Contacts of the helix formed by residues 192 - 199 (chain A) in PDB entry 2HQQ
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 SER 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLU* 5.7 1.7 - - - +
172A VAL 3.1 7.9 + - - -
173A GLU* 2.8 46.4 + - - -
190A PHE 4.2 0.2 - - - -
191A VAL* 1.3 77.1 - - - +
193A LYS* 1.3 64.6 + - - +
194A ASP* 3.4 5.7 + - - +
195A VAL* 2.9 19.2 + - - +
196A ALA* 2.9 22.5 + - - +
223A CYS* 4.5 0.9 - - - -
224A ALA 5.3 0.7 - - - -
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Residues in contact with LYS 193 (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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191A VAL 3.9 1.2 + - - -
192A SER* 1.3 72.5 - - - +
194A ASP* 1.3 57.6 + - - +
196A ALA* 3.1 1.9 + - - +
197A LYS* 2.8 58.7 + - + +
224A ALA 3.7 20.1 + - - +
225A TRP* 3.6 64.9 - - + +
226A ALA* 4.7 13.2 - - + +
227A GLU* 5.5 1.6 + - - -
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Residues in contact with ASP 194 (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 GLU 4.3 4.9 - - - +
175A PRO* 3.4 29.7 - - - +
192A SER* 3.1 9.2 + - - +
193A LYS* 1.3 79.1 - - - +
195A VAL* 1.3 57.3 + - - +
197A LYS* 3.4 7.0 + - - +
198A HIS* 2.9 30.5 + - - +
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Residues in contact with VAL 195 (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 VAL* 3.5 9.9 - - + +
173A GLU 3.4 11.9 - - - +
174A LYS 3.4 30.3 - - - +
175A PRO* 3.7 3.4 - - + -
180A PHE* 3.9 23.8 - - + -
183A PHE* 4.2 4.7 - - + -
191A VAL* 3.7 19.7 - - + -
192A SER* 2.9 23.9 + - - +
194A ASP* 1.3 75.7 - - - +
196A ALA* 1.3 64.3 + - - +
198A HIS* 3.1 8.1 + - - +
199A LEU* 3.0 34.1 + - + +
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Residues in contact with ALA 196 (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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191A VAL* 4.6 4.5 - - + +
192A SER 2.9 13.1 + - - +
193A LYS 3.1 8.5 + - - +
195A VAL* 1.3 77.1 - - - +
197A LYS* 1.3 61.4 + - - +
199A LEU* 3.0 9.9 + - - -
200A GLY 3.1 0.3 + - - -
201A PHE* 3.0 32.3 + - + -
207A ALA* 3.7 22.2 - - + -
211A LEU* 5.3 1.8 - - + -
223A CYS* 4.6 2.7 - - - -
225A TRP* 3.6 25.1 - - + -
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Residues in contact with LYS 197 (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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193A LYS* 2.8 55.8 + - + +
194A ASP* 3.9 7.2 - - - +
196A ALA* 1.3 71.8 - - - +
198A HIS* 1.3 63.5 + - - +
200A GLY* 3.0 13.9 + - - -
201A PHE 3.5 18.8 - - - +
202A GLN* 5.0 13.1 + - - +
225A TRP* 3.7 13.0 - - + -
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Residues in contact with HIS 198 (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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175A PRO* 3.6 39.5 + - + +
177A GLU 6.0 0.4 + - - -
180A PHE* 4.3 11.3 - + - -
194A ASP* 2.9 20.2 + - - +
195A VAL 3.1 4.2 + - - +
197A LYS* 1.3 76.0 - - - +
199A LEU* 1.3 77.7 + - + +
200A GLY 3.3 0.7 + - - -
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Residues in contact with LEU 199 (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 PHE* 3.9 25.4 - - + -
183A PHE* 4.7 5.4 - - + -
195A VAL* 3.0 31.3 + - + +
196A ALA 3.0 9.1 + - - +
198A HIS* 1.3 96.2 - - + +
200A GLY* 1.3 58.3 + - - +
201A PHE* 3.6 21.1 - - + -
211A LEU* 4.1 27.4 - - + -
214A ARG* 5.0 7.6 - - - +
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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