Contacts of the strand formed by residues 166 - 170 (chain A) in PDB entry 5JSJ
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 3.6 43.3 - - + -
132A MET* 4.4 6.5 - - + -
133A ILE* 4.3 11.2 - - + -
155A VAL* 4.2 14.1 - - + -
157A ALA 3.4 14.8 - - - +
158A ARG* 3.9 19.1 - - - -
159A ALA 4.0 0.2 - - - +
164A THR 4.1 9.9 - - - -
165A TRP* 1.3 82.1 - - - +
167A TYR* 1.3 65.0 + - - +
168A ILE* 3.5 3.1 + - - +
178A MET* 3.1 25.9 - - - -
179A TYR 2.9 14.0 + - - +
181A LEU* 3.8 35.0 - - + -
182A LEU* 3.7 31.2 - - + -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.2 14.9 - - + +
78A ASP* 5.2 1.4 - - - +
88A LEU* 4.4 13.7 - - + +
97A VAL* 3.8 19.4 - - + +
155A VAL* 3.7 4.9 - - - +
156A LEU* 2.8 38.2 + - + -
157A ALA* 2.8 31.2 + - + +
158A ARG 4.6 2.2 - - - -
159A ALA* 3.9 20.1 - - + +
160A PRO* 3.2 30.8 - - + +
166A PHE* 1.3 73.2 - - - +
168A ILE* 1.3 57.0 + - - +
176A LEU* 3.6 22.4 - - + -
177A TYR 3.5 7.2 - - - -
178A MET* 4.3 7.0 - - + -
234A HIS* 6.1 0.9 - - - -
244A PHE* 4.1 27.8 - + - -
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Residues in contact with ILE 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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137A VAL* 3.8 22.9 - - + -
139A HIS* 4.5 5.8 - - + +
154A MET 3.1 22.9 - - - +
155A VAL* 4.0 2.5 - - + +
156A LEU* 4.1 5.9 - - - +
166A PHE 4.1 5.8 - - - +
167A TYR* 1.3 76.1 - - - +
169A THR* 1.3 65.1 + - - +
170A TYR* 3.3 39.5 - - + +
176A LEU* 4.1 0.7 - - - +
177A TYR* 2.9 36.0 + - + +
179A TYR* 4.0 16.8 - - + +
181A LEU* 4.0 23.6 - - + -
190A LEU* 5.2 0.2 - - + -
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Residues in contact with THR 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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153A GLY* 3.1 3.6 - - - -
154A MET* 2.9 44.1 + - + +
156A LEU* 4.1 9.8 - - + +
168A ILE* 1.3 75.1 - - - +
170A TYR* 1.3 74.1 + - - +
174A PRO* 3.3 9.1 - - + +
175A VAL 2.8 33.6 + - - -
255A VAL* 3.9 32.8 - - + +
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Residues in contact with TYR 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 VAL* 5.5 0.2 - - + -
139A HIS* 2.7 44.2 + - + -
151A TRP* 3.8 31.4 - + + -
152A ARG 3.4 15.5 - - - +
153A GLY* 3.9 5.2 - - - -
168A ILE* 3.3 36.7 - - + +
169A THR* 1.3 82.2 + - - +
171A GLU* 1.3 64.9 + - - +
172A LYS 4.2 1.1 - - - +
173A ASP 3.2 26.3 + - - +
174A PRO* 3.3 9.4 - - - +
177A TYR* 3.6 44.0 - + + -
179A TYR* 3.5 4.3 - - - -
301A 6PD 3.8 15.3 - - + -
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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