Contacts of the strand formed by residues 169 - 174 (chain A) in PDB entry 1EAK
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 ILE 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A TRP* 4.2 8.1 - - + +
124A ILE* 4.0 22.2 - - + -
125A THR 2.8 9.1 + - - +
126A TYR* 2.9 15.6 - - + +
127A ARG 2.9 24.6 + - - -
148A PHE* 3.6 38.8 - - + -
159A PHE* 4.2 6.1 - - + -
167A ALA* 3.9 1.1 - - - +
168A ASP* 1.3 75.8 - - - +
170A MET* 1.3 59.2 + - - +
171A ILE* 3.7 10.9 + - + -
203A GLY 3.5 23.6 - - - +
205A SER* 3.7 14.6 - - - +
405A PHE* 4.5 0.2 - - + -
408A ALA* 3.9 18.6 - - + -
409A MET* 4.3 6.5 - - - -
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Residues in contact with MET 170 (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* 3.8 9.9 - - - +
129A ILE* 3.4 38.1 - - + -
165A GLY 4.2 4.9 - - - +
166A GLU* 3.3 39.0 - - - +
167A ALA* 3.2 37.9 - - - +
169A ILE* 1.3 70.8 - - - +
171A ILE* 1.3 63.7 + - - +
172A ASN* 3.9 1.0 + - - +
204A ASP* 3.2 31.1 + - - +
205A SER 3.5 17.4 + - - +
206A HIS* 4.3 3.8 + - - -
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 3.7 27.4 - - + -
127A ARG 2.8 12.8 + - - +
128A ILE* 3.9 10.1 - - + -
129A ILE* 2.6 36.7 + - - +
130A GLY 5.1 0.4 - - - -
144A PHE* 3.5 41.7 - - + -
148A PHE* 4.0 3.6 - - + -
169A ILE* 4.2 15.3 - - + +
170A MET* 1.3 72.1 - - - +
172A ASN* 1.3 63.5 + - - +
173A PHE* 5.0 0.7 - - + -
205A SER* 3.5 4.9 - - - -
207A PHE* 3.6 18.6 - - + -
405A PHE* 3.5 27.8 - - + -
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Residues in contact with ASN 172 (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 ILE* 3.6 22.5 - - + +
130A GLY* 3.3 27.0 - - - +
170A MET 4.8 0.9 - - - +
171A ILE* 1.3 80.6 - - - +
173A PHE* 1.3 98.0 + - - +
205A SER 3.2 5.1 + - - +
206A HIS* 3.3 20.6 - - + +
207A PHE* 3.0 25.8 + - - -
753P ALA* 4.4 1.8 + - - -
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Residues in contact with PHE 173 (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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130A GLY 3.5 22.4 - - - -
131A TYR* 3.5 25.4 - - - +
132A THR* 3.6 30.5 - - + -
140A VAL* 4.3 2.5 - - + -
144A PHE* 3.5 34.1 - + - -
171A ILE* 5.0 0.7 - - + -
172A ASN* 1.3 99.9 + - - +
174A GLY* 1.3 58.8 + - - +
207A PHE* 3.3 22.2 - + + -
209A ASP* 4.1 14.3 - - + +
213A TRP* 3.8 28.3 - + - -
397A LEU* 4.0 16.8 - - + -
298C GLN* 5.2 2.8 - - - +
753P ALA* 4.1 5.5 - - - +
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Residues in contact with GLY 174 (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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172A ASN 4.3 0.4 + - - -
173A PHE* 1.3 75.2 - - - +
175A ARG* 1.3 58.2 + - - -
178A HIS* 4.1 18.8 - - - -
184A PHE* 3.3 8.1 - - - -
206A HIS* 5.8 1.4 - - - +
207A PHE 2.9 7.3 + - - +
208A ASP* 3.1 9.0 - - - -
209A ASP* 2.4 36.6 + - - +
298C GLN* 3.7 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