Contacts of the helix formed by residues 165 - 173 (chain A) in PDB entry 2HQR
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 LYS 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A SER* 1.3 75.6 + - - +
166A GLU* 1.3 64.5 + - - +
168A LEU* 3.1 17.2 + - - +
169A LEU 3.3 8.0 + - - -
184A ILE* 3.4 22.7 - - + +
185A GLU* 4.3 19.4 + - - +
207A VAL 5.4 1.3 - - - -
208A ARG* 5.1 11.7 + - - +
210A ARG 4.4 5.6 - - - +
211A GLY* 3.8 22.0 - - - -
212A TYR* 3.5 44.3 + - + +
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Residues in contact with GLU 166 (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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164A SER* 3.4 7.4 + - - +
165A LYS* 1.3 78.5 - - - +
167A GLN* 1.3 72.9 + - - +
169A LEU* 3.0 23.8 + - + +
170A ASP* 2.5 41.3 + - - +
181A PRO* 5.7 7.4 - - + -
184A ILE* 3.9 10.9 - - + +
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Residues in contact with GLN 167 (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 VAL* 3.6 15.9 - - + -
164A SER* 3.3 31.1 + - - +
165A LYS 3.1 0.4 - - - -
166A GLU* 1.3 89.0 + - + +
168A LEU* 1.3 57.9 + - - +
170A ASP* 2.4 32.5 + - - +
171A ALA* 2.7 16.4 + - - +
221B CYS* 6.1 2.4 - - - -
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Residues in contact with LEU 168 (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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151A VAL* 5.2 15.5 - - + -
154A HIS* 4.5 19.1 - - + -
155A LEU* 6.1 0.9 - - + -
163A VAL* 3.8 17.9 - - + -
164A SER 3.8 11.2 - - - +
165A LYS 3.1 7.5 + - - +
167A GLN* 1.3 75.4 - - - +
169A LEU* 1.3 65.8 + - - +
171A ALA* 3.0 13.9 + - - +
172A ILE* 3.3 18.9 + - + +
173A TRP* 4.4 4.2 - - - -
184A ILE* 4.9 9.0 - - + -
188A ILE* 4.5 13.7 - - + -
212A TYR* 3.9 31.2 - - + -
214A PHE* 4.4 19.3 - - + -
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Residues in contact with LEU 169 (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 LYS 3.3 2.2 + - - -
166A GLU* 3.0 20.5 + - + +
168A LEU* 1.3 83.7 - - - +
170A ASP* 1.3 57.2 + - - +
173A TRP* 3.2 46.0 + - + +
179A VAL* 3.8 32.1 - - + +
180A THR 4.6 1.3 - - - +
181A PRO* 3.8 30.5 - - + -
183A VAL* 3.6 26.2 - - + -
184A ILE* 3.5 34.9 - - + +
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Residues in contact with ASP 170 (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 GLU* 2.5 39.9 + - - +
167A GLN* 2.4 39.1 + - - +
169A LEU* 1.3 76.1 - - + +
171A ALA* 1.3 66.3 + - - +
172A ILE 3.5 0.2 - - - -
173A TRP 3.5 12.1 - - - +
174A GLU* 3.3 29.9 - - + +
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Residues in contact with ALA 171 (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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150A GLU* 5.0 0.7 - - - +
154A HIS* 3.9 27.7 - - + +
167A GLN 2.7 19.2 + - - +
168A LEU* 3.0 10.3 + - - +
170A ASP* 1.3 84.9 + - - +
172A ILE* 1.3 74.1 + - + +
174A GLU* 4.5 6.1 + - - +
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Residues in contact with ILE 172 (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 LYS* 4.4 6.7 - - + +
150A GLU* 3.3 51.0 - - + +
151A VAL* 4.1 32.5 - - + +
154A HIS* 4.7 11.2 - - + +
168A LEU* 3.3 10.5 + - + +
171A ALA* 1.3 93.2 - - + +
173A TRP* 1.3 99.5 + - + +
174A GLU* 3.6 3.2 + - - +
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Residues in contact with TRP 173 (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 LYS* 5.3 17.5 - - + +
151A VAL* 6.5 2.0 - - + -
168A LEU* 4.6 2.5 - - + -
169A LEU* 3.2 52.0 + - + +
170A ASP* 3.5 8.8 - - - +
172A ILE* 1.3 103.8 - - + +
174A GLU* 1.3 61.0 + - - +
175A GLU 3.5 5.9 - - - +
177A GLU* 3.3 27.3 + - + +
179A VAL* 3.4 30.3 - - + +
183A VAL* 5.5 5.4 - - + -
184A ILE* 6.3 0.4 - - - -
187A ALA* 4.2 26.7 - - + -
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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