Contacts of the strand formed by residues 238 - 249 (chain F) in PDB entry 2VIG
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 THR 238 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185F TRP* 3.5 39.5 - - + +
186F ILE 3.3 4.3 - - - +
187F THR* 4.6 1.6 + - - -
227F LYS* 3.4 3.7 - - - +
228F GLU* 2.8 46.0 + - + +
230F LYS* 3.1 31.4 + - - +
233F ILE* 5.6 0.2 - - - +
236F SER* 3.9 3.4 + - - -
237F SER* 1.3 76.4 + - - +
239F ALA* 1.3 62.9 + - - +
501F FAD 3.9 22.9 - - + +
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Residues in contact with ALA 239 (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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185F TRP 4.3 2.0 - - - -
186F ILE* 3.0 34.9 + - - +
189F ALA* 3.8 7.7 - - + +
190F TRP* 3.4 22.4 - - + +
224F LEU* 5.2 0.2 - - + -
225F GLY 3.3 23.6 - - - +
226F LYS 3.7 8.1 - - - +
228F GLU* 4.7 4.5 - - - -
238F THR* 1.3 79.3 - - - +
240F ASN* 1.3 69.6 + - - +
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Residues in contact with ASN 240 (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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157F PRO* 4.5 6.9 - - - +
182F THR* 3.5 22.4 - - + +
183F LYS 3.2 11.9 - - - +
184F ALA* 3.3 21.6 - - - +
185F TRP 3.9 1.7 + - - -
224F LEU* 3.5 5.2 - - - +
225F GLY* 2.8 37.7 + - - +
226F LYS 4.7 1.0 + - - -
228F GLU* 4.5 10.6 + - - +
239F ALA* 1.3 77.9 - - - +
241F LEU* 1.3 63.4 + - - +
242F ILE* 4.3 6.5 - - + +
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Residues in contact with LEU 241 (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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153F ALA* 4.0 23.3 - - + -
181F GLY 3.7 2.4 - - - +
182F THR* 3.4 2.6 - - - -
183F LYS* 2.9 41.6 + - + -
186F ILE* 3.8 16.4 - - + +
189F ALA* 3.7 26.2 - - + -
195F ALA* 4.3 19.1 - - + -
217F MET* 4.2 13.9 - - + -
222F LEU* 4.1 13.0 - - + -
223F THR 3.7 2.9 - - - -
224F LEU* 4.0 10.1 - - + -
239F ALA 3.8 0.4 + - - -
240F ASN* 1.3 78.0 - - - +
242F ILE* 1.3 61.3 + - - +
243F PHE* 3.9 24.4 - - + -
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Residues in contact with ILE 242 (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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181F GLY 3.7 2.5 - - - +
182F THR* 3.9 26.9 - - + +
221F GLY 3.3 2.1 - - - +
222F LEU* 3.3 6.4 - - - +
223F THR* 2.8 58.6 + - - +
224F LEU 3.9 2.9 - - - +
225F GLY* 3.6 30.7 - - - +
240F ASN* 4.3 5.2 - - + +
241F LEU* 1.3 73.0 - - - +
243F PHE* 1.3 67.5 - - - +
244F GLU* 4.0 6.0 - - + +
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Residues in contact with PHE 243 (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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168F THR* 4.7 7.2 - - + -
179F LEU* 3.6 39.9 - - + +
180F ASN* 3.4 2.6 - - - +
181F GLY* 2.8 46.8 + - - +
183F LYS* 3.9 25.6 - - + -
197F VAL* 3.8 30.1 - - + -
215F VAL* 4.2 7.6 - - + -
221F GLY 3.3 4.5 - - - -
222F LEU* 3.7 28.7 - - + -
241F LEU* 3.9 20.2 - - + -
242F ILE* 1.3 75.3 - - - +
244F GLU* 1.3 60.5 + - - +
246F CYS* 3.7 25.1 - - + -
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Residues in contact with GLU 244 (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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180F ASN* 3.5 7.4 - - - +
221F GLY* 2.8 25.5 + - - +
242F ILE* 4.0 6.4 + - + +
243F PHE* 1.3 73.5 - - - +
245F ASP* 1.3 78.4 + - + +
246F CYS 3.1 0.7 + - - +
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Residues in contact with ASP 245 (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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171F ARG* 4.4 8.1 + - - -
178F VAL* 3.6 17.7 - - + +
179F LEU 3.4 3.5 + - - -
180F ASN* 2.8 32.9 + - - +
220F PRO 4.8 0.9 - - - +
221F GLY* 4.6 2.4 - - - -
244F GLU* 1.3 78.7 - - + +
246F CYS* 1.3 62.0 + - - +
247F ARG* 3.5 12.6 + - + +
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Residues in contact with CYS 246 (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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177F TRP 3.4 1.9 - - - +
178F VAL* 3.4 2.2 - - - -
179F LEU* 2.7 40.8 + - + +
215F VAL* 4.8 0.2 - - - -
219F THR* 3.5 22.9 - - - -
220F PRO 3.5 20.0 - - - -
221F GLY 3.6 18.6 - - - +
243F PHE* 3.7 31.4 - - + -
244F GLU 3.1 1.3 - - - -
245F ASP* 1.3 75.5 - - - +
247F ARG* 1.3 59.6 + - - +
248F ILE* 4.0 13.0 + - - -
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Residues in contact with ARG 247 (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 GLU* 3.4 36.8 + - - -
176F SER* 3.8 26.6 + - - +
177F TRP 3.3 5.6 - - - +
178F VAL* 3.6 23.5 - - + +
219F THR* 4.5 9.7 + - - -
220F PRO* 4.3 5.4 + - - +
245F ASP* 3.5 14.0 + - + +
246F CYS* 1.3 75.6 - - - +
248F ILE* 1.3 66.7 + - - +
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Residues in contact with ILE 248 (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 SER* 3.2 8.2 - - - -
177F TRP* 2.8 45.7 + - + +
179F LEU* 4.1 12.3 - - + -
213F PHE* 3.7 37.9 - - + -
214F LEU 4.8 0.4 - - - +
215F VAL* 4.0 33.2 - - + -
216F PRO* 4.6 8.7 - - + -
219F THR* 5.2 2.0 - - + +
246F CYS* 4.4 11.4 - - - +
247F ARG* 1.3 79.5 - - - +
249F PRO* 1.3 75.1 - - + +
252F SER* 3.8 15.3 - - - +
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Residues in contact with PRO 249 (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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175F ASP* 3.7 9.4 - - - +
176F SER* 4.4 2.0 - - - +
177F TRP* 3.5 4.6 - - - -
216F PRO* 6.0 4.3 - - + -
248F ILE* 1.3 86.1 - - + +
250F LYS* 1.3 61.1 + - - +
251F ASP* 4.2 12.1 - - + +
252F SER* 2.9 43.9 + - - +
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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