Contacts of the helix formed by residues 176 - 181 (chain X) in PDB entry 2BOD
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 ASP 176 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138X ALA* 4.0 4.9 - - + -
142X LYS* 2.8 33.5 + - - +
173X GLN 3.0 16.1 + - - -
174X GLN 3.1 3.8 - - - +
175X ALA* 1.3 78.7 - - - +
177X ILE* 1.3 64.6 + - - +
178X SER* 3.2 3.5 + - - -
179X ASN* 3.0 32.6 + - - +
180X SER* 2.7 26.6 + - - +
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Residues in contact with ILE 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155X PHE* 4.0 21.5 - - + -
172X LEU* 3.1 36.0 + - + +
173X GLN* 4.2 5.1 + - + +
175X ALA 3.2 3.7 + - - -
176X ASP* 1.3 75.7 - - - +
178X SER* 1.3 64.0 + - - +
180X SER 4.4 0.2 - - - +
181X ALA* 3.0 43.5 + - + +
183X GLY 3.6 23.1 - - - +
184X ILE* 3.7 20.4 - - + -
208X ILE* 4.2 25.6 - - + -
213X LEU* 4.2 16.2 - - + -
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Residues in contact with SER 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X LYS* 5.4 1.6 + - - -
176X ASP* 3.2 1.6 - - - -
177X ILE* 1.3 80.8 - - - +
179X ASN* 1.3 69.6 + - - +
181X ALA 4.6 4.7 - - - +
208X ILE* 4.4 4.9 - - - +
210X ASN* 2.9 39.9 + - - +
213X LEU* 4.3 8.0 - - - +
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Residues in contact with ASN 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X LYS* 4.0 15.5 - - - +
145X LYS* 3.6 19.4 + - - +
176X ASP* 3.0 37.3 + - - +
178X SER* 1.3 86.7 - - - +
180X SER* 1.3 58.6 + - - +
181X ALA 3.9 0.7 - - - -
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Residues in contact with SER 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138X ALA* 3.5 16.7 + - - -
141X GLY* 3.0 27.9 - - - +
142X LYS* 2.9 32.7 + - - -
145X LYS* 3.8 9.9 - - - +
153X ILE* 3.9 2.1 - - - +
155X PHE* 3.8 17.3 - - - -
175X ALA 3.8 0.9 + - - -
176X ASP* 2.7 25.0 + - - +
179X ASN* 1.3 78.2 - - - +
181X ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X LYS* 4.3 8.5 + - - +
153X ILE* 3.5 18.2 - - + +
155X PHE* 3.9 23.8 - - + -
177X ILE* 3.0 30.6 + - + +
178X SER 4.6 5.0 - - - +
179X ASN 3.9 0.6 - - - -
180X SER* 1.3 81.1 - - - +
182X HIS* 1.3 61.7 + - - +
183X GLY 3.4 4.7 - - - +
213X LEU* 3.7 9.4 - - - +
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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
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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