Contacts of the strand formed by residues 202 - 207 (chain F) in PDB entry 2HU4
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 VAL 202 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193F GLY 3.9 0.3 - - - +
194F ILE* 3.6 4.7 - - - -
195F SER* 3.1 28.4 + - - +
201F ALA* 1.3 76.4 - - - +
203F ALA* 1.3 72.7 + - - +
204F VAL* 3.7 13.5 + - + +
214F THR* 4.1 22.4 - - + +
215F ILE 3.3 11.0 - - - +
216F LYS* 4.4 4.3 - - + -
98G ALA* 5.9 1.3 - - + -
99G VAL* 5.7 7.8 - - + +
452G ASP 4.2 7.0 - - - +
453G THR* 4.8 2.5 - - + -
454G VAL* 3.3 43.7 - - + +
458G TRP* 6.1 0.2 - - + -
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Residues in contact with ALA 203 (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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192F ILE* 4.1 7.4 - - + -
193F GLY 3.5 5.6 - - - -
194F ILE* 3.4 25.4 - - + -
202F VAL* 1.3 73.9 - - - +
204F VAL* 1.3 59.4 + - - +
205F LEU* 3.9 4.0 + - + +
214F THR* 3.5 5.7 - - - -
215F ILE* 2.7 45.3 + - + +
223F LEU* 4.1 5.1 - - + +
241F MET* 3.9 20.9 - - + -
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Residues in contact with VAL 204 (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 SER* 4.4 11.0 + - - +
176F VAL 5.9 1.3 - - - +
191F THR 3.5 1.4 - - - +
192F ILE* 3.5 4.9 - - - -
193F GLY 2.8 34.0 + - - +
195F SER* 6.5 0.4 - - - -
202F VAL* 4.4 14.6 - - + +
203F ALA* 1.3 75.8 - - - +
205F LEU* 1.3 66.7 + - - +
206F LYS* 4.4 7.3 - - + +
211F ILE* 3.7 36.3 - - + -
213F ASP 4.1 2.7 - - - -
214F THR* 4.5 1.8 - - - +
98G ALA* 4.2 17.3 - - + -
99G VAL* 3.9 30.1 - - + +
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Residues in contact with LEU 205 (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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190F LEU* 4.5 4.0 - - + -
191F THR 3.5 2.9 - - - +
192F ILE* 3.4 42.2 - - + -
203F ALA* 4.5 9.0 - - + +
204F VAL* 1.3 74.4 - - - +
206F LYS* 1.3 62.4 + - - +
211F ILE* 3.1 8.3 - - - +
212F THR* 2.8 24.1 + - - -
213F ASP* 3.0 27.9 + - + +
214F THR 4.7 0.7 - - - +
215F ILE* 4.8 10.5 - - + -
257F MET* 3.8 25.6 - - - -
260F GLY* 3.5 26.5 - - - +
262F VAL* 4.0 14.8 - - + -
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Residues in contact with LYS 206 (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 PHE* 4.4 2.6 - - - -
174F GLU 3.0 28.4 + - - +
175F SER* 4.0 13.0 - - - +
189F TRP 3.4 0.5 - - - +
190F LEU* 3.2 11.2 - - - +
191F THR* 3.1 44.3 + - - +
204F VAL* 4.4 6.7 - - + +
205F LEU* 1.3 79.4 - - - +
207F TYR* 1.3 60.5 + - - +
208F ASN 3.9 0.7 - - - -
209F GLY* 3.6 26.2 + - - +
210F ILE 3.6 6.1 - - - +
211F ILE* 3.9 15.9 - - + +
212F THR* 3.9 2.2 - - - -
100G TYR* 3.0 53.5 + - - +
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Residues in contact with TYR 207 (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 ASP* 2.7 34.5 + - + -
187F THR* 3.6 14.8 - - + +
188F SER* 2.6 34.9 + - - -
189F TRP 3.4 6.1 - - - -
190F LEU* 4.5 9.6 - - + -
206F LYS* 1.3 73.2 - - - +
208F ASN* 1.3 72.6 + - + +
209F GLY 3.3 0.2 - - - -
210F ILE* 3.1 26.0 + - + +
212F THR* 3.7 10.7 + - + +
237F CYS* 6.2 1.3 - - - -
259F LYS* 3.3 61.1 - - + +
260F GLY* 3.5 4.9 - - - +
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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