Contacts of the helix formed by residues 179 - 186 (chain A) in PDB entry 3H9R
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 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A SER* 1.3 78.2 - - - +
180A LEU* 1.3 63.3 + - - +
181A ALA* 3.6 10.0 + - - +
182A ASP* 3.3 19.3 + - - +
183A LEU* 3.1 21.1 + - - +
227A TRP* 4.3 2.9 - - - -
230A GLU* 3.6 16.8 - - + +
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Residues in contact with LEU 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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6A PG4 3.9 15.3 - - - +
179A THR* 1.3 71.8 - - - +
181A ALA* 1.3 57.0 + - - +
183A LEU* 3.5 6.9 - - + +
184A LEU* 2.6 46.3 + - + +
196A LEU* 4.1 27.6 - - + -
204A VAL* 4.3 8.1 - - + -
227A TRP* 3.7 26.0 - - + -
230A GLU* 3.1 33.8 + - + +
232A VAL* 3.9 28.5 - - + -
266A ILE* 4.0 18.8 - - + -
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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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6A PG4 4.7 12.9 + - - -
179A THR* 3.3 9.0 + - - +
180A LEU* 1.3 77.4 - - - +
182A ASP* 1.3 62.7 + - - +
184A LEU* 3.5 8.7 + - - +
185A ASP* 3.1 24.9 + - - +
230A GLU* 4.9 1.0 + - - +
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Residues in contact with ASP 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 SER* 2.8 27.4 + - - -
179A THR* 3.3 19.3 + - - +
180A LEU 3.2 0.4 - - - -
181A ALA* 1.3 78.9 - - - +
183A LEU* 1.3 61.7 + - - +
185A ASP* 3.2 14.8 + - - +
186A HIS* 3.3 21.9 + - - -
45B LYS* 3.1 30.8 + - - -
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Residues in contact with LEU 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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178A SER* 3.7 21.1 - - - +
179A THR 3.1 21.6 + - - +
180A LEU* 3.7 7.2 - - + +
182A ASP* 1.3 77.7 - - - +
184A LEU* 1.3 59.6 + - - +
185A ASP 3.5 0.3 + - - -
186A HIS* 4.0 3.5 + - - +
187A SER* 3.7 14.9 + - - -
196A LEU* 3.3 23.6 - - + -
197A PRO* 3.7 15.5 - - + +
200A VAL* 4.6 23.8 - - + -
204A VAL* 4.6 1.8 - - + -
227A TRP* 3.9 28.3 - - + -
45B LYS* 4.2 16.4 + - + +
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Residues in contact with LEU 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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6A PG4 3.4 40.8 - - - +
180A LEU* 2.6 28.1 + - + +
181A ALA* 4.0 6.3 - - - +
183A LEU* 1.3 73.0 - - - +
185A ASP* 1.3 57.0 + - - +
187A SER* 3.6 6.1 - - - -
194A SER 4.2 1.3 - - - +
195A GLY* 3.7 33.9 - - - +
196A LEU* 3.8 14.8 - - + +
258A ARG* 2.7 44.0 + - - +
265A PHE 4.1 9.9 - - - +
266A ILE* 4.5 6.3 - - + -
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Residues in contact with ASP 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 17.7 + - - +
182A ASP* 3.2 8.3 + - - +
184A LEU* 1.3 76.1 - - - +
186A HIS* 1.3 75.7 + - - +
187A SER 2.9 13.3 + - - -
188A CYS* 4.5 2.8 + - - +
258A ARG* 4.6 4.2 + - - +
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Residues in contact with HIS 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 ASP* 3.3 22.1 + - - +
183A LEU 4.0 2.8 + - - +
184A LEU 3.6 0.4 - - - -
185A ASP* 1.3 89.2 + - - +
187A SER* 1.3 56.5 + - - +
188A CYS 3.7 3.7 + - - -
43B ARG* 3.5 46.3 - - + +
45B LYS* 2.9 38.8 + - - +
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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