Contacts of the strand formed by residues 300 - 306 (chain F) in PDB entry 2CEA
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 300 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179F PHE* 4.9 1.2 - - - -
194F PRO 5.3 0.3 - - - +
195F LYS* 4.6 3.6 - - - +
246F PHE* 5.9 1.8 - - + -
249F ALA* 3.5 28.0 - - + +
250F LYS* 3.6 35.7 - - + +
253F ALA* 3.5 21.1 - - + -
255F CYS* 3.7 8.7 - - - +
257F VAL* 4.5 18.6 - - + -
294F PHE* 3.5 45.7 - - + -
295F ASP 4.8 0.7 - - - +
296F SER* 3.8 10.7 + - - +
298F GLU* 4.6 9.6 - - + +
299F GLY* 1.3 76.1 - - - +
301F ILE* 1.3 67.0 + - - +
302F VAL* 4.9 2.2 - - + -
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Residues in contact with ILE 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F VAL* 2.9 41.1 - - + -
179F PHE* 3.9 16.6 - - + -
180F LEU* 2.7 41.1 - - + -
193F MET* 4.7 4.9 - - + -
194F PRO 4.3 17.3 - - - +
195F LYS 4.0 3.8 - - - +
197F ILE* 4.6 17.0 - - + -
255F CYS 3.2 5.6 + - - +
256F ILE* 3.4 11.8 - - + +
257F VAL* 3.0 22.5 + - - +
300F ILE* 1.3 78.5 - - - +
302F VAL* 1.3 65.2 + - - +
303F MET* 3.9 10.2 + - + -
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Residues in contact with VAL 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F LYS 3.1 8.3 + - - -
196F GLY* 3.0 5.9 - - - -
197F ILE 3.0 21.5 + - - +
246F PHE* 4.3 15.7 - - + -
257F VAL* 3.2 34.3 - - + +
259F ILE* 3.4 31.2 - - + -
291F MET* 3.8 28.7 - - + +
294F PHE* 4.7 2.5 - - + -
300F ILE* 4.3 2.4 - - + -
301F ILE* 1.3 72.1 - - - +
303F MET* 1.3 61.9 + - - +
322F PHE* 3.8 18.0 - - + -
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Residues in contact with MET 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F LEU* 3.2 48.2 - - + -
176F VAL* 4.1 17.9 - - + -
197F ILE* 3.3 33.0 - - + +
199F LEU* 4.6 11.0 - - + -
211F ALA* 4.4 14.8 - - + -
214F VAL* 4.7 3.6 - - + -
256F ILE* 4.1 24.8 - - + +
257F VAL 2.9 6.8 + - - +
258F PHE* 3.2 22.4 - - + -
259F ILE* 2.8 25.1 + - - +
301F ILE* 3.9 7.0 + - + -
302F VAL* 1.3 75.2 - - - +
304F ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 304 (chain F).
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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197F ILE 2.9 6.1 + - - -
198F LEU* 3.0 12.5 - - + +
199F LEU* 2.7 33.6 + - - +
258F PHE* 4.8 1.6 - - - -
259F ILE* 3.5 11.2 - - + +
262F ILE* 2.9 38.1 - - + -
302F VAL 4.1 0.2 + - - -
303F MET* 1.3 76.2 - - - +
305F ALA* 1.3 55.2 + - - +
322F PHE* 3.5 15.0 - - + -
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Residues in contact with ALA 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F LEU* 3.3 8.5 - - + +
207F LYS* 3.9 29.8 - - + +
258F PHE* 3.9 21.9 - - + -
259F ILE 3.3 6.7 + - - -
260F ASP* 4.0 13.0 - - - +
261F GLU 3.4 3.1 + - - -
262F ILE* 3.1 23.4 + - - +
304F ALA* 1.3 74.6 - - - +
306F THR* 1.3 68.2 + - - +
1607F ADP 5.4 0.7 - - - +
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Residues in contact with THR 306 (chain F).
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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198F LEU* 4.2 13.2 - - + -
199F LEU 3.0 5.1 + - - +
200F VAL* 3.3 26.7 - - + +
201F GLY 3.5 4.0 + - - -
207F LYS* 4.1 6.7 - - - +
260F ASP* 5.7 0.4 - - - -
261F GLU* 5.0 2.0 - - - +
262F ILE* 3.7 15.0 - - + -
263F ASP* 2.8 31.9 + - - +
305F ALA* 1.3 81.1 - - - +
307F ASN* 1.3 56.4 + - - +
308F ARG* 3.0 19.3 + - - +
309F PRO* 4.3 17.5 - - + -
312F LEU* 4.8 4.5 - - + -
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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