Contacts of the strand formed by residues 35 - 43 (chain A) in PDB entry 1JEY
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 ARG 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLY* 1.3 81.6 - - - +
36A ASP* 1.3 66.6 + - - +
80A ARG* 2.5 76.5 + - + +
81A ASP* 4.4 2.5 - - - -
82A LEU* 3.9 14.0 - - + +
110A ASN* 2.9 24.4 + - - +
159A PHE* 3.5 47.9 - - - -
160A LYS 3.9 9.0 + - - +
161A MET* 3.3 10.9 - - - +
162A SER* 3.2 17.3 + - - -
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Residues in contact with ASP 36 (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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34A GLY 4.1 2.3 + - - +
35A ARG* 1.3 76.7 + - - +
37A SER* 1.3 60.0 + - - +
81A ASP* 3.1 28.5 + - - +
82A LEU* 3.1 24.4 + - - +
162A SER* 3.0 28.2 + - - -
163A HIS* 3.2 23.5 + - + +
252A ARG* 4.0 33.4 + - - +
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Residues in contact with SER 37 (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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36A ASP* 1.3 76.8 + - - +
38A LEU* 1.3 61.2 + - - +
82A LEU* 3.7 10.9 - - - +
108A LEU* 3.9 10.8 - - - +
154A PHE* 3.4 27.4 - - - -
161A MET* 2.8 29.4 - - - +
163A HIS 2.7 14.9 + - - +
165A ARG 2.8 27.1 + - - -
252A ARG* 3.2 8.7 + - - -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 1.3 75.1 - - - +
39A ILE* 1.3 63.8 + - - +
40A PHE* 3.4 36.3 + - + -
70A VAL* 4.8 2.5 - - + -
81A ASP* 5.9 1.8 - - + +
82A LEU 3.1 10.9 + - - +
83A LEU* 3.4 17.0 - - + +
84A ALA 3.0 22.2 + - - +
108A LEU* 3.8 0.7 - - - +
165A ARG* 3.3 32.5 - - + +
167A MET* 3.9 29.6 - - + -
250A GLU* 4.3 29.2 - - - +
252A ARG* 4.5 8.5 - - - +
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Residues in contact with ILE 39 (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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38A LEU* 1.3 76.1 - - - +
40A PHE* 1.3 66.6 + - - +
41A LEU 3.7 1.0 + - - +
84A ALA* 3.8 17.7 - - + -
86A VAL* 3.9 27.4 - - + -
108A LEU* 4.3 4.0 - - + -
150A CYS* 3.2 45.5 - - + +
153A LEU* 3.8 15.3 - - + -
154A PHE* 3.6 30.3 - - + -
165A ARG 2.9 10.2 + - - +
166A ILE* 3.5 7.0 - - + +
167A MET* 2.9 27.7 + - - +
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Residues in contact with PHE 40 (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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38A LEU* 3.4 35.9 - - + -
39A ILE* 1.3 71.9 - - - +
41A LEU* 1.3 59.5 + - - +
42A VAL* 4.1 1.4 + - - +
67A ILE* 3.6 39.3 - - + -
70A VAL* 3.9 31.0 - - + -
71A TYR* 3.8 21.8 - + - -
83A LEU* 4.3 12.6 - - + -
84A ALA 2.8 27.3 + - - +
85A VAL* 3.5 3.9 - - + +
86A VAL* 2.9 28.6 + - - +
167A MET* 3.8 18.6 - - + -
169A PHE* 3.9 22.0 - + + -
246A VAL* 4.7 1.1 - - + -
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Residues in contact with LEU 41 (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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39A ILE* 3.7 0.6 + - + -
40A PHE* 1.3 71.2 - - - +
42A VAL* 1.3 62.1 + - - +
86A VAL* 3.4 29.6 - - + +
88A TYR* 3.7 14.4 - - + -
143A LEU* 5.5 1.8 - - + -
146A VAL* 3.6 34.3 - - + -
147A LEU* 4.5 12.3 - - + -
150A CYS* 3.9 15.7 - - - -
166A ILE* 4.1 18.8 - - + -
167A MET 2.8 15.3 + - - +
168A LEU* 3.5 25.5 - - + +
169A PHE* 2.8 29.7 + - - -
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Residues in contact with VAL 42 (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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40A PHE 4.7 1.1 - - - +
41A LEU* 1.3 79.8 - - - +
43A ASP* 1.3 75.8 + - - +
44A ALA 3.6 0.3 + - - -
48A MET* 4.4 4.3 - - + -
60A PHE* 3.9 14.4 - - + -
63A SER* 4.3 16.4 - - - -
64A ILE* 5.1 1.1 - - + -
67A ILE* 3.6 31.4 - - + -
85A VAL* 5.6 0.7 - - + -
86A VAL 2.8 11.3 + - - +
87A PHE* 3.3 36.6 - - + +
88A TYR* 3.1 28.9 + - - -
169A PHE* 3.9 10.1 - - + +
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Residues in contact with ASP 43 (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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42A VAL* 1.3 84.7 - - - +
44A ALA* 1.3 64.8 + - - +
45A SER* 2.9 32.1 + - - -
48A MET* 3.0 33.9 - - + +
60A PHE* 4.0 2.4 - - - -
88A TYR* 3.4 37.1 - - - +
141A TYR* 4.5 2.2 + - - -
169A PHE 3.0 21.5 + - - +
170A THR* 2.9 18.7 + - - +
171A ASN* 4.4 1.0 - - - +
172A GLU* 4.1 9.4 - - - +
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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