Contacts of the helix formed by residues 168 - 177 (chain H) in PDB entry 5EIG
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 168 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H SER* 5.8 1.0 - - - +
140H ILE* 6.0 5.6 - - + -
166H VAL 4.2 0.2 + - - -
167H ILE* 1.3 72.0 - - - +
169H ILE* 1.3 58.1 + - - +
170H GLU* 3.3 9.2 + - - +
171H GLY* 3.1 23.0 + - - +
172H CYS* 2.9 28.3 + - - +
302H LEU* 3.6 34.8 - - + +
305H ARG* 5.3 2.3 + - - -
306H GLN* 3.9 3.7 - - - +
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Residues in contact with ILE 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H ILE* 4.5 4.7 - - + -
158H THR* 3.7 18.2 - - + -
167H ILE* 3.0 16.9 + - - +
168H ASP* 1.3 71.0 - - - +
170H GLU* 1.3 58.4 + - - +
172H CYS* 3.2 5.9 + - - +
173H ALA* 2.8 29.3 + - - +
184H LEU* 4.5 3.9 - - + +
186H VAL* 3.8 34.8 - - + -
196H GLN* 3.2 28.9 - - - +
198H PRO* 4.2 11.4 - - + +
201H LEU* 3.7 31.4 - - + +
203H ALA* 4.5 5.2 - - + +
306H GLN* 3.3 11.1 + - - +
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Residues in contact with GLU 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ASP* 3.3 7.9 + - - +
169H ILE* 1.3 78.6 - - - +
171H GLY* 1.3 61.4 + - - +
173H ALA* 3.6 2.6 + - - +
174H HIS* 3.2 22.0 + - - +
201H LEU* 3.1 41.5 + - + +
306H GLN* 4.7 1.2 + - - +
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Residues in contact with GLY 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H ILE* 5.6 2.0 - - - -
168H ASP* 3.1 22.2 + - - -
170H GLU* 1.3 74.0 - - - +
172H CYS* 1.3 65.4 + - - +
174H HIS* 3.3 7.6 + - - +
175H ILE* 3.1 32.8 + - - +
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Residues in contact with CYS 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H CYS* 4.9 6.7 - - - +
140H ILE* 5.4 4.3 - - + +
143H LEU* 3.6 24.2 - - - -
154H VAL* 4.9 0.9 - - - -
156H ILE* 4.5 16.4 - - + -
167H ILE* 4.2 12.1 - - + -
168H ASP 2.9 18.9 + - - +
169H ILE* 3.6 5.4 - - - +
171H GLY* 1.3 74.9 - - - +
173H ALA* 1.3 59.7 + - - +
175H ILE* 3.3 9.3 + - - +
176H VAL* 2.9 41.9 + - - +
184H LEU* 4.3 17.3 - - + -
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Residues in contact with ALA 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H ILE 2.8 20.6 + - - +
170H GLU 3.8 4.9 - - - +
172H CYS* 1.3 74.6 - - - +
174H HIS* 1.3 55.7 + - - +
176H VAL* 3.9 1.1 - - - -
177H HIS* 2.9 40.7 + - - +
184H LEU* 3.6 15.8 - - + +
201H LEU 3.9 0.4 - - - +
202H GLY* 3.5 39.9 - - - +
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Residues in contact with HIS 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H GLU 3.2 11.5 + - - +
171H GLY* 3.5 11.4 - - - +
173H ALA* 1.3 79.8 - - - +
175H ILE* 1.3 64.7 + - + +
177H HIS* 3.7 2.4 + - - +
178H LYS* 3.5 43.7 + - + +
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Residues in contact with ILE 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H ILE* 3.5 47.6 - - + -
143H LEU* 4.0 18.6 - - + -
144H GLU* 3.6 34.5 - - + +
147H ILE* 4.3 10.9 - - + +
171H GLY 3.1 17.7 + - - +
172H CYS* 3.6 7.9 - - - +
174H HIS* 1.3 83.1 - - + +
176H VAL* 1.3 61.3 + - - +
178H LYS* 3.6 24.6 - - - +
179H HIS* 4.3 7.3 + - + -
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Residues in contact with VAL 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H LEU* 4.2 18.8 - - + -
147H ILE* 4.4 10.1 - - + -
154H VAL* 3.9 22.0 - - + -
172H CYS* 2.9 28.7 + - - +
173H ALA* 3.9 4.5 - - - +
175H ILE* 1.3 78.4 - - - +
177H HIS* 1.3 72.9 + - + +
178H LYS 3.2 1.6 + - - -
179H HIS* 3.4 18.5 + - - +
182H ILE* 3.6 37.5 - - + +
184H LEU* 4.2 14.6 - - + -
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Residues in contact with HIS 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H ALA* 2.9 27.0 + - + +
174H HIS* 4.2 3.4 - - - +
176H VAL* 1.3 78.3 - - + +
178H LYS* 1.3 63.0 + - - +
179H HIS* 3.2 4.2 + - - -
180H GLY 4.6 8.5 - - - +
182H ILE 3.6 15.9 - - - +
184H LEU* 4.3 5.9 - - + +
202H GLY* 3.0 28.8 + - - -
204H ASP* 2.6 38.6 + - - -
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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