + - - +
184C VAL* 3.2 2.3 + - - +
185C ARG* 2.9 22.9 + - - +
193C LEU* 4.4 7.5 - - + +
195C LEU* 4.1 3.2 - - + +
213C LEU* 3.4 21.4 - - + +
216C TYR* 3.6 33.2 - - + -
218C ILE* 4.1 12.6 - - + -
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU 3.0 19.4 + - - +
179C GLU* 3.9 4.9 - - - +
181C THR* 1.3 77.0 - - - +
183C ALA* 1.3 59.1 + - - +
185C ARG* 3.3 2.4 + - - +
186C GLY* 2.9 27.4 + - - -
216C TYR* 3.5 35.2 - - + +
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ALA* 3.9 31.2 - - + +
152C ALA* 3.6 8.6 - - + +
179C GLU 3.0 18.8 + - - +
180C ILE 3.6 4.3 - - - +
182C ALA* 1.3 77.3 - - - +
184C VAL* 1.3 62.4 + - - +
186C GLY* 3.4 8.4 + - - -
187C GLU* 3.5 20.8 + - - +
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Residues in contact with VAL 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LEU* 3.7 33.9 - - + -
151C LEU* 4.0 28.5 - - + +
152C ALA* 4.4 1.6 - - - +
155C ALA* 4.0 12.8 - - + -
166C PHE* 5.1 0.2 - - + -
168C LEU* 4.1 11.9 - - + -
180C ILE 2.9 20.9 + - - +
181C THR 3.8 3.1 - - - +
183C ALA* 1.3 72.5 - - - +
185C ARG* 1.3 68.8 + - - +
187C GLU* 2.9 13.0 + - - +
188C ILE* 3.3 19.9 + - + +
193C LEU* 3.9 21.5 - - + -
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Residues in contact with ARG 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C THR 2.9 17.1 + - - +
182C ALA* 3.5 8.1 - - - +
184C VAL* 1.3 78.1 - - - +
186C GLY* 1.3 63.4 + - - +
187C GLU 3.1 1.6 + - - -
188C ILE* 3.3 28.0 + - - +
189C GLY 2.9 34.2 + - - +
190C ASP* 3.2 11.7 - - - -
191C ALA 2.5 32.5 + - - +
193C LEU* 3.8 14.5 - - + +
215C LYS 5.7 0.4 - - - +
216C TYR* 2.9 37.3 + - + +
217C ASP* 3.1 36.4 + - - +
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Residues in contact with GLY 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C ALA 2.9 16.7 + - - -
183C ALA* 3.4 3.6 + - - -
184C VAL 3.1 0.4 - - - -
185C ARG* 1.3 77.0 - - - +
187C GLU* 1.3 69.3 + - - +
189C GLY 4.9 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