Contacts of the strand formed by residues 255 - 261 (chain J) in PDB entry 3EOA
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 255 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231J THR* 3.9 21.8 - - - +
232J LYS 3.1 11.9 + - - +
233J VAL* 3.3 12.0 - - + +
234J LEU 2.7 32.2 + - - +
253J ASP 4.1 2.6 + - - +
254J ILE* 1.3 72.1 - - - +
256J ARG* 1.3 56.7 + - - +
257J TYR* 3.9 16.2 - - + +
279J SER* 3.6 5.8 - - - +
285J PHE* 3.7 29.4 - - + -
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Residues in contact with ARG 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J ILE* 4.7 4.3 - - - -
234J LEU* 3.4 19.3 - - + +
236J ILE* 4.8 7.0 - - + -
248J ILE* 3.7 19.1 - - - +
251J ALA* 2.8 38.6 + - - -
252J LYS* 3.9 20.8 + - - +
254J ILE* 2.8 43.2 + - + +
255J ILE* 1.3 74.3 - - - +
257J TYR* 1.3 63.0 + - - +
277J PHE 2.7 28.2 + - - +
278J ALA* 3.1 29.7 + - - +
279J SER* 2.7 44.6 + - - +
280J LYS 5.0 0.4 - - - +
285J PHE* 3.6 8.4 - - - -
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Residues in contact with TYR 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233J VAL* 4.1 15.7 - - + -
234J LEU 2.7 9.2 + - - +
235J ILE* 3.9 30.5 - - + -
236J ILE* 2.7 37.0 + - - +
255J ILE* 3.9 18.2 - - + +
256J ARG* 1.3 76.3 - - - +
258J ILE* 1.3 57.2 + - - +
259J ILE* 5.4 4.3 - - + -
284J GLU 4.3 8.3 - - - -
285J PHE* 3.3 43.8 - + - +
287J LYS* 6.5 0.2 - - + -
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Residues in contact with ILE 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208J THR* 4.8 2.5 - - + -
236J ILE* 3.4 31.9 - - + +
238J THR* 4.2 8.5 - - + -
256J ARG 4.4 0.2 + - - -
257J TYR* 1.3 75.6 - - - +
259J ILE* 1.3 62.2 + - - +
260J GLY 3.9 0.9 + - - -
274J LEU* 3.7 40.2 - - + +
277J PHE* 3.9 25.1 - - + -
278J ALA* 3.6 23.8 - - + -
285J PHE 3.1 5.4 + - - -
286J VAL* 3.6 22.7 - - + +
287J LYS* 2.7 32.6 + - - +
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Residues in contact with ILE 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J PHE* 4.2 15.0 - - + -
235J ILE* 4.1 28.0 - - + -
236J ILE 2.7 13.0 + - - +
237J ILE* 3.6 8.0 - - + -
238J THR 3.0 29.0 + - - +
257J TYR* 5.4 4.7 - - + -
258J ILE* 1.3 80.0 - - - +
260J GLY* 1.3 58.9 + - - +
261J ILE* 3.7 23.3 + - + +
287J LYS* 3.3 22.4 - - + +
289J LEU* 4.4 8.7 - - + -
295J LEU* 4.6 3.6 - - + -
298J LEU* 3.8 30.1 - - + -
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Residues in contact with GLY 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238J THR* 3.4 6.3 - - - -
258J ILE 3.9 2.2 + - - -
259J ILE* 1.3 72.3 - - - +
261J ILE* 1.3 60.2 + - - -
265J PHE* 3.6 22.7 - - - -
274J LEU* 3.7 15.7 - - - +
287J LYS 2.9 10.5 + - - -
288J ILE* 3.5 7.7 - - - +
289J LEU* 2.8 29.3 + - - +
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Residues in contact with ILE 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J ILE* 4.2 2.9 - - + -
237J ILE* 3.6 27.6 - - + -
238J THR 2.9 14.3 + - - +
239J ASP* 3.4 26.2 - - + +
259J ILE* 3.9 14.4 - - + -
260J GLY* 1.3 76.3 - - - +
262J GLY* 1.3 64.9 + - - +
263J LYS 3.9 0.5 + - - -
265J PHE* 3.7 5.5 - - - -
289J LEU* 3.4 9.9 - - + +
291J THR 3.8 7.0 - - - +
292J PHE* 3.6 56.4 - - + +
295J LEU* 3.8 28.3 - - + -
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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