Contacts of the strand formed by residues 130 - 136 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B CYS* 3.7 7.0 - - - -
66B ALA 3.6 28.5 - - - -
67B LEU* 3.8 34.7 - - + +
89B ASP* 2.3 38.4 + - - +
113B ARG* 3.6 14.4 + - - -
116B PHE* 3.9 7.8 - - - -
123B PHE* 4.9 1.9 - - - -
125B PRO* 4.0 14.5 - - + +
126B GLU 5.1 0.9 - - - -
129B SER* 1.3 97.4 - - - +
131B ASP* 1.3 63.3 + - - +
132B VAL 3.9 6.1 - - - +
133B ILE* 3.8 18.2 - - + -
157B SER* 3.1 20.0 + - - +
158B LEU* 3.4 9.5 - - - +
159B ARG* 2.8 27.6 + - - +
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR* 3.3 3.9 - - + +
62B GLY* 3.3 41.3 + - - +
64B SER* 2.6 40.9 + - - -
65B CYS 2.8 14.5 + - - +
85B PHE* 4.1 3.1 - - + -
130B TYR* 1.3 74.7 - - - +
132B VAL* 1.3 65.6 + - - +
159B ARG* 3.6 20.6 - - - +
160B PRO 4.7 4.0 - - - +
161B ASN 6.1 0.2 - - - -
162B GLY* 3.1 8.1 - - - -
163B ILE 2.9 25.5 + - - -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.9 21.5 - - + -
61B THR* 3.8 13.9 - - + -
65B CYS 3.5 3.0 + - - -
66B ALA* 3.1 11.6 - - + +
67B LEU 2.9 23.0 + - - +
81B LEU* 5.0 1.6 - - + -
85B PHE* 3.4 32.8 - - + -
130B TYR* 3.9 1.6 - - - +
131B ASP* 1.3 86.7 - - - +
133B ILE* 1.3 75.5 + - - +
134B TRP* 4.1 25.4 - - + +
163B ILE* 3.3 14.6 - - + +
165B VAL* 4.6 1.8 - - + -
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 3.5 15.5 - - + -
69B CYS* 3.6 27.6 - - - -
130B TYR* 3.8 17.7 - - + -
132B VAL* 1.3 76.9 - - - +
134B TRP* 1.3 55.8 + - - +
135B ILE* 4.0 7.4 - - + -
154B CYS* 3.5 38.1 - - + +
157B SER* 3.3 26.9 - - - +
158B LEU* 3.6 14.8 - - + -
163B ILE 3.0 7.5 + - - -
164B ILE* 3.3 9.3 - - + +
165B VAL* 2.8 32.1 + - - +
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Residues in contact with TRP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 3.5 44.6 - - - -
48B PHE* 4.7 5.8 - + - -
49B LEU* 4.0 20.0 - - + -
67B LEU 2.8 14.3 + - - +
68B ASP* 3.8 3.8 - - - +
69B CYS* 2.8 31.5 + - - +
76B ILE* 3.8 22.3 - - + +
80B LEU* 3.7 19.7 - - + -
81B LEU* 4.3 16.4 - - + -
132B VAL* 4.0 13.8 - - + -
133B ILE* 1.3 70.3 - - - +
135B ILE* 1.3 64.8 + - - +
136B GLN* 2.9 36.2 + - + +
165B VAL* 3.6 47.1 - - + -
167B LYS* 4.4 6.9 - - + +
220B SER* 5.8 0.4 - - - -
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B CYS* 3.9 20.0 - - + -
120B LEU* 4.5 6.1 - - + -
133B ILE* 4.0 9.2 - - + +
134B TRP* 1.3 77.2 - - - +
136B GLN* 1.3 59.5 + - - +
137B TRP 4.3 0.2 + - - -
138B VAL* 3.5 23.6 - - + -
139B ILE* 3.7 19.5 - - + -
147B LEU* 5.9 0.9 - - + -
150B PHE* 3.8 17.9 - - + -
151B LEU* 3.8 20.0 - - + -
154B CYS* 4.5 0.7 - - - -
164B ILE* 3.7 24.9 - - + -
165B VAL 2.7 15.4 + - - +
166B ILE* 3.4 9.1 - - + +
167B LYS 3.0 24.1 + - - +
168B ASP* 4.7 1.4 - - - +
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP* 2.8 30.1 + - - +
42B ILE* 6.1 0.2 - - - +
45B SER* 4.0 2.4 + - - -
68B ASP* 5.7 0.2 + - - -
69B CYS 3.9 6.7 + - - -
75B ARG* 3.9 0.7 - - - -
76B ILE* 3.6 22.3 - - + +
134B TRP* 2.9 32.1 + - - +
135B ILE* 1.3 75.0 - - - +
137B TRP* 1.3 103.0 + - + +
138B VAL* 3.2 6.8 + - - +
167B LYS* 3.2 33.0 - - + +
1402B SAH 2.8 25.5 + - - -
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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