Contacts of the helix formed by residues 180 - 185 (chain A) in PDB entry 1QHP
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 ARG 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A TRP 5.4 0.4 + - - -
178A ASP 3.5 1.7 + - - +
179A ASP* 1.3 75.3 + - - +
181A TYR* 1.3 64.3 + - - +
183A ALA* 3.4 20.9 + - - +
184A GLN* 2.9 60.4 + - - +
230A VAL 5.2 0.4 + - - -
231A LYS* 2.9 44.1 + - - +
235A SER* 5.2 0.4 + - - -
257A TRP* 3.6 19.1 - - - -
260A ASP* 5.7 0.2 - - - -
266A ASN* 3.6 36.1 - - - +
269A GLU* 2.9 43.1 + - - +
599A LYS* 6.2 2.2 - - - +
628A LEU* 4.2 16.6 - - + -
637A TYR* 4.7 0.4 + - - -
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Residues in contact with TYR 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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171A ASN* 3.8 18.6 + - + +
179A ASP* 3.4 10.1 + - - +
180A ARG* 1.3 78.3 - - - +
182A GLU* 1.3 66.0 + - + +
184A GLN 3.7 0.2 - - - -
185A TRP* 2.8 71.6 + + + +
186A LYS* 4.4 19.1 - - + -
628A LEU* 3.8 22.5 - - + +
630A PRO* 3.7 42.0 - - + +
636A PHE* 4.1 11.9 - + - -
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Residues in contact with GLU 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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174A ILE* 3.3 13.9 - - + +
175A SER* 2.8 38.6 + - - -
176A ASN* 2.9 31.0 + - - +
179A ASP* 3.0 27.5 + - - +
181A TYR* 1.3 78.1 - - + +
183A ALA* 1.3 64.4 + - - +
186A LYS* 2.9 55.7 + - + +
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Residues in contact with ALA 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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174A ILE* 3.9 16.4 - - - +
177A TRP 3.7 18.2 - - - +
179A ASP 2.9 16.8 + - - +
180A ARG* 3.6 26.5 - - - +
181A TYR 3.3 0.4 - - - -
182A GLU* 1.3 77.7 - - - +
184A GLN* 1.3 59.2 + - - +
186A LYS 4.4 2.1 - - - +
231A LYS* 5.4 1.1 - - + -
232A HIS* 2.8 40.0 + - + +
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Residues in contact with GLN 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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169A HIS* 4.0 6.1 + - - -
180A ARG* 2.9 47.3 + - - +
182A GLU 3.1 0.4 - - - -
183A ALA* 1.3 78.8 - - - +
185A TRP* 1.3 82.3 + - + +
186A LYS 3.6 0.4 - - - -
198A ASP* 3.3 2.1 - - - +
231A LYS 3.3 20.0 - - - +
232A HIS 3.2 13.8 - - - +
233A PHE* 3.4 9.1 - - - +
234A ASN* 3.4 13.7 - - - +
235A SER* 4.8 0.2 + - - -
269A GLU* 4.8 1.2 + - - -
628A LEU* 4.0 3.8 - - - +
637A TYR* 2.6 38.1 + - - -
697A CA 2.6 24.4 - - - -
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Residues in contact with TRP 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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169A HIS* 3.5 45.9 + + - +
171A ASN* 3.0 30.7 + - - +
181A TYR* 2.8 57.9 + + + +
184A GLN* 1.3 104.7 - - + +
186A LYS* 1.3 63.0 + - - +
187A ASN* 5.0 0.3 - - - +
198A ASP* 4.0 1.8 - - - -
202A GLU* 3.6 27.1 + - + +
234A ASN* 4.0 11.2 - - + -
628A LEU* 3.9 20.6 - - + -
636A PHE* 3.4 31.2 - + - -
637A TYR* 3.9 14.8 - + - -
638A VAL* 4.0 5.4 - - + -
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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