Contacts of the strand formed by residues 173 - 182 (chain A) in PDB entry 2EYR
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 PHE 173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASN* 5.6 7.0 - - + -
143A ASP* 4.5 8.3 - - + -
167A ASP* 3.7 0.9 + - - -
168A MET* 2.8 49.8 + - + +
171A MET* 3.9 23.3 - - + +
172A ASP* 1.3 74.9 - - - +
174A LYS* 1.3 68.5 + - - +
175A SER* 3.5 19.5 - - - -
143B LYS* 3.6 31.0 - - + +
198B ARG* 3.2 31.2 - - - -
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Residues in contact with LYS 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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14A GLU* 2.9 39.0 + - - +
81A GLN* 5.0 7.1 - - - +
82A LEU* 3.6 25.1 - - + -
116A PRO* 4.1 16.2 - - + -
118A ILE* 4.4 15.2 - - + +
165A VAL* 4.6 1.8 - - + -
166A LEU 3.3 9.0 - - - +
167A ASP* 3.6 29.6 - - - +
172A ASP* 4.3 15.0 + - - +
173A PHE* 1.3 91.6 - - - +
175A SER* 1.3 64.0 + - - +
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 5.1 5.4 - - - -
142A THR* 4.6 0.9 + - - -
143A ASP* 3.6 15.0 - - - +
164A CYS 3.5 1.2 - - - +
165A VAL* 3.5 4.6 - - - +
166A LEU* 2.8 56.9 + - - +
173A PHE* 3.5 8.5 - - - -
174A LYS* 1.3 75.6 - - - +
176A ASN* 1.3 63.0 + - - +
198B ARG* 3.1 30.3 + - - -
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Residues in contact with ASN 176 (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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116A PRO* 4.7 0.2 - - - -
118A ILE* 3.4 12.8 - - - +
142A THR* 3.0 7.3 + - - -
143A ASP* 3.0 25.6 + - - +
144A PHE* 3.2 47.3 + - + +
145A ASP 3.6 1.2 + - - -
146A SER* 3.0 32.0 + - - +
163A LYS* 3.8 13.2 - - + +
164A CYS 3.4 5.2 - - - +
165A VAL* 3.1 27.1 - - - +
175A SER* 1.3 75.1 - - - +
177A SER* 1.3 60.4 + - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 3.7 13.6 - - - +
141A PHE 3.0 14.1 - - - -
142A THR* 3.6 10.8 - - - -
144A PHE* 3.9 3.4 - - - -
163A LYS* 3.3 4.9 - - - -
164A CYS 2.8 31.3 + - - -
166A LEU* 5.5 4.5 - - - +
176A ASN* 1.3 78.8 - - - +
178A ALA* 1.3 59.8 + - - +
145B THR* 5.7 1.7 - - - +
196B ARG* 2.9 38.7 + - - +
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Residues in contact with ALA 178 (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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140A LEU* 3.7 3.9 - - - +
141A PHE* 2.7 38.1 + - + +
144A PHE* 4.3 0.2 - - - -
150A VAL* 3.7 33.7 - - + -
161A THR 3.2 20.0 - - - +
162A ASP 4.1 2.0 - - - -
177A SER* 1.3 75.6 - - - +
179A VAL* 1.3 63.0 + - - +
193A PHE* 3.6 14.4 - - + -
196B ARG* 4.1 1.6 - - - +
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Residues in contact with VAL 179 (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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138A VAL* 3.8 24.2 - - + -
139A CYS 3.7 2.5 - - - -
140A LEU* 4.3 4.3 - - + -
159A TYR 3.8 0.3 - - - +
160A ILE* 3.3 4.2 - - - +
161A THR* 2.8 40.7 + - - +
178A ALA* 1.3 74.8 - - - +
180A ALA* 1.3 63.6 + - - +
181A TRP* 3.6 18.6 - - + -
193A PHE* 4.3 0.9 - - - -
147B VAL* 4.1 25.6 - - + -
149B LEU* 4.2 1.8 - - + -
194B SER* 3.1 28.3 - - - +
196B ARG* 3.5 23.1 - - + +
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Residues in contact with ALA 180 (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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137A SER 3.6 0.5 - - - +
138A VAL* 3.4 3.8 - - - +
139A CYS* 2.8 37.8 + - + +
158A VAL* 5.1 0.2 - - + -
159A TYR 3.1 8.5 - - - +
160A ILE* 3.9 15.0 - - + -
179A VAL* 1.3 75.1 - - - +
181A TRP* 1.3 61.9 + - - +
187A PHE* 3.8 19.2 - - + -
192A ALA* 4.4 4.5 - - + -
193A PHE* 3.6 25.4 - - + -
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Residues in contact with TRP 181 (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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136A LYS* 3.6 28.0 - - + +
137A SER 3.2 13.5 - - - +
138A VAL* 3.9 13.7 - - + -
158A VAL* 3.7 0.6 - - - -
159A TYR* 2.9 71.3 + + + -
161A THR* 3.5 33.2 - - + -
179A VAL* 3.6 25.1 - - + -
180A ALA* 1.3 74.8 - - - +
182A SER* 1.3 62.4 + - - +
187A PHE* 4.1 4.6 - - - -
149B LEU* 3.6 21.6 - - + +
151B THR* 4.2 12.1 - - + +
180B LEU* 4.0 9.4 - - + -
182B GLU* 5.5 0.4 + - - -
192B ALA* 3.7 27.3 - - + +
193B LEU 5.0 0.4 - - - -
194B SER* 4.1 13.0 - - - -
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Residues in contact with SER 182 (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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135A ASP 4.4 0.2 - - - +
136A LYS* 3.6 6.5 - - - -
137A SER* 3.0 32.9 + - - +
157A ASP 2.7 24.9 + - - -
158A VAL* 3.7 5.1 - - - +
159A TYR* 5.3 1.1 - - - -
181A TRP* 1.3 78.6 - - - +
183A ASN* 1.3 64.6 + - - +
184A LYS* 3.1 22.0 - - - +
187A PHE* 3.6 31.5 - - - -
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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