Contacts of the strand formed by residues 163 - 169 (chain A) in PDB entry 2EZT
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 VAL 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.3 50.0 - - + +
97A ALA* 3.6 20.9 - - + -
98A ARG* 4.0 6.1 - - - +
104A VAL* 3.4 9.9 - - + +
106A ALA* 4.7 1.3 - - + -
133A VAL* 4.0 18.4 + - + +
134A ALA* 3.5 3.3 - - - -
135A ASP* 2.7 38.6 + - - +
136A TYR 3.4 0.7 + - - -
157A ALA* 4.8 0.7 - - - -
162A GLY* 1.3 71.9 - - - -
164A ALA* 1.3 63.9 + - - +
165A VAL* 3.6 25.1 - - + -
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Residues in contact with ALA 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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104A VAL 2.9 7.5 + - - +
105A LEU* 3.5 7.2 - - + +
106A ALA 2.9 26.2 + - - +
136A TYR* 3.3 15.9 - - + -
153A ALA* 3.2 44.6 - - + +
157A ALA* 4.0 8.5 - - + +
162A GLY 3.8 0.6 + - - -
163A VAL* 1.3 73.1 - - - +
165A VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 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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94A LEU* 4.3 2.9 - - + -
106A ALA* 3.4 11.4 - - + +
108A ILE* 3.4 33.4 - - + -
130A TYR* 3.7 22.7 - - + -
133A VAL* 4.7 0.9 - - + -
134A ALA* 3.8 14.1 - - + -
136A TYR* 2.7 12.8 + - - +
137A ASN* 3.4 11.2 + - - +
138A VAL* 3.1 23.9 + - - +
163A VAL* 3.6 21.8 - - + -
164A ALA* 1.3 78.1 - - - +
166A VAL* 1.3 64.4 + - - +
167A GLN* 3.5 15.3 - - - +
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Residues in contact with VAL 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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105A LEU* 4.4 3.8 - - + -
106A ALA 3.0 7.3 + - - -
107A LEU* 3.5 8.0 - - + -
108A ILE 2.8 30.4 + - - +
136A TYR* 4.6 0.4 - - + -
138A VAL* 3.4 13.0 - - + +
140A ALA* 4.3 7.9 - - + -
146A LEU* 4.6 0.7 - - + -
149A VAL* 3.8 28.5 - - + -
150A ILE* 3.9 21.8 - - + -
153A ALA* 3.8 28.3 - - + -
165A VAL* 1.3 78.7 - - - +
167A GLN* 1.3 63.1 + - - +
168A ILE* 3.8 18.8 - - + +
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Residues in contact with GLN 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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108A ILE* 3.4 20.0 - - + +
110A GLN* 4.8 3.8 - - + +
126A GLU* 4.0 28.0 - - + +
127A ASN* 3.0 25.1 + - - +
130A TYR* 3.8 7.9 - - + -
137A ASN* 2.7 26.9 + - - -
138A VAL 2.9 14.1 + - - +
139A THR* 2.6 34.9 + - + +
140A ALA* 2.9 28.8 + - - +
165A VAL* 3.5 20.2 - - - +
166A VAL* 1.3 71.6 - - - +
168A ILE* 1.3 58.6 + - - +
169A PRO* 3.6 3.4 - - - +
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 5.6 0.7 - - + -
36A SER 4.0 4.3 - - - +
37A ILE* 5.7 2.9 - - + -
40A ILE* 4.4 18.6 - - + -
107A LEU* 4.2 36.6 - - + -
108A ILE 2.8 14.3 + - - +
109A GLY* 4.0 0.6 - - - -
110A GLN* 3.2 19.6 + - - +
140A ALA* 4.7 1.1 - - - -
146A LEU* 4.0 18.2 - - + -
150A ILE* 4.3 11.7 - - + -
166A VAL* 3.8 18.2 - - + +
167A GLN* 1.3 76.3 - - - +
169A PRO* 1.3 79.6 - - + +
170A VAL* 3.3 1.6 + - - -
172A LEU* 4.9 1.8 - - + -
173A PRO* 3.7 25.1 - - + -
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Residues in contact with PRO 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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110A GLN* 3.5 5.3 - - + +
111A PHE 3.4 20.4 - - - +
113A THR* 3.7 14.6 - - + -
116A MET* 3.5 24.7 - - + -
139A THR* 4.3 2.9 - - + -
140A ALA 3.0 29.4 - - - +
141A VAL* 5.7 0.2 - - + -
167A GLN 3.6 6.3 - - - +
168A ILE* 1.3 84.4 - - - +
170A VAL* 1.3 64.5 + - - +
171A ASP* 3.1 16.9 + - - +
172A LEU* 3.2 21.5 + - + +
173A PRO* 3.3 8.0 - - - +
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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