Contacts of the helix formed by residues 172 - 186 (chain A) in PDB entry 2GH0
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 ASN 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A LEU 3.5 8.5 + - - +
169A CYS 2.9 9.4 + - - +
171A LEU* 1.3 77.7 - - - +
173A ASP* 1.3 67.5 + - - +
174A LYS* 3.2 18.1 + - - +
175A CYS* 2.9 29.7 + - + +
176A ASP* 2.8 23.7 + - - +
211A HIS* 3.7 32.7 + - + +
146C ARG* 3.4 0.9 - - - -
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Residues in contact with ASP 173 (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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171A LEU 4.2 2.8 - - - +
172A ASN* 1.3 72.7 - - - +
174A LYS* 1.3 62.3 - - - +
176A ASP* 3.5 2.3 + - - +
177A ARG* 3.2 30.9 + - + +
146C ARG* 2.8 39.4 + - - +
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Residues in contact with LYS 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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172A ASN* 3.2 15.5 + - - +
173A ASP* 1.3 79.3 - - - +
175A CYS* 1.3 61.3 + - - +
177A ARG* 3.4 5.8 + - - +
178A LEU* 3.3 36.6 + - + +
206A LYS* 3.7 22.6 + - + +
207A ALA* 4.9 0.2 - - - -
208A ALA* 4.0 25.2 - - - +
211A HIS* 5.7 0.2 - - - -
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Residues in contact with CYS 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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169A CYS* 2.1 61.8 - - - +
172A ASN* 2.9 19.0 + - + +
174A LYS* 1.3 77.1 - - - +
176A ASP* 1.3 67.0 + - - +
178A LEU* 3.3 7.5 + - - +
179A ARG* 2.9 21.1 + - - +
203A PHE* 3.8 17.5 - - - -
207A ALA* 4.5 6.1 - - + -
208A ALA 5.8 0.4 - - - +
211A HIS* 3.8 24.0 - - + +
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Residues in contact with ASP 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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169A CYS* 3.2 7.2 + - - +
170A THR* 3.4 41.3 + - - +
172A ASN 2.8 17.9 + - - +
173A ASP 3.6 5.7 - - - +
175A CYS* 1.3 76.7 - - - +
177A ARG* 1.3 68.0 + - - +
179A ARG* 3.9 5.0 + - - +
180A LYS* 2.9 49.1 + - - +
146C ARG* 3.7 27.7 + - - +
148C ARG* 4.8 5.4 + - - -
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Residues in contact with ARG 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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173A ASP* 3.2 18.1 + - + +
174A LYS* 3.4 6.0 + - - +
175A CYS 3.2 0.4 - - - -
176A ASP* 1.3 86.3 - - - +
178A LEU* 1.3 60.2 + - + +
180A LYS* 3.5 6.3 + - - +
181A ALA* 3.0 28.8 + - - +
148C ARG* 4.4 28.7 - - - +
194C GLU* 5.5 9.5 + - - -
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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 LYS* 3.3 26.8 + - + +
175A CYS 3.8 1.8 - - - +
176A ASP 3.2 0.6 - - - -
177A ARG* 1.3 77.7 - - + +
179A ARG* 1.3 64.4 + - - +
181A ALA* 3.5 8.6 + - + +
182A TYR* 3.3 23.6 + - - +
199A GLN 4.8 1.2 - - - +
202A THR* 4.0 27.8 - - + +
203A PHE* 3.5 21.7 - - + +
206A LYS* 3.6 17.0 - - + -
207A ALA* 3.5 36.8 - - + +
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Residues in contact with ARG 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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166A ALA* 4.0 8.3 - - - +
167A MET* 4.1 1.2 - - - +
169A CYS* 3.8 23.8 - - - -
170A THR* 3.6 19.1 + - - -
175A CYS 2.9 16.9 + - - +
176A ASP* 3.9 7.2 + - - +
178A LEU* 1.3 74.0 - - - +
180A LYS* 1.3 64.7 + - - +
182A TYR* 3.4 20.9 + - + -
183A GLY* 2.9 28.1 + - - -
203A PHE* 3.7 4.6 - - + -
215A LEU* 4.0 24.5 - - - +
230A ARG* 3.5 10.9 - - - +
