Contacts of the strand formed by residues 162 - 167 (chain A) in PDB entry 3O46
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 ILE 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A UNX 3.7 16.7 - - - -
153A ILE* 3.7 38.8 - - + -
154A LYS 4.0 2.2 - - - +
155A LYS* 3.7 35.7 - - + +
160A GLY 3.7 0.4 + - - -
161A ALA* 1.3 69.7 - - - +
163A ILE* 1.3 60.2 + - - +
184A GLU* 3.3 8.6 - - - +
185A LEU* 2.8 49.1 + - + +
193A VAL* 4.2 16.6 - - + +
196A LYS 5.6 3.8 - - - +
198A PRO* 4.5 15.7 - - + -
201A ILE* 4.9 9.0 - - + -
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Residues in contact with ILE 163 (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 UNX 3.9 21.1 - - - -
153A ILE* 3.3 5.3 - - - -
154A LYS* 2.9 37.0 + - + +
156A ASP* 4.7 9.2 - - + +
161A ALA* 3.6 31.9 - - + +
162A ILE* 1.3 74.9 - - - +
164A VAL* 1.3 77.0 + - - +
165A ALA* 3.3 2.2 + - + +
182A GLY* 3.7 24.0 - - - +
183A ASP 3.4 2.0 - - - +
184A GLU* 3.7 23.1 - - + +
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Residues in contact with VAL 164 (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 ALA* 4.6 4.9 - - + -
152A THR 3.5 11.4 - - - +
153A ILE* 4.3 8.1 - - + -
162A ILE 4.3 0.2 + - - -
163A ILE* 1.3 73.3 - - - +
165A ALA* 1.3 60.4 + - - +
166A ARG 4.0 5.8 - - - +
167A ILE* 3.8 27.1 - - + -
179A ILE* 3.9 28.0 - - + -
180A HIS 3.5 22.4 - - - +
181A VAL* 3.4 7.2 - - - +
182A GLY 2.9 24.6 + - - -
183A ASP* 2.8 20.4 + - + +
185A LEU* 4.2 13.2 - - + -
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Residues in contact with ALA 165 (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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13A UNX 4.5 5.4 - - - -
152A THR* 2.8 21.6 + - - +
153A ILE 4.4 1.1 - - - +
154A LYS* 4.2 27.6 - - + -
163A ILE* 3.3 2.8 + - - +
164A VAL* 1.3 73.7 - - - +
166A ARG* 1.3 62.1 + - - +
181A VAL* 3.7 16.3 - - - +
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Residues in contact with ARG 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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13A UNX 3.5 15.7 - - - -
151A ALA* 3.2 7.7 - - - +
152A THR* 3.0 39.9 + - + +
164A VAL* 3.7 1.3 - - - +
165A ALA* 1.3 81.3 - - - +
167A ILE* 1.3 73.4 + - - +
168A MSE 3.6 41.1 - - - +
169A ARG 5.4 2.2 - - - +
181A VAL* 3.8 5.6 - - - +
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Residues in contact with ILE 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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150A GLY 3.6 1.8 - - - +
151A ALA* 3.8 13.9 - - + -
164A VAL* 3.8 20.4 - - + -
166A ARG* 1.3 84.6 + - - +
168A MSE 1.3 65.6 + - - +
169A ARG 3.4 2.8 + - - -
173A ALA* 4.0 9.6 - - + -
174A ASP* 3.6 41.5 - - + +
179A ILE* 3.7 28.0 - - + +
180A HIS* 4.2 0.9 - - - -
181A VAL* 3.9 26.0 - - + +
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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