Contacts of the strand formed by residues 206 - 210 (chain B) in PDB entry 3UXA
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 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 3.8 27.8 - - + +
37B ILE* 4.0 23.6 - - + -
38B LEU* 3.9 32.3 - - + -
175B ARG 2.9 14.8 + - - +
176B ILE* 3.3 19.9 - - + +
177B ILE 2.8 27.2 + - - +
204B ASN 3.7 3.5 + - - +
205B VAL* 1.3 71.9 - - - +
207B LYS* 1.3 63.2 + - - +
208B VAL* 4.6 0.7 - - + -
228B ASN* 3.3 18.2 - - + +
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Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 3.4 4.3 - - + +
179B ILE* 3.5 18.8 - - + -
198B ILE* 4.4 18.4 - - + +
201B ILE* 4.0 32.1 - - + -
202B PRO 3.6 21.2 + - - -
203B SER* 3.9 12.0 + - - +
205B VAL 3.1 16.4 + - - +
206B VAL* 1.3 73.2 - - - +
208B VAL* 1.3 62.7 + - - +
209B ALA 4.2 0.4 - - - -
225B LEU 5.4 1.6 - - - -
226B GLY* 3.2 27.8 + - - +
227B VAL* 3.7 6.4 - - + +
228B ASN* 2.8 54.5 + - - +
229B ALA 3.5 1.6 + - - -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 6.0 0.7 - - + -
37B ILE* 4.2 11.2 - - + -
49B ILE* 4.0 26.9 - - + -
176B ILE* 4.6 12.6 - - + -
177B ILE 2.9 13.8 + - - +
178B ILE* 3.4 18.4 - - + +
179B ILE* 3.0 27.3 + - - -
206B VAL* 4.6 1.6 - - + -
207B LYS* 1.3 76.6 - - - +
209B ALA* 1.3 71.2 + - - +
210B ALA 3.6 0.5 + - - -
229B ALA* 3.2 24.7 - - + +
231B GLU* 3.7 19.3 - - + +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 3.7 9.6 - - - +
194B GLN* 4.4 12.6 - - - +
198B ILE* 4.8 2.9 - - + -
208B VAL* 1.3 71.7 - - - +
210B ALA* 1.3 58.2 + - - +
213B ILE* 3.3 17.2 - - + +
222B LEU* 4.1 17.0 - - + -
227B VAL* 3.6 24.8 - - + +
229B ALA 3.1 5.9 + - - -
230B PHE* 3.4 4.0 - - + -
231B GLU 2.8 25.3 + - - -
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE* 3.4 17.3 - - + -
179B ILE 2.9 9.5 + - - +
180B SER* 4.2 4.5 - - - -
181B SER* 3.3 5.2 + - - -
194B GLN* 3.2 15.8 + - - +
208B VAL 3.6 0.2 + - - -
209B ALA* 1.3 74.5 - - - +
211B SER* 1.3 80.4 + - - +
213B ILE* 4.2 2.9 - - - -
231B GLU* 3.3 39.5 - - + +
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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