Contacts of the strand formed by residues 130 - 136 (chain A) in PDB entry 2EX4
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A CYS* 3.6 26.5 - - - -
66A ALA 3.8 11.9 - - - -
67A LEU* 3.8 36.9 - - + +
89A ASP* 2.6 36.8 + - - +
113A ARG* 3.9 6.6 + - - -
116A PHE* 3.9 9.5 - - - -
123A PHE* 4.9 1.9 - - - -
125A PRO* 3.9 8.5 - - + +
126A GLU* 4.7 3.8 + - - +
129A SER* 1.3 88.6 - - - +
131A ASP* 1.3 63.7 + - - +
132A VAL 4.0 5.8 - - - +
133A ILE* 3.8 22.0 - - + -
157A SER* 3.0 32.9 + - - +
158A LEU* 3.4 9.2 - - - +
159A ARG* 2.8 26.8 + - - +
162A GLY* 4.3 0.2 - - - -
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Residues in contact with ASP 131 (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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61A THR* 3.4 3.4 - - + +
62A GLY* 3.1 42.9 + - - +
64A SER* 2.9 25.7 + - - -
65A CYS 2.8 20.0 + - - +
85A PHE* 4.1 3.4 - - + -
129A SER 4.4 0.2 + - - -
130A TYR* 1.3 73.2 - - - +
132A VAL* 1.3 65.1 + - - +
158A LEU* 4.6 0.2 - - - -
159A ARG* 3.2 30.4 + - - +
160A PRO 4.7 3.1 - - - +
162A GLY* 3.0 8.9 - - - -
163A ILE 2.9 25.3 + - - -
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Residues in contact with VAL 132 (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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49A LEU* 3.9 22.7 - - + -
61A THR* 3.8 13.2 - - + -
65A CYS 3.5 2.6 + - - -
66A ALA* 3.1 7.5 - - + +
67A LEU 2.8 25.1 + - - +
81A LEU* 4.7 5.8 - - + -
85A PHE* 3.4 33.2 - - + -
130A TYR* 4.0 1.3 - - - +
131A ASP* 1.3 86.7 - - - +
133A ILE* 1.3 71.3 + - - +
134A TRP* 4.1 27.6 - - + +
163A ILE* 3.3 14.6 - - + +
165A VAL* 4.9 1.3 - - + -
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Residues in contact with ILE 133 (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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67A LEU* 3.4 10.5 - - + -
69A CYS* 3.7 26.5 - - - -
130A TYR* 3.8 22.2 - - + -
132A VAL* 1.3 78.9 - - - +
134A TRP* 1.3 55.7 + - - +
135A ILE* 4.2 7.2 - - + -
154A CYS* 3.4 52.9 - - + +
157A SER* 4.0 13.0 - - - -
158A LEU* 3.8 15.9 - - + -
163A ILE 3.0 7.1 + - - -
164A ILE* 3.3 10.0 - - + +
165A VAL* 2.8 32.4 + - - +
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Residues in contact with TRP 134 (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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45A SER* 3.5 40.6 - - - -
48A PHE* 4.8 5.4 - + - -
49A LEU* 4.1 18.8 - - + -
67A LEU 2.8 14.5 + - - +
68A ASP* 3.9 3.7 - - - +
69A CYS* 2.9 29.8 + - - +
76A ILE* 3.8 21.3 - - + +
80A LEU* 3.6 23.8 - - + -
81A LEU* 4.3 17.5 - - + -
132A VAL* 4.0 13.4 - - + -
133A ILE* 1.3 73.6 - - - +
135A ILE* 1.3 63.5 + - - +
136A GLN* 2.9 35.9 + - + +
165A VAL* 3.6 46.7 - - + -
167A LYS* 4.4 7.1 - - + +
220A SER* 5.9 0.4 - - - -
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Residues in contact with ILE 135 (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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69A CYS* 3.9 20.2 - - + -
120A LEU* 4.5 6.3 - - + -
133A ILE* 4.2 8.5 - - + +
134A TRP* 1.3 78.2 - - - +
136A GLN* 1.3 59.2 + - - +
138A VAL* 3.5 23.6 - - + -
139A ILE* 3.7 20.7 - - + +
147A LEU* 6.1 0.4 - - + -
150A PHE* 3.9 21.5 - - + -
151A LEU* 3.9 16.4 - - + -
154A CYS* 4.5 0.9 - - - -
164A ILE* 3.7 25.4 - - + -
165A VAL 2.7 13.9 + - - +
166A ILE* 3.3 11.0 - - + +
167A LYS 2.9 24.0 + - - +
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Residues in contact with GLN 136 (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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41A ASP* 2.8 29.3 + - - +
42A ILE* 6.1 0.2 - - - +
45A SER* 4.1 2.9 + - - -
68A ASP* 5.7 0.2 + - - -
69A CYS 4.0 5.9 + - - -
75A ARG* 3.9 1.6 - - - -
76A ILE* 3.6 23.0 - - + +
134A TRP* 2.9 32.7 + - - +
135A ILE* 1.3 74.2 - - - +
137A TRP* 1.3 103.9 + - + +
138A VAL* 3.2 7.2 + - - +
167A LYS* 3.2 30.8 - - + +
1401A SAH 2.9 25.0 + - - +
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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