Contacts of the strand formed by residues 234 - 241 (chain A) in PDB entry 1EUT
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A PHE* 3.5 31.9 - + - -
156A ALA* 6.1 3.8 - - + -
200A ARG* 5.7 0.2 - - - -
226A THR* 4.4 5.6 - - + -
227A ILE 3.2 8.1 - - - +
228A ILE* 4.0 21.8 - - + -
232A GLY 3.7 14.4 - - - -
233A ALA* 1.3 78.5 - - - +
235A GLN* 1.3 63.2 + - - +
256A VAL* 3.6 2.4 - - - -
257A GLY* 3.2 23.6 + - - +
258A MET* 3.3 29.7 + - - +
259A ASP* 4.8 7.0 - - - -
278A SER* 4.3 15.7 - - - +
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Residues in contact with GLN 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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199A TRP* 4.6 3.6 - - - -
226A THR* 3.1 29.8 + - - +
227A ILE* 3.1 28.4 + - + +
229A ASN* 2.9 35.8 + - - +
233A ALA* 4.4 3.8 - - + +
234A PHE* 1.3 78.4 - - - +
236A ALA* 1.3 61.1 + - - +
253A ALA* 4.0 16.7 + - + +
254A VAL* 3.6 22.2 - - - +
255A GLY 2.7 26.9 + - - +
256A VAL* 4.9 0.7 - - - -
258A MET* 3.8 6.1 - - - -
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Residues in contact with ALA 236 (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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225A TYR 3.5 5.8 - - - -
235A GLN* 1.3 76.1 - - - +
237A VAL* 1.3 61.1 + - - +
253A ALA* 3.2 3.4 - - - -
254A VAL* 2.8 48.9 + - + +
258A MET* 3.8 21.9 - - + +
261A ASN* 3.8 26.0 - - + +
273A LEU* 4.3 6.5 - - + -
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Residues in contact with VAL 237 (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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193A ILE 5.8 0.9 - - - +
199A TRP* 4.9 7.0 - - + +
224A GLN* 3.8 5.4 - - - +
225A TYR* 2.9 45.8 + - + +
227A ILE* 3.5 31.6 - - + -
236A ALA* 1.3 75.5 - - - +
238A SER* 1.3 68.9 + - - +
239A VAL* 4.8 6.3 - - + -
250A ALA* 4.2 9.2 - - + -
251A GLY 3.3 31.2 - - - +
252A GLU 4.5 1.6 - - - -
253A ALA* 4.2 15.3 - - + +
254A VAL* 5.3 0.9 - - - -
261A ASN* 4.7 0.4 + - - +
273A LEU* 6.3 0.2 - - - -
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Residues in contact with SER 238 (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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222A ILE* 3.6 10.6 - - - +
223A GLN 4.0 2.2 - - - -
224A GLN* 2.7 33.5 + - - -
237A VAL* 1.3 74.4 - - - +
239A VAL* 1.3 60.6 + - - +
240A TYR* 3.8 6.2 - - - -
250A ALA* 3.7 1.2 - - - -
251A GLY* 3.0 27.5 + - - +
252A GLU 4.9 3.2 + - - -
294A HIS* 4.5 19.1 - - - -
296A TYR* 3.0 24.6 + - - -
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Residues in contact with VAL 239 (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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146A PHE* 4.9 2.9 - - + -
189A ILE* 4.7 2.7 - - + -
193A ILE* 3.6 38.6 - - + -
221A LEU 3.9 0.2 - - - +
222A ILE* 3.5 1.4 - - - -
223A GLN* 2.9 33.7 + - - +
225A TYR* 3.2 46.0 - - + -
237A VAL* 4.7 3.8 - - + +
238A SER* 1.3 76.3 - - - +
240A TYR* 1.3 64.2 + - - +
248A TRP* 4.0 23.8 - - + -
249A ARG 3.6 5.8 - - - +
250A ALA* 4.2 9.0 - - + -
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Residues in contact with TYR 240 (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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220A ARG* 3.5 44.0 - - - -
221A LEU 3.0 19.3 - - - +
222A ILE* 4.3 4.7 - - + -
238A SER* 3.8 13.2 - - - -
239A VAL* 1.3 74.9 - - - +
241A SER* 1.3 59.0 + - - +
242A ASP* 3.9 6.3 - - - -
248A TRP* 3.5 6.8 - - - -
249A ARG* 2.9 76.5 + - + +
250A ALA 4.8 1.6 + - - -
251A GLY* 3.8 27.6 - - - -
293A GLY* 3.1 24.6 - - - -
294A HIS* 4.2 20.6 - + + -
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Residues in contact with SER 241 (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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219A GLY 4.6 0.2 - - - +
220A ARG* 3.4 6.7 - - - +
221A LEU* 3.1 30.9 + - - +
240A TYR* 1.3 76.3 - - - +
242A ASP* 1.3 64.2 + - - +
243A ASP* 3.4 5.9 + - - -
244A HIS 4.7 0.8 + - - -
245A GLY* 2.5 36.7 + - - -
247A THR 3.0 20.2 + - - -
248A TRP* 3.4 20.8 - - - -
249A ARG* 5.4 0.9 - - - -
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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