Contacts of the strand formed by residues 160 - 167 (chain A) in PDB entry 5J6Y
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 TYR 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLY* 4.1 0.3 - - - -
56A ARG* 3.2 6.3 - - - +
57A GLY* 3.0 48.0 + - - -
58A SER 2.7 40.7 + - - -
60A ASP 3.4 1.6 - - - -
61A VAL* 3.4 31.6 - - + -
66A HIS* 3.2 27.8 - - + +
69A GLU* 4.5 4.9 + - + +
70A PHE* 3.6 32.8 - + + -
110A ASP* 3.3 7.8 - - - +
153A TRP* 3.7 22.7 - - + -
155A ASP* 3.8 5.4 - - - -
158A GLY 3.3 11.0 - - - -
159A ASP* 1.3 76.1 - - - +
161A VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 161 (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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54A TYR 3.4 16.4 - - - +
55A GLY 4.1 0.9 - - - +
56A ARG* 3.9 26.7 - - + +
70A PHE* 4.0 5.3 - - - -
108A THR* 4.3 10.3 - - + -
109A ALA* 3.2 11.9 - - - +
110A ASP* 3.0 41.1 + - + +
131A VAL* 3.8 23.8 - - + -
153A TRP* 3.2 9.7 + - - -
160A TYR* 1.3 77.1 - - - +
162A PHE* 1.3 66.3 + - - +
163A GLN* 5.0 4.3 - - + +
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Residues in contact with PHE 162 (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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52A ILE* 4.1 4.7 - - + -
53A SER* 3.7 2.4 + - - -
54A TYR* 2.8 49.8 + + + +
70A PHE* 3.9 10.9 - - + -
90A ILE* 4.4 8.5 - - + -
92A LEU* 4.9 0.4 - - + -
107A VAL* 3.9 16.4 - - + -
108A THR 3.4 2.2 - - - -
109A ALA* 4.2 8.1 - - + -
113A TYR* 3.7 25.4 - + + -
115A ILE* 4.6 3.6 - - + -
151A MET* 3.8 27.6 - - + -
152A ILE 4.6 0.7 - - - -
153A TRP* 3.5 40.6 - + + +
161A VAL* 1.3 76.8 - - - +
163A GLN* 1.3 63.5 + - - +
164A PRO* 3.5 28.3 - - + +
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Residues in contact with GLN 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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52A ILE 4.2 2.0 - - - +
53A SER* 2.9 32.5 + - - +
54A TYR 4.9 1.3 - - - +
106A LYS 3.7 1.4 - - - +
107A VAL* 3.5 2.8 - - - -
108A THR* 2.9 47.7 + - - +
161A VAL* 5.3 4.5 - - + -
162A PHE* 1.3 75.3 - - - +
164A PRO* 1.3 60.9 - - - +
165A THR* 3.5 30.2 + - + +
176A VAL* 4.4 9.6 - - + +
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Residues in contact with PRO 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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52A ILE* 3.4 23.9 - - + +
105A PHE* 4.0 9.6 - - + -
107A VAL* 3.8 18.8 - - + -
115A ILE* 3.5 27.1 - - + -
151A MET* 3.9 15.0 - - + -
162A PHE* 3.5 30.5 - - + -
163A GLN* 1.3 85.9 - - - +
165A THR* 1.3 62.9 + - - +
175A PHE 4.5 1.2 - - - +
176A VAL* 4.9 0.8 - - - -
177A LEU* 4.5 13.9 + - - +
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Residues in contact with THR 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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105A PHE* 3.2 8.4 - - - -
106A LYS* 2.8 49.9 + - - +
163A GLN* 3.5 35.4 - - + +
164A PRO* 1.3 75.1 - - - +
166A LEU* 1.3 61.1 + - - +
174A TYR* 3.3 28.1 - - + +
175A PHE 3.3 14.4 - - - +
176A VAL* 4.3 9.6 - - + -
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Residues in contact with LEU 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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96A VAL* 5.6 0.4 - - + -
98A LEU* 3.9 34.5 - - + -
103A TYR* 3.9 24.2 - - + -
104A ASN 3.4 23.8 - - - +
105A PHE* 3.8 33.4 - - + -
117A ILE* 5.6 0.2 - - + -
139A PHE* 4.1 2.5 - - + -
165A THR* 1.3 75.1 - - - +
167A SER* 1.3 61.3 + - - +
174A TYR* 3.2 4.1 - - - -
175A PHE* 2.8 60.3 + - + +
177A LEU* 4.2 13.9 - - + -
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Residues in contact with SER 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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103A TYR* 3.1 12.7 - - - +
104A ASN* 2.9 34.7 + - - +
166A LEU* 1.3 74.1 - - - +
168A ALA* 1.3 58.5 + - - +
169A ASP* 2.8 17.3 + - - -
170A GLY 5.1 0.5 + - - -
171A GLY 2.8 21.4 + - - -
173A THR 2.8 22.6 + - - -
174A TYR* 3.5 21.7 - - - -
175A PHE* 4.6 0.7 - - - -
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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