Contacts of the strand formed by residues 166 - 171 (chain A) in PDB entry 1E0W
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 LYS 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL* 3.0 25.3 + - + +
122A GLN* 3.2 9.2 - - + +
123A TRP 2.9 26.0 + - - +
164A SER 3.9 2.2 + - - +
165A ALA* 1.3 72.4 - - - +
167A LEU* 1.3 61.2 + - - +
168A CYS 3.8 0.2 + - - -
200A ASP* 3.5 15.9 - - + +
201A CYS* 4.0 14.6 - - - -
231A ASP* 2.7 30.5 + - - +
261A LEU* 4.1 25.2 - - + +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET* 4.4 8.3 - - + -
123A TRP* 3.9 4.7 - - + -
125A VAL* 3.9 20.2 - - + -
155A PHE* 3.8 25.8 - - + +
158A ALA* 4.0 13.9 - - + +
159A ARG* 3.6 47.8 - - + +
162A ASP 5.1 1.1 - - - +
165A ALA* 4.0 18.2 - - + +
166A LYS* 1.3 76.7 - - - +
168A CYS* 1.3 60.2 + - - +
198A PRO 4.6 4.7 - - - +
199A ILE* 3.9 3.6 - - - +
200A ASP* 2.9 44.9 + - - +
201A CYS* 3.1 7.1 + - - +
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Residues in contact with CYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.7 21.1 - - - +
122A GLN* 3.7 13.7 - - - -
123A TRP 2.8 18.3 + - - +
124A ASP* 3.7 14.1 - - - +
125A VAL* 2.9 26.0 + - - +
126A VAL 3.9 0.9 + - - +
155A PHE* 3.6 9.4 - - - -
167A LEU* 1.3 72.0 - - - +
169A TYR* 1.3 63.9 + - - +
201A CYS* 2.1 49.6 - - - +
202A VAL 4.9 0.7 - - - -
203A GLY* 4.6 6.3 - - - +
233A ALA* 5.7 2.0 - - - -
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Residues in contact with TYR 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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126A VAL* 3.7 39.9 - - + -
129A ALA* 2.9 23.2 + - + +
130A PHE* 3.4 17.1 - + - -
151A ILE* 4.8 2.5 - - + -
155A PHE* 3.7 10.8 - + + -
168A CYS* 1.3 72.0 - - - +
170A ASN* 1.3 58.1 + - - +
171A ASP* 2.6 33.6 + - + -
185A MET* 3.6 39.5 - - + -
188A MET* 3.9 18.2 - - + -
189A VAL* 5.7 0.2 - - + -
199A ILE* 3.9 22.0 - - + -
201A CYS 3.1 7.0 + - - +
202A VAL* 3.5 7.3 - - + +
203A GLY 2.8 29.2 + - - +
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Residues in contact with ASN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A HIS* 4.1 0.6 - - - -
124A ASP* 3.8 33.0 + - + +
126A VAL 3.1 10.0 + - - +
127A ASN* 2.9 25.5 + - - +
128A GLU 2.9 24.4 + - - -
169A TYR* 1.3 76.3 - - - +
171A ASP* 1.3 62.6 + - - +
203A GLY* 3.4 15.8 - - - +
205A GLN* 3.5 10.1 - - - +
235A THR* 2.8 26.5 + - - +
236A GLU* 3.3 23.8 + - - -
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 3.5 17.5 - - - +
130A PHE* 3.5 23.0 + - - +
169A TYR* 2.6 34.5 + - + -
170A ASN* 1.3 74.8 - - - +
172A TYR* 1.3 77.0 + - - +
174A VAL* 3.6 21.5 - - + +
181A LYS* 3.4 21.6 + - - -
185A MET* 4.5 0.9 - - - -
203A GLY 3.2 9.1 + - - +
205A GLN* 2.9 34.4 + - - +
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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