Contacts of the strand formed by residues 209 - 215 (chain F) in PDB entry 6IWQ
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 SER 209 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208F THR* 1.3 76.4 + - - +
210F SER* 1.3 63.1 + - - +
211F VAL* 4.0 2.5 - - - -
238F TYR 2.9 7.0 + - - +
239F LEU* 3.8 4.9 - - - +
240F ALA* 2.8 32.3 + - - +
241F GLU 3.7 2.1 + - - +
294F GLY* 4.0 0.9 - - - -
296F VAL* 3.2 27.2 - - - +
298F ILE* 3.4 26.6 - - - +
311F TYR* 2.9 25.6 + - - -
315F VAL* 4.2 1.2 - - - +
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Residues in contact with SER 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F SER* 1.3 73.8 + - - +
211F VAL* 1.3 64.2 + - - +
212F VAL* 3.8 1.8 + - - -
241F GLU* 3.1 34.0 + - - +
291F ALA* 4.0 16.3 + - - -
294F GLY* 2.6 34.4 + - - -
296F VAL 2.9 6.9 + - - +
297F LEU* 3.6 12.9 - - - +
298F ILE 2.9 22.0 + - - -
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Residues in contact with VAL 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F SER* 5.0 1.1 - - - +
210F SER* 1.3 75.6 - - - +
212F VAL* 1.3 60.8 + - - +
213F ILE* 4.5 12.6 - - + -
230F VAL* 4.6 10.3 - - + -
239F LEU* 4.0 19.3 - - + -
241F GLU 3.2 5.9 + - - -
242F ILE* 3.5 35.4 - - + +
243F VAL* 2.8 26.5 + - - +
298F ILE* 3.1 36.6 - - + +
300F LEU* 4.5 6.5 - - + -
310F TRP* 4.5 11.7 - - + -
311F TYR* 6.1 0.2 - - + -
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Residues in contact with VAL 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F SER 4.3 7.6 - - - +
211F VAL* 1.3 78.2 - - - +
213F ILE* 1.3 60.3 + - - +
214F VAL* 4.0 5.3 + - + -
243F VAL* 3.2 11.9 - - + +
245F ILE* 4.8 2.7 - - + -
287F GLY* 4.1 29.8 - - - +
291F ALA* 4.1 16.8 - - + -
297F LEU* 4.4 9.4 - - + -
298F ILE 2.9 5.6 + - - +
299F TYR* 3.1 43.1 - - + +
300F LEU 3.0 24.6 + - - +
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Residues in contact with ILE 213 (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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211F VAL* 4.5 9.4 - - + -
212F VAL* 1.3 74.2 - - - +
214F VAL* 1.3 62.0 + - - +
215F PHE* 4.7 1.0 - - - -
223F LEU* 4.0 12.3 - - + -
226F THR* 4.5 11.4 - - - +
227F VAL* 4.2 19.3 - - + -
230F VAL* 5.5 1.3 - - + -
242F ILE* 4.2 11.9 - - + -
243F VAL 3.0 5.1 + - - -
244F LEU* 3.4 25.7 - - + +
245F ILE* 3.0 22.3 + - - +
300F LEU* 3.3 29.4 - - + +
301F ASP 4.0 0.2 - - - +
302F ALA* 3.5 37.2 - - + -
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Residues in contact with VAL 214 (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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212F VAL* 4.0 8.2 + - + +
213F ILE* 1.3 73.3 - - - +
215F PHE* 1.3 72.7 + - - +
245F ILE* 3.5 19.1 - - + +
247F ASP* 4.8 5.6 - - + -
280F LEU* 4.7 19.1 - - + +
283F ALA* 3.5 29.8 - - + +
284F ARG* 4.0 37.7 - - + +
287F GLY* 6.0 0.2 - - - -
299F TYR* 5.4 0.7 - - + -
300F LEU 4.1 3.6 + - - -
301F ASP* 5.3 1.6 - - - +
302F ALA* 3.4 19.1 + - - +
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Residues in contact with PHE 215 (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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213F ILE 4.7 0.9 - - - -
214F VAL* 1.3 80.9 - - - +
216F HIS* 1.3 65.6 + - - +
217F ASN 4.0 0.9 - - - -
218F GLU* 4.2 10.5 - - + -
223F LEU* 4.2 20.9 - - + -
244F LEU* 4.6 16.6 - - + -
245F ILE 2.7 24.5 + - - -
246F ASP* 2.9 38.8 - - + -
247F ASP* 3.1 26.7 + - - +
249F SER* 4.0 0.7 - - - -
254F LEU* 2.8 45.8 - - + -
258F LEU* 4.2 21.1 - - + -
271F VAL* 4.7 2.0 - - + -
302F ALA* 3.9 17.3 - - + -
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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