Contacts of the helix formed by residues 177 - 186 (chain A) in PDB entry 2GC5
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 THR 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLY 3.4 0.4 - - - -
176A HIS* 1.3 85.7 - - + +
178A ILE* 1.3 64.7 + - - +
179A THR* 3.8 10.2 + - - -
180A ALA* 3.1 24.8 + - - +
181A ILE* 3.3 27.9 + - - +
203A ASP* 6.0 0.9 - - - -
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Residues in contact with ILE 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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166A VAL* 3.8 11.7 - - + +
167A ALA* 4.1 32.8 - - - +
168A LEU* 4.2 6.3 - - + +
177A THR* 1.3 73.7 - - - +
179A THR* 1.3 51.9 + - - +
181A ILE* 3.4 4.5 + - + +
182A ALA* 2.7 37.1 + - - +
201A VAL* 3.7 20.6 - - + -
203A ASP* 3.6 31.8 + - + +
204A ALA* 3.6 19.3 - - + +
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Residues in contact with THR 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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177A THR* 3.2 9.3 - - - -
178A ILE* 1.3 77.6 - - - +
180A ALA* 1.3 58.1 + - - +
182A ALA* 3.2 2.0 + - - +
183A LYS* 2.8 59.7 + - - +
203A ASP* 3.7 24.6 + - - +
207A VAL* 3.8 18.4 - - + -
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Residues in contact with ALA 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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174A LEU 4.2 5.4 - - - +
175A GLY* 4.1 20.2 - - - -
176A HIS 4.7 0.4 - - - +
177A THR* 3.1 22.5 + - - +
179A THR* 1.3 77.3 - - - +
181A ILE* 1.3 62.0 + - - +
183A LYS* 3.6 9.8 + - - +
184A HIS* 3.3 27.2 + - - -
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Residues in contact with ILE 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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47A THR* 4.6 5.6 - - - +
166A VAL* 3.8 14.8 - - + -
167A ALA 3.9 19.3 - - - +
168A LEU* 4.4 4.7 - - - +
170A HIS* 4.1 15.9 - - + +
171A GLN* 4.3 8.5 - - + -
174A LEU* 3.7 26.2 - - + -
175A GLY 3.6 22.2 - - - +
177A THR 3.3 21.6 + - - +
178A ILE* 3.8 6.1 - - + +
180A ALA* 1.3 73.2 - - - +
182A ALA* 1.3 66.2 + - - +
184A HIS* 3.3 4.7 + - - +
185A KCX 3.1 44.0 + - - +
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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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163A LEU* 4.8 1.8 - - - +
166A VAL* 3.9 13.6 - - + +
178A ILE 2.7 22.5 + - - +
179A THR 3.6 4.7 - - - +
181A ILE* 1.3 72.9 - - - +
183A LYS* 1.3 51.7 + - - +
185A KCX 3.3 2.8 + - - +
186A ALA* 2.8 36.0 + - - +
204A ALA* 3.8 32.8 - - + +
207A VAL* 3.7 16.1 - - + +
208A VAL* 5.7 2.2 - - + +
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Residues in contact with LYS 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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149A ASP* 4.7 4.0 - - - +
179A THR* 2.8 42.1 + - + +
180A ALA* 3.7 9.0 - - - +
181A ILE 3.3 0.2 - - - -
182A ALA* 1.3 74.0 - - - +
184A HIS* 1.3 63.1 + - - +
186A ALA* 3.5 8.5 + - - +
187A GLY* 3.6 6.9 + - - -
207A VAL* 3.8 21.9 - - + +
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Residues in contact with HIS 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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147A GLY* 4.4 14.8 - - - -
148A GLY 4.1 1.5 + - - -
149A ASP* 2.7 56.9 + - + +
150A THR* 4.3 20.3 + - + -
173A LEU 4.8 2.8 + - - -
174A LEU* 3.2 43.1 + - + -
180A ALA 3.3 13.7 + - - -
181A ILE 3.3 8.6 + - - +
183A LYS* 1.3 77.9 - - - +
185A KCX 1.3 59.7 + - - +
187A GLY 3.0 5.7 + - - -
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Residues in contact with KCX 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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45A THR* 3.6 16.3 + - + +
46A GLY* 3.1 32.0 + - - +
47A THR* 3.3 23.3 + - - -
50A LYS* 4.1 9.5 + - - +
144A VAL* 5.1 0.3 - - - +
146A ILE* 4.1 3.3 - - - -
147A GLY* 3.0 44.7 + - - +
163A LEU* 3.8 23.2 - - + +
165A GLU 4.8 1.1 - - - -
166A VAL* 4.0 12.6 - - + -
170A HIS* 2.6 45.9 + - - +
174A LEU* 6.2 0.2 - - - -
181A ILE* 3.1 28.7 + - + +
182A ALA* 3.5 5.2 - - - +
184A HIS* 1.3 70.6 + - - +
186A ALA* 1.3 58.8 + - - +
187A GLY 2.8 11.8 + - - -
188A ILE* 3.2 24.9 + - - +
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Residues in contact with ALA 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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163A LEU* 4.3 5.8 - - + -
182A ALA 2.8 20.9 + - - +
183A LYS* 3.8 7.6 - - - +
184A HIS 3.2 0.6 - - - -
185A KCX 1.3 72.0 + - - +
187A GLY* 1.3 55.6 + - - +
188A ILE 3.1 0.9 - - - -
189A ILE* 3.0 46.8 + - + +
207A VAL* 4.0 18.2 - - + -
208A VAL* 4.9 2.0 - - + -
211A LYS* 3.5 23.2 - - + -
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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