Contacts of the helix formed by residues 166 - 174 (chain A) in PDB entry 4ACR
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 PHE 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ALA* 3.9 23.6 - - + -
141A PHE* 4.2 20.4 - + - -
144A LEU* 3.8 55.6 - - + -
167A TRP* 1.3 112.9 + + + +
168A ALA* 3.2 6.3 - - - +
169A ARG* 3.3 33.9 + - + +
170A LEU* 2.9 37.8 + - + +
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Residues in contact with TRP 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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144A LEU* 6.2 0.4 - - + -
166A PHE* 1.3 99.9 - + + +
168A ALA* 1.3 61.1 + - - +
170A LEU* 3.6 34.2 - - + +
171A LEU* 2.9 31.2 + - - +
206A PRO* 3.7 43.6 + - + +
209A LEU* 4.2 23.1 - - + +
210A ARG* 6.3 0.6 - - - +
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Residues in contact with ALA 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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166A PHE 3.2 4.1 - - - +
167A TRP* 1.3 77.7 - - - +
169A ARG* 1.3 59.5 + - - +
171A LEU* 3.4 5.6 + - - +
172A GLU* 2.9 49.3 + - - +
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Residues in contact with ARG 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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140A ALA* 6.2 4.2 - - - +
143A ASP* 5.1 15.4 + - - +
147A GLU* 6.2 2.6 - - - +
166A PHE* 3.3 34.1 + - + +
168A ALA* 1.3 79.6 - - - +
170A LEU* 1.3 60.2 + - - +
172A GLU* 3.6 7.8 + - - +
173A ARG* 3.1 68.7 + - - +
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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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137A ASN* 4.5 21.8 - - + +
141A PHE* 5.4 9.6 - - + -
166A PHE* 2.9 28.2 + - + +
167A TRP* 3.6 37.9 - - + +
169A ARG* 1.3 75.6 - - - +
171A LEU* 1.3 51.1 + - - +
173A ARG* 2.8 10.7 + - + +
174A LEU* 2.7 63.5 + - + +
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Residues in contact with LEU 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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167A TRP 2.9 21.7 + - - +
168A ALA* 3.9 5.8 - - - +
170A LEU* 1.3 74.1 - - - +
172A GLU* 1.3 62.7 + - + +
174A LEU* 3.5 34.9 + - + +
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Residues in contact with GLU 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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168A ALA* 2.9 33.7 + - - +
169A ARG* 3.9 7.4 - - - +
171A LEU* 1.3 78.1 - - + +
173A ARG* 1.3 63.8 + - + +
174A LEU 3.6 3.1 + - - +
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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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137A ASN* 5.5 9.5 - - - +
139A ARG* 5.5 8.3 - - - +
140A ALA* 4.9 14.6 - - - +
169A ARG* 3.1 50.9 + - - +
170A LEU* 2.8 7.8 + - + +
172A GLU* 1.3 79.0 - - + +
174A LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 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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133A LEU* 5.8 9.2 - - + -
137A ASN* 5.3 6.3 - - - +
170A LEU* 2.7 47.7 + - + +
171A LEU* 3.6 39.3 - - + +
172A GLU 3.3 4.5 - - - +
173A ARG* 1.3 81.6 - - - +
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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