Contacts of the strand formed by residues 161 - 168 (chain A) in PDB entry 2EA3
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 GLY 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A CYS* 4.7 4.9 - - - -
156A GLY* 3.5 5.0 - - - -
157A ASN 2.9 28.9 + - - +
158A CYS* 4.3 1.9 - - - -
159A ARG 3.6 1.6 - - - +
160A THR* 1.3 84.9 + - - +
162A GLY* 1.3 58.5 + - - -
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Residues in contact with GLY 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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129A THR* 3.5 25.1 + - - +
130A VAL 4.1 4.7 - - - -
131A CYS* 4.3 8.1 - - - +
155A SER* 3.2 15.5 - - - -
156A GLY* 4.0 2.2 - - - -
157A ASN 3.8 2.3 + - - -
161A GLY* 1.3 75.0 - - - -
163A THR* 1.3 64.5 + - - -
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Residues in contact with THR 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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127A ARG* 3.7 42.4 + - + +
128A THR 3.4 17.9 + - - +
129A THR* 5.6 0.3 - - - -
154A GLY* 3.2 3.9 - - - -
155A SER* 2.9 44.5 + - - +
162A GLY* 1.3 73.8 + - - -
164A THR* 1.3 64.8 + - - +
165A PHE* 3.8 17.7 - - + -
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Residues in contact with THR 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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128A THR* 2.9 37.7 + - - -
130A VAL 2.6 24.8 + - - -
131A CYS* 3.4 0.7 - - - -
132A ALA* 3.3 27.4 + - + +
151A THR* 3.8 17.7 - - + -
153A GLY 3.4 12.7 - - - +
154A GLY* 5.3 0.3 - - - -
155A SER 5.1 0.9 + - - -
163A THR* 1.3 74.9 + - - +
165A PHE* 1.3 71.3 + - - +
166A PHE* 3.6 31.0 - - + -
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Residues in contact with PHE 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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113A SER* 3.8 20.0 - - - -
114A SER 4.7 2.2 - - - -
115A VAL* 3.5 33.2 - - + -
117A TYR* 4.7 2.9 - - - +
125A LEU* 3.8 20.0 - - + -
126A ILE 3.1 5.4 - - - +
127A ARG* 3.4 55.9 - - + -
152A SER* 2.9 24.0 + - - -
153A GLY 2.7 24.7 + - - +
154A GLY* 4.0 13.0 - - - -
155A SER* 5.5 0.9 - - - -
163A THR* 3.8 14.4 - - + -
164A THR* 1.3 76.0 - - - +
166A PHE* 1.3 66.4 - - - +
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Residues in contact with PHE 166 (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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96A ARG* 3.9 15.7 - - + -
125A LEU* 3.4 9.2 - - - -
126A ILE* 2.7 45.4 + - + +
128A THR* 3.3 42.6 - - + -
130A VAL* 4.4 3.6 - - + -
141A LEU* 3.6 48.0 - - + -
149A GLY* 4.5 0.2 - - - -
150A VAL 3.3 11.9 - - - +
151A THR* 3.1 44.6 - - - -
152A SER 4.1 0.4 - - - +
164A THR* 3.6 23.8 - - + -
165A PHE* 1.3 75.5 - - - +
167A GLN* 1.3 61.6 + - - +
168A PRO* 3.4 1.2 - - - +
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Residues in contact with GLN 167 (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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55A ASN* 3.7 9.6 + - - +
56A ASP* 2.9 51.2 + - + +
57A TYR* 3.7 20.9 - - + -
123A ARG 5.0 2.7 - - - +
124A GLY 5.6 0.2 - - - -
125A LEU* 3.7 13.5 - - + +
149A GLY* 3.0 1.1 - - - -
150A VAL* 2.9 37.6 + - + +
152A SER* 4.3 2.3 - - - -
166A PHE* 1.3 70.1 - - - +
168A PRO* 1.3 100.9 + - - +
171A PRO* 4.1 14.5 - - - +
172A ILE* 3.8 15.2 - - + +
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Residues in contact with PRO 168 (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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124A GLY 3.2 28.3 - - - +
126A ILE* 4.0 17.3 - - + -
148A GLN 3.4 11.2 - - - +
166A PHE 3.4 7.8 - - - +
167A GLN* 1.3 112.1 + - - +
169A VAL* 1.3 63.9 + - - +
170A ASN* 4.5 1.1 - - + +
171A PRO* 3.5 20.3 - - + +
172A ILE* 3.5 5.9 - - - +
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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