Contacts of the strand formed by residues 175 - 179 (chain B) in PDB entry 1O69
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 PHE 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ALA* 3.8 36.3 - - + -
66B VAL* 4.1 15.0 - - + -
67B ALA* 4.3 6.3 - - + -
151B VAL* 4.2 9.0 - - + -
152B LEU 3.4 3.6 + - - +
153B ILE* 3.5 26.9 - - + -
154B GLU* 2.9 22.1 + - - +
170B GLY 4.1 4.2 - - - +
173B GLY* 3.9 6.8 - - - -
174B GLU* 1.4 103.2 - - + +
176B GLY* 1.3 59.6 + - - +
194B LEU* 4.0 12.8 - - + -
195B ILE 3.3 4.9 - - - +
196B GLY* 4.2 0.4 - - - -
198B ASN 6.4 0.2 - - - -
201B LYS* 3.9 36.3 - - + -
202B ILE* 3.8 30.5 - - + -
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLU* 3.3 12.6 - - - -
170B GLY* 3.3 21.7 + - - -
175B PHE* 1.3 75.4 - - - +
177B VAL* 1.3 68.1 + - - +
178B TYR* 5.8 0.2 - - - -
194B LEU* 3.6 1.4 - - - +
195B ILE* 2.9 39.1 + - - +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 3.5 34.8 - - + +
59B ALA* 3.6 31.2 - - + -
60B LEU* 3.7 31.6 - - + +
153B ILE* 4.8 3.1 - - + -
154B GLU 2.9 10.8 + - - +
155B ASP* 4.7 4.7 - - - +
156B ALA* 2.9 33.8 + - - +
157B ALA 3.2 0.3 + - - -
170B GLY* 5.0 0.2 - - - -
176B GLY* 1.3 80.0 - - - +
178B TYR* 1.3 66.1 + - - +
193B MET 3.2 4.9 - - - +
194B LEU* 3.9 10.8 - - + -
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Residues in contact with TYR 178 (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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41B VAL* 3.7 31.0 - - + -
45B SER* 3.6 15.3 - - - -
56B ALA* 4.0 0.2 - - - +
156B ALA* 3.5 27.8 - - + -
157B ALA* 4.2 1.3 - - - -
160B LEU* 3.9 41.7 - - + +
168B ALA* 4.3 2.6 - - - +
169B LEU 2.6 30.4 + - - -
170B GLY* 4.0 1.5 - - - -
171B THR* 4.2 1.2 - - - +
177B VAL* 1.3 82.7 - - - +
179B SER* 1.3 61.3 + - - +
180B TYR* 3.8 19.7 - - + +
192B GLY* 3.2 4.9 - - - -
193B MET* 2.9 36.2 + - + +
195B ILE* 3.5 32.0 - - + +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 3.9 2.0 - - - -
157B ALA* 3.4 41.3 + - - +
160B LEU* 4.9 6.4 - - - +
178B TYR* 1.3 73.7 - - - +
180B TYR* 1.3 75.1 + - - +
181B ASN 4.3 4.6 + - - -
182B GLY 4.9 3.2 + - - -
191B GLY 3.8 5.4 - - - -
395B X04 2.9 39.4 + - - -
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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
------------------------------------------------------------
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