Contacts of the strand formed by residues 170 - 177 (chain A) in PDB entry 3HJW
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 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.9 20.8 - - + +
117A MET 3.4 2.4 - - - +
118A HIS* 2.7 37.1 + - - +
165A GLU 3.9 0.9 - - - +
166A ILE* 3.3 6.6 - - - +
167A GLU 2.8 38.6 + - - +
168A GLY 3.4 0.2 - - - -
169A ARG* 1.3 78.9 - - - +
171A VAL* 1.3 61.8 + - - +
201A SER* 5.1 1.2 + - - -
4B ARG* 2.8 33.2 + - - +
16B LEU* 4.4 7.1 - - + +
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA 3.6 1.2 - - - +
116A LEU* 3.4 4.2 - - - +
117A MET* 2.8 55.8 + - + +
119A LEU* 3.7 31.4 - - + -
128A ILE* 4.0 20.2 - - + -
132A MET* 4.0 26.7 - - + -
163A VAL* 4.2 17.5 - - + -
165A GLU 3.6 2.2 - - - -
166A ILE* 4.2 6.3 - - + -
170A ASP* 1.3 78.7 - - - +
172A LEU* 1.3 62.7 + - - +
173A PHE* 3.8 6.8 - - + -
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Residues in contact with LEU 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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114A VAL* 3.7 18.6 - - + -
115A ALA 3.3 19.3 - - - +
116A LEU* 4.0 11.8 - - + +
163A VAL* 3.7 3.1 - - - +
164A LEU* 2.8 37.4 + - + -
165A GLU* 2.8 24.5 + - + +
170A ASP 4.1 0.4 - - - -
171A VAL* 1.3 72.3 - - - +
173A PHE* 1.3 63.4 + - - +
5B ILE* 4.1 20.6 - - + -
14B TYR* 4.0 10.1 - - + +
15B THR* 3.8 40.4 - - - +
16B LEU* 4.2 10.3 - - + +
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Residues in contact with PHE 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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113A TYR 3.9 0.3 - - - +
114A VAL* 3.4 5.4 - - - +
115A ALA* 2.8 66.5 + - + -
117A MET* 3.8 24.0 - - + -
132A MET* 3.5 31.9 - - + -
161A ILE* 4.3 6.7 - - + -
162A GLU 3.2 14.4 - - - +
163A VAL* 3.8 9.4 - - + -
164A LEU* 4.2 2.7 - - - +
171A VAL* 3.8 11.7 - - + -
172A LEU* 1.3 75.3 - - - +
174A ARG* 1.3 72.5 + - - +
175A VAL* 4.0 24.5 - - + -
183A ILE* 5.1 1.6 - - + -
186A LEU* 5.1 7.0 - - + -
187A ILE* 3.7 21.3 - - + -
190A ILE* 5.0 3.6 - - + -
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Residues in contact with ARG 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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112A GLU* 2.4 43.7 + - - +
113A TYR 3.2 4.7 - - - +
114A VAL* 4.0 9.2 - - + -
160A TYR* 4.6 6.5 - - + -
161A ILE* 3.4 2.8 - - - -
162A GLU* 2.7 55.6 + - + +
164A LEU* 3.9 25.5 - - + +
173A PHE* 1.3 76.4 - - - +
175A VAL* 1.3 60.6 + - - +
206A THR* 3.6 13.9 + - - -
213A GLU* 4.8 1.8 + - - -
7B LYS* 5.6 0.2 - - - +
12B GLY 4.1 8.9 + - - -
13B ARG* 5.6 0.6 - - - +
14B TYR* 3.2 36.7 - - - +
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Residues in contact with VAL 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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111A LYS 3.9 0.3 - - - +
112A GLU* 3.2 7.8 - - - +
113A TYR* 2.8 53.8 + - + +
115A ALA* 5.5 1.6 - - + -
158A VAL* 3.9 7.0 - - + -
160A TYR* 3.3 17.7 - - - +
161A ILE* 3.7 14.1 - - + -
173A PHE* 4.0 19.5 - - + +
174A ARG* 1.3 76.2 - - - +
176A GLY* 1.3 58.5 + - - +
177A VAL* 3.7 18.6 + - + -
183A ILE* 4.3 21.1 - - + -
186A LEU* 4.2 10.3 - - + -
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Residues in contact with GLY 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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13A LEU* 4.1 2.7 - - - -
111A LYS 3.4 7.9 - - - -
158A VAL* 3.5 1.2 - - - -
159A TYR* 2.7 34.8 + - - -
160A TYR* 3.0 41.3 + - - +
175A VAL* 1.3 70.8 - - - +
177A VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 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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13A LEU* 4.3 0.2 - - - +
110A GLY* 3.3 4.0 - - - -
111A LYS* 2.7 50.3 + - + +
113A TYR* 4.0 24.0 - - + -
157A LYS 3.5 8.1 - - - +
158A VAL* 4.3 7.4 - - + -
159A TYR* 3.6 7.7 - - - -
175A VAL* 3.7 21.8 - - + -
176A GLY* 1.3 80.7 - - - +
178A GLU* 1.3 69.3 + - - +
181A THR* 3.7 31.6 - - + +
183A ILE* 4.3 9.6 - - + -
186A LEU* 5.2 1.1 - - + -
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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