234A THR* 6.0 0.4 - - - +
143C GLU* 3.0 40.6 + - - -
144C LEU 5.6 0.8 + - - -
145C VAL* 6.2 1.2 - - - +
197C SER 4.9 6.5 + - - -
199C MET* 4.6 0.4 - - - +
205C TRP* 3.7 34.5 - - + -
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Residues in contact with LYS 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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176A ASP* 2.9 37.5 + - - +
177A ARG* 3.7 7.2 - - - +
179A ARG* 1.3 83.6 - - + +
181A ALA* 1.3 55.6 + - - +
183A GLY 4.6 0.2 - - - +
184A GLU* 3.0 32.2 + - - +
145C VAL* 4.4 7.7 - - - +
146C ARG* 3.0 38.6 + - - +
148C ARG* 5.0 6.1 - - - +
194C GLU* 5.3 7.5 + - - +
195C ALA 4.7 8.8 + - - +
196C VAL* 4.1 18.2 - - - +
197C SER* 3.9 43.3 + - - +
205C TRP* 5.6 1.1 - - - -
212C SER* 5.4 1.6 + - - -
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Residues in contact with ALA 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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177A ARG 3.0 18.0 + - - +
178A LEU* 3.6 12.8 - - + +
179A ARG 3.2 0.2 - - - -
180A LYS* 1.3 78.4 - - - +
182A TYR* 1.3 61.1 + - - +
184A GLU* 3.7 7.5 - - - +
185A ALA* 3.1 22.3 + - - +
199A GLN* 3.3 24.3 - - + +
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Residues in contact with TYR 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 3.3 20.4 + - - -
179A ARG* 3.7 19.7 + - + +
181A ALA* 1.3 76.3 - - - +
183A GLY* 1.3 62.2 + - - +
185A ALA* 4.2 0.4 - - - -
186A CYS* 2.9 46.0 + - + -
199A GLN* 3.5 34.5 - - + +
200A LEU* 3.6 25.8 - - + +
203A PHE* 3.9 29.2 - + + -
204A PHE* 5.8 0.7 - + - -
215A LEU* 3.6 11.2 - - + +
234A THR* 2.7 42.6 + - - +
235A ILE* 4.4 4.2 - - + +
236A ALA* 5.2 0.2 - - + -
205C TRP* 3.7 24.9 - + - -
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Residues in contact with GLY 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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179A ARG 2.9 13.6 + - - -
180A LYS 3.9 1.1 - - - -
182A TYR* 1.3 80.4 - - - +
184A GLU* 1.3 54.5 + - - +
186A CYS* 3.9 1.4 - - - +
187A SER* 2.5 36.0 + - - -
197C SER* 4.1 5.2 - - - -
205C TRP* 3.5 38.5 - - - -
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Residues in contact with GLU 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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180A LYS 3.0 18.3 + - - +
181A ALA* 3.7 7.5 - - - +
183A GLY* 1.3 79.1 - - - +
185A ALA* 1.3 63.2 + - - +
186A CYS 3.4 0.5 + - - -
187A SER* 3.6 12.5 + - - +
195C ALA* 3.8 26.2 + - - +
197C SER* 3.6 12.4 + - - +
207C THR* 3.7 14.9 + - + +
209C ASP* 4.9 3.3 - - - +
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Residues in contact with ALA 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 ALA 3.1 15.3 + - - +
182A TYR 3.2 4.0 + - - +
184A GLU* 1.3 79.8 - - - +
186A CYS* 1.3 59.3 + - - +
187A SER 3.6 0.4 - - - -
191A CYS* 3.9 14.0 - - - +
192A GLN* 4.2 5.0 + - - +
195A VAL* 4.0 15.1 - - + +
196A CYS* 3.5 23.1 + - - +
199A GLN* 3.6 22.7 - - + -
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Residues in contact with CYS 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 TYR* 2.9 38.4 + - + +
183A GLY* 3.9 2.9 - - - +
185A ALA* 1.3 76.0 - - - +
187A SER* 1.3 61.7 + - - +
188A GLY 4.0 1.4 + - - +
191A CYS* 4.2 0.7 - - - -
196A CYS* 2.1 58.8 - - - -
200A LEU* 4.3 2.9 - - - -
236A ALA* 3.4 26.9 - - + +
239A CYS* 3.4 20.1 - - - +
205C TRP* 4.9 3.1 - - + +
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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