Contacts of the helix formed by residues 173 - 186 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171G GLY 3.3 5.5 + - - -
172G ARG* 1.3 78.2 - - - +
174G GLU* 1.3 66.4 + - - -
175G LYS 3.5 2.0 - - - -
176G LEU 3.6 1.9 + - - -
177G ASP* 2.9 27.8 + - - +
201G TRP* 5.7 2.1 - - - +
209G MSE 5.4 0.4 - - - -
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Residues in contact with GLU 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ASP 5.6 1.9 - - - +
192B ARG* 5.8 3.8 - - - +
217B ASP* 5.1 0.3 - - - +
173G GLY* 1.3 71.3 - - - +
175G LYS* 1.3 65.3 + - - +
177G ASP* 3.6 0.5 - - - +
178G LEU* 3.0 45.3 + - + +
208G ASN* 5.9 1.7 - - - +
209G MSE 3.6 29.1 - - - +
212G LYS* 2.9 42.4 + - + +
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Residues in contact with LYS 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G GLY 3.5 0.6 - - - -
174G GLU* 1.3 79.6 - - - +
176G LEU* 1.3 61.6 + - - +
178G LEU* 3.6 5.4 + - - +
179G GLU* 2.9 59.6 + - - +
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Residues in contact with LEU 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G GLU 4.4 13.9 - - - +
147G THR* 5.2 1.3 - - - -
148G ALA* 4.8 8.7 - - + +
172G ARG* 3.9 39.5 - - + +
173G GLY* 3.6 2.0 + - - -
175G LYS* 1.3 76.8 - - - +
177G ASP* 1.3 61.2 + - - +
179G GLU* 4.1 17.5 - - + +
180G ILE* 2.8 55.3 + - + +
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Residues in contact with ASP 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G VAL* 3.3 18.0 - - + +
171G GLY* 2.7 31.1 + - - -
172G ARG* 2.8 25.4 + - - +
173G GLY 2.9 24.5 + - - +
174G GLU 3.6 3.4 - - - +
176G LEU* 1.3 77.6 - - - +
178G LEU* 1.3 63.7 + - - +
180G ILE* 3.3 6.5 - - - +
181G THR* 2.8 31.2 + - - -
201G TRP* 3.7 13.9 + - - -
209G MSE 3.8 15.2 - - + +
213G LEU* 4.7 1.8 - - + -
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Residues in contact with LEU 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G GLU* 3.0 43.7 + - + +
175G LYS* 4.0 4.9 - - - +
177G ASP* 1.3 75.5 - - - +
179G GLU* 1.3 58.1 + - + +
181G THR* 3.9 4.0 - - - -
182G ALA* 2.9 31.9 + - - +
209G MSE 4.1 6.1 - - + -
212G LYS* 3.6 39.7 - - + +
213G LEU* 3.8 18.6 - - + -
216G TYR* 3.8 15.4 + - + +
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Residues in contact with GLU 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G ALA* 4.1 10.6 - - + +
175G LYS* 2.9 59.2 + - - +
176G LEU* 3.2 22.1 + - + +
178G LEU* 1.3 78.4 - - + +
180G ILE* 1.3 56.9 + - - +
182G ALA* 3.6 5.9 - - - +
183G ALA* 3.0 26.2 + - - +
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Residues in contact with ILE 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G GLU 5.4 0.2 - - - +
147G THR* 4.4 0.9 - - - -
148G ALA* 3.8 24.7 - - - +
151G LEU* 3.8 20.9 - - + -
168G LEU* 4.1 12.8 - - + -
169G LYS 3.6 11.9 - - - +
170G VAL* 4.6 2.0 - - + -
172G ARG* 3.5 37.2 - - - +
176G LEU* 2.8 41.6 + - + +
177G ASP* 3.3 18.2 - - - +
179G GLU* 1.3 70.8 - - - +
181G THR* 1.3 64.2 + - - +
183G ALA* 3.7 2.0 - - - +
184G VAL* 2.9 34.7 + - - +
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Residues in contact with THR 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G LEU* 3.8 10.7 - - - +
170G VAL* 3.9 15.6 - - - +
177G ASP 2.8 21.9 + - - -
178G LEU 3.9 2.7 - - - -
180G ILE* 1.3 77.3 - - - +
182G ALA* 1.3 62.5 + - - +
184G VAL* 4.0 1.0 - - - +
185G ARG* 3.0 24.3 + - - +
193G LEU* 4.1 7.5 - - + +
195G LEU* 4.2 3.6 - - + +
213G LEU* 3.5 21.0 - - + +
216G TYR* 3.6 33.0 - - + -
218G ILE* 4.1 14.8 - - + -
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Residues in contact with ALA 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G LEU 2.9 19.8 + - - +
179G GLU* 3.6 6.7 - - - +
181G THR* 1.3 78.0 - - - +
183G ALA* 1.3 62.4 + - - +
185G ARG* 3.8 1.9 - - - +
186G GLY* 3.0 21.1 + - - -
216G TYR* 3.5 31.3 - - + +
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Residues in contact with ALA 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G ALA* 3.7 32.1 - - + +
152G ALA* 4.1 11.2 - - + +
179G GLU 3.0 18.3 + - - +
180G ILE* 3.3 5.3 + - - +
182G ALA* 1.3 77.2 - - - +
184G VAL* 1.3 63.3 + - + +
186G GLY* 3.4 8.6 + - - -
187G GLU* 3.6 18.7 + - - +
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Residues in contact with VAL 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G LEU* 3.9 19.5 - - + -
151G LEU* 4.1 31.4 - - + +
152G ALA* 5.0 0.7 - - - +
155G ALA* 4.0 13.7 - - + -
166G PHE* 5.0 0.2 - - + -
168G LEU* 3.8 17.0 - - + -
180G ILE 2.9 20.5 + - - +
181G THR 4.0 2.9 - - - +
183G ALA* 1.3 74.6 - - - +
185G ARG* 1.3 66.4 + - - +
187G GLU* 2.9 13.0 + - - +
188G ILE* 3.3 20.7 + - + +
193G LEU* 3.9 26.7 - - + -
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Residues in contact with ARG 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G THR 3.0 18.8 + - - +
182G ALA 3.8 3.6 - - - +
184G VAL* 1.3 75.5 - - - +
186G GLY* 1.3 63.0 + - - +
187G GLU 3.1 1.2 + - - -
188G ILE* 3.3 30.3 + - - +
189G GLY* 2.9 29.9 + - - +
190G ASP* 3.4 8.9 - - - +
191G ALA 2.7 31.3 + - - +
192G ARG* 4.8 0.2 - - - +
193G LEU* 3.5 18.3 - - + +
216G TYR* 2.9 36.5 + - + +
217G ASP* 2.8 38.8 + - - +
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Residues in contact with GLY 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G ALA 3.0 16.4 + - - -
183G ALA* 3.8 3.4 - - - -
184G VAL 3.1 0.6 - - - -
185G ARG* 1.3 78.7 - - - +
187G GLU* 1.3 66.5 + - - +
189G 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