Contacts of the helix formed by residues 208 - 217 (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 ALA 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A LYS* 4.0 19.8 - - - +
175A CYS* 5.8 0.6 - - - +
206A LYS 3.7 2.0 + - - -
207A ALA* 1.3 70.8 - - - +
209A GLU* 1.4 67.0 + - - +
210A PRO* 3.9 11.0 - - + -
211A HIS* 3.0 32.3 + - + +
212A ALA* 2.9 20.4 + - - +
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Residues in contact with GLU 209 (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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204A PHE 5.8 3.4 - - - +
207A ALA 3.3 5.1 + - - +
208A ALA* 1.4 69.7 - - - +
210A PRO* 1.3 73.4 - - + +
212A ALA* 3.3 5.5 + - - -
213A GLN* 2.9 46.7 + - - +
286A SER* 4.9 2.6 - - - +
290A ARG* 2.4 56.7 + - + +
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Residues in contact with PRO 210 (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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165A PHE* 5.9 0.2 - - - -
208A ALA* 3.3 12.3 - - + -
209A GLU* 1.3 95.6 - - + +
211A HIS* 1.3 60.0 + - + +
213A GLN* 4.0 5.7 - - + +
214A GLY* 3.1 23.4 + - - -
351A PHE* 6.4 1.6 - - + -
352A HIS* 4.7 3.6 + - - -
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Residues in contact with HIS 211 (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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165A PHE 5.3 1.0 - - - +
168A LEU* 4.6 30.6 + - + +
169A CYS* 5.1 3.6 - - - +
172A ASN* 3.7 37.7 + - - +
174A LYS* 5.7 0.4 - - - -
175A CYS* 3.8 27.4 - - + +
208A ALA* 3.0 30.5 + - + +
210A PRO* 1.3 78.4 - - + +
212A ALA* 1.3 67.4 + - - +
214A GLY* 3.4 1.5 + - - -
215A LEU* 3.0 24.6 + - - +
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Residues in contact with ALA 212 (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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203A PHE* 3.8 28.7 - - + -
204A PHE* 3.9 24.6 - - + +
207A ALA* 4.1 10.5 - - + +
208A ALA 2.9 15.7 + - - +
209A GLU* 3.9 7.0 - - - +
211A HIS* 1.3 78.2 - - - +
213A GLN* 1.3 60.9 + - - +
215A LEU* 3.4 4.1 + - - +
216A LEU* 3.2 24.4 + - - +
293A LEU* 4.5 4.9 - - + -
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Residues in contact with GLN 213 (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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209A GLU* 2.9 40.1 + - - +
210A PRO* 4.2 5.4 - - + +
212A ALA* 1.3 72.6 - - + +
214A GLY* 1.3 61.7 + - - +
217A LEU* 2.8 46.6 + - + +
286A SER* 4.8 3.8 + - - +
289A LEU* 3.8 25.9 - - - +
290A ARG* 4.2 11.9 - - - +
293A LEU* 3.4 26.7 - - + +
348A LYS* 3.7 26.5 + - + -
352A HIS* 3.2 11.3 - - + +
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Residues in contact with GLY 214 (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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165A PHE* 3.1 36.6 - - - +
210A PRO 3.1 17.1 + - - -
211A HIS* 3.4 2.0 + - - -
213A GLN* 1.3 75.0 - - - +
215A LEU* 1.3 65.3 + - - +
216A LEU 3.5 0.2 + - - -
218A CYS* 3.4 16.5 - - - +
352A HIS* 3.4 19.7 - - - -
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Residues in contact with LEU 215 (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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162A CYS 5.1 2.9 - - - +
165A PHE* 4.2 10.2 + - - +
166A ALA* 3.7 30.5 - - + -
169A CYS* 4.8 4.9 - - + -
179A ARG* 4.0 22.2 - - - +
182A TYR* 3.6 23.1 - - + +
203A PHE* 3.6 32.1 - - + -
204A PHE* 5.5 4.3 - - + -
211A HIS 3.0 16.3 + - - +
212A ALA* 3.5 6.3 - - - +
214A GLY* 1.3 81.2 - - - +
216A LEU* 1.3 59.3 + - + +
218A CYS* 3.6 14.0 - - - -
234A THR* 3.8 23.5 + - + +
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Residues in contact with LEU 216 (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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204A PHE* 4.0 13.2 - - + -
212A ALA 3.2 12.5 + - - +
215A LEU* 1.3 81.4 - - + +
217A LEU* 1.3 64.4 + - + +
218A CYS 3.1 9.3 + - - -
231A ARG* 3.4 24.0 - - - +
234A THR* 4.3 11.0 - - + -
235A ILE* 4.2 18.6 - - + +
292A TYR* 5.2 3.1 - - + -
293A LEU* 3.5 18.2 - - + -
296A ILE* 3.4 33.2 - - + -
303A ASN* 4.8 4.9 - - - +
304A PHE* 3.4 35.0 - - + -
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Residues in contact with LEU 217 (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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213A GLN* 2.8 37.1 + - + +
216A LEU* 1.3 84.4 - - + +
218A CYS* 1.3 58.2 + - - +
289A LEU* 3.9 39.5 - - + -
292A TYR* 4.9 4.5 - - + -
293A LEU* 4.6 15.3 - - + -
304A PHE* 4.0 18.4 - - + -
345A ILE* 4.4 20.6 - - + -
348A LYS* 4.2 14.8 - - + -
349A MET* 3.2 26.0 - - + +
352A HIS* 2.8 18.6 + - - -
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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