Contacts of the helix formed by residues 164 - 175 (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 SER 164 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162X TRP 4.0 0.4 + - - -
163X HIS* 1.3 75.7 - - - +
165X PRO* 1.3 72.1 - - - +
166X ALA* 3.6 7.8 + - - +
167X GLN* 3.1 25.1 + - - +
168X MET* 3.1 19.6 + - - +
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Residues in contact with PRO 165 (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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163X HIS 3.6 4.7 - - - +
164X SER* 1.3 84.0 - - - +
166X ALA* 1.3 57.1 + - - +
168X MET* 3.3 2.3 + - - +
169X ALA* 2.9 30.7 + - - +
200X TYR* 4.3 15.7 - - + -
203X ALA* 3.5 43.7 - - + +
204X VAL* 3.9 15.7 - - + +
207X ALA* 4.7 2.2 - - + -
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Residues in contact with ALA 166 (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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164X SER* 3.1 7.8 + - - +
165X PRO* 1.3 78.3 - - - +
167X GLN* 1.3 62.4 + - - +
169X ALA* 3.4 7.7 + - - +
170X SER* 3.0 22.7 + - - -
207X ALA* 4.4 9.8 - - + +
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Residues in contact with GLN 167 (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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163X HIS* 4.9 3.6 - - + +
164X SER* 3.1 26.3 + - - +
166X ALA* 1.3 73.1 - - - +
168X MET* 1.3 66.0 + - - +
170X SER* 3.2 13.4 + - - -
171X TRP* 3.0 67.9 + - + +
174X GLN* 5.2 0.8 - - - +
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Residues in contact with MET 168 (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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119X ILE* 3.9 21.1 - - + -
120X SER* 3.3 26.2 - - - +
157X ALA* 3.4 31.0 - - + +
163X HIS* 4.0 13.2 - - + +
164X SER 3.1 12.2 + - - +
165X PRO 3.7 6.3 - - - +
167X GLN* 1.3 77.0 - - - +
169X ALA* 1.3 63.0 + - - +
171X TRP* 3.3 20.4 + - + +
172X LEU* 2.9 47.5 + - + +
200X TYR* 3.5 20.2 - - - +
204X VAL* 4.0 8.7 - - + -
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Residues in contact with ALA 169 (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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165X PRO 2.9 18.0 + - - +
166X ALA 3.6 4.5 - - - +
168X MET* 1.3 75.8 - - - +
170X SER* 1.3 58.1 + - - +
172X LEU* 3.3 2.5 + - - +
173X GLN* 2.9 36.0 + - - +
204X VAL* 3.9 7.5 - - - +
207X ALA* 3.5 32.3 - - + +
208X ILE* 3.7 23.0 - - + +
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Residues in contact with SER 170 (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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166X ALA 3.0 14.1 + - - -
167X GLN* 3.2 18.8 + - - -
169X ALA* 1.3 77.4 - - - +
171X TRP* 1.3 62.0 + - - +
173X GLN* 3.3 14.9 + - - +
174X GLN* 3.1 37.7 + - - +
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Residues in contact with TRP 171 (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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119X ILE* 3.5 34.3 - - + -
122X MET* 3.5 26.5 - - + +
123X SER* 3.4 26.2 - - - -
130X GLN* 4.4 8.1 + - - -
134X LEU* 3.8 12.1 - - + +
163X HIS* 3.6 39.9 - + + -
167X GLN* 3.0 52.5 + - + +
168X MET* 3.6 14.8 - - + +
170X SER* 1.3 76.2 - - - +
172X LEU* 1.3 56.6 + - - +
174X GLN* 3.2 22.1 + - - +
175X ALA* 3.0 27.0 + - - +
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Residues in contact with LEU 172 (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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119X ILE* 3.6 25.1 - - + -
155X PHE* 3.9 30.1 - - + -
156X ASP 4.6 3.8 - - - +
157X ALA* 4.2 1.8 - - + -
168X MET* 2.9 36.5 + - + +
169X ALA 3.8 3.8 - - - +
171X TRP* 1.3 76.3 - - - +
173X GLN* 1.3 59.3 + - - +
175X ALA* 3.2 11.2 + - - +
177X ILE* 3.1 39.7 + - + +
184X ILE* 3.7 18.8 - - + -
204X VAL* 3.6 27.6 - - + -
208X ILE* 4.1 5.6 - - + -
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Residues in contact with GLN 173 (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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169X ALA* 2.9 22.0 + - - +
170X SER* 3.6 13.6 - - - +
171X TRP 3.2 0.2 - - - -
172X LEU* 1.3 75.7 - - - +
174X GLN* 1.3 58.2 + - + +
176X ASP* 3.0 19.1 + - - -
177X ILE* 4.4 5.4 - - + +
207X ALA 4.1 5.6 + - - +
208X ILE* 3.2 45.6 + - + +
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Residues in contact with GLN 174 (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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131X GLN* 3.4 31.7 + - - +
134X LEU* 3.5 21.0 - - + +
135X GLU* 5.8 0.5 - - - -
138X ALA* 5.3 1.0 - - - +
167X GLN* 5.2 1.0 - - - +
170X SER* 3.1 34.3 + - - +
171X TRP* 3.4 26.5 - - - +
173X GLN* 1.3 75.3 - - + +
175X ALA* 1.3 56.2 + - - +
176X ASP* 3.1 7.5 + - - +
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Residues in contact with ALA 175 (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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119X ILE* 4.9 2.0 - - + -
134X LEU* 3.5 31.8 - - + +
137X MET* 4.0 17.0 - - + -
138X ALA* 3.2 19.2 - - - +
155X PHE* 3.6 12.8 - - + -
171X TRP 3.0 12.0 + - - +
172X LEU* 3.6 11.0 - - - +
173X GLN 3.2 0.8 - - - -
174X GLN* 1.3 73.8 - - - +
176X ASP* 1.3 70.2 + - - +
177X ILE 3.2 2.7 + - - -
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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