Contacts of the strand formed by residues 202 - 207 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLY 3.7 0.2 - - - +
194B ILE* 3.4 5.6 - - - -
195B SER* 3.0 32.8 + - - +
200B GLY 4.6 0.9 - - - +
201B ALA* 1.3 74.8 - - - +
203B ALA* 1.3 68.7 + - - +
204B VAL* 3.7 13.7 + - + +
214B THR* 3.4 33.9 - - + +
215B ILE 3.5 5.4 - - - +
216B LYS* 4.6 4.9 - - + +
98C ALA* 6.0 2.7 - - + -
99C VAL* 5.5 8.7 - - + -
452C ASP 4.2 5.6 - - - +
453C THR* 5.0 2.9 - - + -
454C VAL* 3.3 35.4 - - + +
458C TRP* 6.1 0.2 - - + -
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ILE* 4.4 7.0 - - + -
193B GLY 3.6 4.9 - - - -
194B ILE* 4.0 10.3 - - + -
202B VAL* 1.3 73.1 - - - +
204B VAL* 1.3 60.5 + - - +
205B LEU* 3.8 1.8 + - + +
214B THR* 3.2 6.9 - - - -
215B ILE* 2.8 52.6 + - + +
223B LEU* 4.3 4.8 - - + +
241B MET* 3.9 27.6 - - + -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B SER* 4.6 8.0 + - - +
176B VAL 5.9 1.8 - - - +
191B THR 3.6 3.1 - - - +
192B ILE* 3.8 1.0 - - - -
193B GLY 2.9 35.2 + - - +
195B SER* 6.0 1.6 - - - +
202B VAL* 4.4 15.9 - - + +
203B ALA* 1.3 75.8 - - - +
205B LEU* 1.3 63.0 + - - +
206B LYS* 4.0 10.7 + - + +
211B ILE* 3.5 41.7 - - + -
213B ASP 4.0 2.9 - - - -
214B THR* 4.5 0.7 - - - +
98C ALA* 4.3 15.5 - - + -
99C VAL* 4.0 26.5 - - + +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LEU* 4.5 6.3 - - + -
191B THR 3.6 2.5 - - - +
192B ILE* 3.4 41.3 - - + -
203B ALA* 4.6 4.7 - - + +
204B VAL* 1.3 75.0 - - - +
206B LYS* 1.3 55.7 + - - +
211B ILE* 3.3 7.1 - - - +
212B THR* 2.8 29.2 + - - -
213B ASP* 3.0 27.8 + - + +
214B THR 4.7 0.2 - - - +
215B ILE* 4.5 16.2 - - + -
257B MET* 3.8 26.9 - - - -
260B GLY 3.5 26.2 - - - +
262B VAL* 4.1 14.4 - - + -
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PHE* 4.2 2.2 - - - -
174B GLU 2.9 29.5 + - - +
175B SER* 3.8 15.1 + - - +
189B TRP 3.6 0.3 - - - +
190B LEU* 3.2 9.8 - - - +
191B THR* 3.0 45.0 + - - +
204B VAL* 4.4 7.9 - - + +
205B LEU* 1.3 80.0 - - - +
207B TYR* 1.3 60.6 + - - +
208B ASN 4.1 0.7 - - - -
209B GLY* 3.8 20.8 + - - +
210B ILE 3.5 6.5 - - - +
211B ILE* 3.8 31.2 - - + +
212B THR* 3.8 2.5 - - - -
99C VAL 4.7 0.2 - - - -
100C TYR* 2.8 43.6 + - - +
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Residues in contact with TYR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ASP* 2.7 35.1 + - - -
187B THR* 3.7 12.8 - - + +
188B SER* 2.2 38.0 + - - -
189B TRP 3.4 7.0 - - - -
190B LEU* 4.5 8.7 - - + -
206B LYS* 1.3 73.4 - - - +
208B ASN* 1.3 74.8 + - + +
210B ILE* 3.0 28.6 + - + +
212B THR* 3.6 13.4 + - + +
237B CYS* 6.3 0.7 - - - -
259B LYS* 3.5 58.8 - - + +
260B GLY* 3.6 5.8 - - - -
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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