Contacts of the strand formed by residues 226 - 235 (chain A) in PDB entry 2EJU
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 TYR 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ARG 5.5 3.4 - - - -
32A MET* 3.8 29.6 - - + -
34A LEU* 4.8 6.1 - - - +
35A ASN* 3.2 46.9 + - + +
163A THR* 4.2 8.3 - - + -
164A ALA 3.4 12.1 - - - +
165A THR* 4.2 11.0 - - + -
221A TYR* 3.7 19.6 + + - -
222A TYR* 3.5 5.8 - - - -
223A LYS* 2.8 59.9 + - + +
224A ASP* 4.0 11.2 - - + +
225A HIS* 1.3 77.8 - - - +
227A PHE* 1.3 73.0 + - - +
228A ARG* 4.0 11.0 - - + -
308A LEU* 5.6 0.2 - - - +
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Residues in contact with PHE 227 (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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162A VAL 3.7 0.3 - - - +
163A THR* 3.2 7.6 - - - +
164A ALA* 2.8 44.7 + - + +
167A GLY* 3.6 26.5 - - - -
170A LEU* 3.8 24.0 - - + -
171A CYS* 4.3 17.5 - - - -
193A HIS 3.4 21.3 - - - -
196A GLY* 3.8 8.5 - - - -
197A THR* 3.3 33.4 - - - +
200A LEU* 3.9 19.0 - - + +
221A TYR 3.8 3.4 - - - +
222A TYR* 3.7 27.8 - + - -
225A HIS 4.8 0.4 - - - -
226A TYR* 1.3 79.7 - - - +
228A ARG* 1.3 60.3 + - - +
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Residues in contact with ARG 228 (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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35A ASN* 3.4 29.6 + - - +
39A VAL* 3.8 7.1 - - - +
61A ARG* 3.1 12.3 - - - +
136A ASP* 2.7 43.0 + - - -
161A GLY 3.3 22.2 + - - -
162A VAL* 3.3 7.7 - - - +
163A THR* 3.0 21.8 + - - +
197A THR* 4.5 2.3 - - - +
200A LEU* 4.5 1.6 - - - -
219A LEU 4.7 0.4 - - - -
220A ALA* 3.1 4.3 - - - +
221A TYR* 2.9 67.1 + - + +
226A TYR* 4.0 4.7 - - + -
227A PHE* 1.3 72.9 - - - +
229A ALA* 1.3 65.2 + - - +
230A PHE* 3.3 32.7 - - - -
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Residues in contact with ALA 229 (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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160A LEU 3.4 2.8 - - - +
161A GLY* 3.5 0.6 - - - -
162A VAL* 2.8 40.0 + - - +
197A THR* 5.8 0.2 - - + -
200A LEU* 4.0 17.5 - - + -
201A VAL* 4.1 25.1 - - + -
204A ILE* 4.3 15.1 - - + +
219A LEU 3.5 4.7 - - - -
220A ALA* 4.0 1.6 - - + +
228A ARG* 1.3 77.9 - - - +
230A PHE* 1.3 63.3 + - - +
231A VAL* 4.1 4.4 - - + +
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Residues in contact with PHE 230 (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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38A ILE* 4.3 4.7 - - + -
39A VAL* 4.0 30.1 - - + -
42A LEU* 3.4 32.5 - - + -
134A PHE* 4.4 8.1 - + - -
159A ILE* 5.1 1.1 - - + -
160A LEU 3.2 5.2 - - - +
161A GLY* 3.9 15.3 - - - -
217A VAL* 3.8 1.6 - - - +
218A ILE* 2.9 33.9 + - + -
219A LEU* 2.6 46.3 + - + +
220A ALA* 4.9 0.2 - - - +
221A TYR* 4.1 18.4 - + - -
228A ARG* 3.3 44.9 - - - -
229A ALA* 1.3 74.1 - - - +
231A VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 231 (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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159A ILE* 3.3 5.9 - - - +
160A LEU* 2.9 54.6 + - + +
201A VAL* 4.9 4.0 - - + -
204A ILE* 4.1 32.8 - - + -
215A ILE* 4.1 32.5 - - + -
216A ASP 3.5 9.4 - - - +
217A VAL* 4.4 11.2 - - + -
218A ILE* 3.8 4.7 - - - -
229A ALA* 4.8 3.6 - - + -
230A PHE* 1.3 82.4 - - - +
232A LYS* 1.3 61.3 + - - +
233A LEU* 4.0 6.2 + - + -
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Residues in contact with LYS 232 (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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46A LEU* 5.7 2.8 - - + +
157A ARG* 2.7 36.5 + - - +
158A GLY 3.8 4.5 - - - +
159A ILE* 4.1 19.1 - - + +
215A ILE* 3.3 4.6 - - - -
216A ASP* 2.9 40.8 + - + +
218A ILE* 3.8 16.1 - - + +
231A VAL* 1.3 72.1 - - - +
233A LEU* 1.3 69.2 + - - +
234A LYS* 3.6 10.8 + - + +
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Residues in contact with LEU 233 (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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151A LEU* 4.0 30.7 - - + +
154A ALA* 4.0 17.5 - - + -
155A LYS 3.5 19.7 - - - +
156A ARG 3.6 13.0 - - - +
157A ARG* 3.3 20.4 - - - +
158A GLY 2.9 21.3 + - - +
160A LEU* 5.3 6.7 - - + -
208A ALA* 4.7 1.3 - - + -
213A LEU* 4.3 21.1 - - + -
214A GLY 3.5 3.6 - - - +
215A ILE* 3.9 22.4 - - + -
231A VAL* 4.7 11.2 - - + +
232A LYS* 1.3 78.5 - - - +
234A LYS* 1.3 63.8 + - - +
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Residues in contact with LYS 234 (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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156A ARG 3.8 2.7 - - - -
157A ARG* 5.5 0.4 - - - -
213A LEU* 3.1 9.4 - - - +
214A GLY* 2.8 52.8 + - - +
215A ILE* 3.8 8.1 - - - +
216A ASP* 2.7 37.0 + - + +
232A LYS* 3.8 15.5 - - + +
233A LEU* 1.3 80.1 - - - +
235A ASP* 1.3 62.0 + - - +
236A GLY 3.5 0.3 + - - -
239A LYS* 3.8 30.6 - - + +
243A THR* 5.4 0.7 - - - +
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Residues in contact with ASP 235 (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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156A ARG* 2.9 58.1 + - - +
157A ARG* 4.0 28.2 + - + +
213A LEU* 4.0 4.7 - - - -
233A LEU 4.2 0.4 + - - -
234A LYS* 1.3 70.0 - - - +
236A GLY* 1.3 61.6 + - - +
238A ARG* 3.7 2.6 + - - -
239A LYS* 3.2 26.6 + - - +
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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