Contacts of the helix formed by residues 166 - 179 (chain A) in PDB entry 3ARE
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 ASP 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A MET* 2.9 24.8 + - + +
164A LEU 3.5 0.2 - - - -
165A ASN* 1.3 90.1 - - - +
167A THR* 1.3 65.4 + - - +
168A CYS 3.6 1.3 - - - -
169A PRO* 3.4 2.9 - - - +
170A LEU* 3.3 25.4 + - - +
501A NAG 5.5 2.1 - - - +
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Residues in contact with THR 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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58A LEU* 5.9 2.0 - - + -
66A LEU* 4.3 22.2 - - + -
162A MET* 3.0 24.3 + - - +
163A LEU* 3.4 32.9 - - + +
166A ASP* 1.3 72.4 - - - +
168A CYS* 1.3 60.3 + - - +
170A LEU* 3.3 4.2 + - - +
171A PHE* 2.8 39.6 + - + +
601A 4GH 4.6 6.3 - - + -
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Residues in contact with CYS 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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10A PHE* 4.1 2.5 - - - -
103A GLY* 3.5 11.7 - - - -
104A CYS* 2.0 57.0 - - + -
114A SER* 4.3 1.1 - - - +
163A LEU 2.9 21.2 + - - +
164A LEU* 4.1 4.9 - - - +
167A THR* 1.3 71.9 - - - +
169A PRO* 1.4 61.8 - - + +
171A PHE* 3.7 0.8 - - - -
172A VAL* 2.8 41.4 + - - +
601A 4GH 4.0 23.5 - - + +
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Residues in contact with PRO 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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104A CYS* 4.1 4.3 - - - -
106A MET* 3.3 15.7 - - + +
110A ASN 5.4 3.6 - - - +
112A SER* 3.3 31.4 - - - +
114A SER* 4.5 2.5 - - - +
164A LEU 3.7 13.2 - - - +
165A ASN 3.8 13.2 - - - +
166A ASP 3.4 13.5 - - - +
168A CYS* 1.4 95.7 - - + +
170A LEU* 1.3 55.3 + - - +
173A ARG* 3.2 31.0 + - - +
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Residues in contact with LEU 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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57A LYS* 5.9 0.7 - - - +
58A LEU* 5.4 5.1 - - + +
166A ASP 3.3 17.7 + - - +
167A THR* 3.3 4.2 + - - +
168A CYS 3.3 0.6 - - - -
169A PRO* 1.3 77.6 - - - +
171A PHE* 1.3 61.9 + - - +
173A ARG* 4.3 5.0 - - - +
174A GLY* 3.7 12.6 + - - -
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Residues in contact with PHE 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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10A PHE* 4.0 14.6 - + - -
38A HIS* 4.1 10.1 - + - -
54A SER 3.7 17.5 - - - -
55A GLN* 3.6 25.1 - - - -
56A GLY* 4.2 4.7 - - - -
57A LYS 5.1 0.4 + - - -
58A LEU* 3.4 35.7 - - + -
63A TRP* 4.8 6.3 - + - -
66A LEU* 5.6 0.7 - - + -
167A THR* 2.8 25.2 + - + +
168A CYS 3.7 1.1 - - - +
170A LEU* 1.3 77.2 - - - +
172A VAL* 1.3 62.6 + - + +
174A GLY* 2.9 16.7 + - - -
175A LEU* 3.0 33.9 + - + +
601A 4GH 3.7 35.9 - - + -
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Residues in contact with VAL 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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10A PHE* 3.5 43.3 - - + -
32A LEU* 3.8 24.5 - - + -
104A CYS* 3.8 9.9 - - - -
106A MET* 3.7 32.3 - - + -
168A CYS* 2.8 24.4 + - - +
171A PHE* 1.3 71.0 - - + +
173A ARG* 1.3 60.0 + - - +
174A GLY 3.0 1.6 - - - -
175A LEU* 3.1 6.6 + - - +
176A LEU* 3.0 32.0 + - + +
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Residues in contact with ARG 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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106A MET* 3.6 10.6 - - + +
169A PRO 3.2 20.6 + - - +
170A LEU* 4.3 5.6 - - - +
172A VAL* 1.3 76.0 - - - +
174A GLY* 1.3 61.0 + - - +
176A LEU* 4.0 9.3 + - + +
177A GLU* 3.8 20.4 + - - +
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Residues in contact with GLY 174 (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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57A LYS* 3.9 33.7 + - - +
170A LEU 3.7 6.6 + - - -
171A PHE* 2.9 11.9 + - - -
173A ARG* 1.3 78.7 - - - +
175A LEU* 1.3 58.1 + - - +
177A GLU* 3.6 4.1 + - - +
178A ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 175 (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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10A PHE* 3.7 33.7 - - + -
32A LEU* 4.0 19.0 - - + +
37A THR* 4.7 6.5 - - + +
38A HIS* 4.6 5.4 - - + -
53A TRP* 3.4 41.2 - - + +
54A SER* 3.5 19.1 - - - +
56A GLY* 3.7 6.1 - - - -
171A PHE* 3.0 31.6 + - + +
172A VAL* 3.1 8.7 + - - +
174A GLY* 1.3 74.3 - - - +
176A LEU* 1.3 57.1 + - - +
178A ALA* 3.0 3.2 + - - -
179A GLY* 2.7 33.4 + - - -
183A LEU* 5.3 0.2 - - - +
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Residues in contact with LEU 176 (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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8A TYR* 3.7 39.7 - - + -
32A LEU* 4.2 10.1 - - + -
106A MET* 3.8 32.3 - - + -
172A VAL* 3.0 26.3 + - + +
173A ARG* 4.3 9.9 - - + +
174A GLY 3.4 0.2 - - - -
175A LEU* 1.3 75.2 - - - +
177A GLU* 1.3 59.6 + - - +
179A GLY 4.0 1.0 - - - -
180A LYS* 3.5 20.8 + - - +
183A LEU* 3.9 24.6 - - + +
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Residues in contact with GLU 177 (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 ARG 3.8 11.0 + - - +
174A GLY* 3.6 7.7 + - - +
176A LEU* 1.3 76.5 - - - +
178A ALA* 1.3 65.8 + - - +
179A GLY 3.3 0.6 + - - -
180A LYS* 3.5 18.1 + - + +
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Residues in contact with ALA 178 (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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53A TRP* 3.6 37.3 - - + +
56A GLY* 4.0 14.8 - - - +
57A LYS* 5.7 0.2 - - - -
174A GLY 3.0 18.7 + - - +
175A LEU* 3.0 7.3 + - - +
177A GLU* 1.3 78.8 - - - +
179A GLY* 1.3 57.5 + - - +
180A LYS 3.9 0.5 + - - -
181A SER* 5.2 1.9 + - - -
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Residues in contact with GLY 179 (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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53A TRP* 3.5 31.5 - - - -
175A LEU 2.7 15.6 + - - -
176A LEU 4.0 4.5 - - - -
178A ALA* 1.3 74.5 - - - +
180A LYS* 1.3 61.9 + - - -
181A SER* 3.2 3.1 - - - -
182A ASP* 3.7 3.8 + - - +
183A LEU* 3.2 31.3 + - - +
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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