Contacts of the helix formed by residues 170 - 181 (chain C) in PDB entry 5GOU
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 170 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C MET 4.3 2.7 + - - -
166C GLY* 2.9 21.7 + - - -
167C ALA* 4.5 1.2 - - - -
168C PRO 4.0 2.9 - - - +
169C GLU* 1.3 73.7 - - - +
171C GLY* 1.3 58.3 + - - +
172C LEU* 3.6 9.9 + - - +
173C ALA* 3.0 43.0 + - - +
174C GLU* 3.4 11.1 + - - +
172F LEU* 5.6 3.1 - - - +
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LYS* 3.2 38.2 + - - +
165A MET* 4.3 2.5 - - - +
168C PRO 4.2 3.5 + - - -
169C GLU 3.5 6.1 + - - -
170C SER* 1.3 72.4 - - - +
172C LEU* 1.3 55.9 + - - +
174C GLU* 3.7 8.9 + - - +
175C TYR* 3.1 26.7 + - - +
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LYS 3.8 4.2 + - - -
165A MET* 4.0 47.1 - - + +
172A LEU* 5.1 14.6 - - + +
173A ALA* 5.2 4.9 - - + -
176A LEU* 4.0 18.2 - - + -
170C SER* 3.1 8.6 + - - +
171C GLY* 1.3 76.3 - - - +
173C ALA* 1.3 59.6 + - - +
175C TYR* 3.3 3.3 + - + -
176C LEU* 2.8 61.4 + - + +
172F LEU* 4.9 11.4 - - + -
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Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C LEU* 5.1 1.1 - - - -
165C MET* 3.5 50.1 - - + +
167C ALA* 4.1 10.1 - - + +
170C SER* 3.0 24.5 + - - +
172C LEU* 1.3 77.6 - - - +
174C GLU* 1.3 57.5 + - - +
176C LEU* 3.9 1.9 - - - -
177C PHE* 3.0 30.2 + - - +
172F LEU* 4.9 5.8 - - + +
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LYS* 5.8 3.8 - - - +
48C LEU* 4.2 19.3 - - + +
51C PHE* 3.7 5.9 - - + -
95C SER* 3.5 12.9 + - - -
96C GLY* 2.9 34.1 + - - -
97C LEU* 3.1 11.8 + - - +
162C LEU* 4.3 15.0 - - + -
167C ALA* 4.0 17.7 - - + -
168C PRO* 4.0 13.8 - - + +
170C SER 3.4 7.2 + - - +
171C GLY* 3.7 7.7 + - - +
173C ALA* 1.3 75.0 - - - +
175C TYR* 1.3 61.0 + - - +
178C ASP* 3.0 30.1 + - - +
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Residues in contact with TYR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASN* 3.2 26.9 - - - +
165A MET* 3.5 43.5 - - + -
176A LEU* 4.3 4.3 - - + -
177A PHE* 3.5 12.5 - + - -
180A HIS* 3.3 29.8 - - + +
181A THR* 2.7 30.5 + - - -
48C LEU* 4.7 7.1 - - + +
49C LYS* 5.8 1.8 - - - -
171C GLY 3.1 20.1 + - - +
172C LEU* 3.6 4.9 - - + +
173C ALA 3.3 0.2 - - - -
174C GLU* 1.3 77.2 - - - +
176C LEU* 1.3 82.1 + - + +
178C ASP* 3.3 9.4 + - - +
179C LYS* 3.2 33.5 + - + +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 4.0 24.2 - - + -
180A HIS* 4.2 8.5 - - + +
172C LEU* 2.8 37.6 + - + +
173C ALA* 4.0 3.4 - - - +
175C TYR* 1.3 90.2 - - + +
177C PHE* 1.3 58.2 + - - +
179C LYS* 3.2 2.3 + - - +
180C HIS* 2.8 58.0 + - + +
172F LEU* 3.9 24.9 - - + -
175F TYR* 3.6 11.2 + - + -
176F LEU* 4.1 17.3 - - + -
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Residues in contact with PHE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C PHE* 3.5 23.6 - + - -
100C MET* 4.5 1.6 - - - -
158C HIS* 3.4 42.6 - + + -
161C ASN* 4.1 17.3 - - + -
162C LEU* 3.6 19.7 - - + -
165C MET* 3.4 26.8 - - + -
173C ALA 3.0 17.4 + - - +
174C GLU 4.0 1.1 - - - +
176C LEU* 1.3 72.4 - - - +
178C ASP* 1.3 65.6 + - - +
181C THR* 3.1 46.9 + - + -
182C LEU* 3.2 32.3 + - + -
175F TYR* 3.5 7.4 - - - -
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 3.7 15.5 - - + +
49C LYS* 3.7 15.5 + - - +
50C ASN* 2.6 52.1 + - - +
51C PHE* 2.8 49.4 + - + -
174C GLU 3.0 20.0 + - - +
175C TYR* 3.5 6.8 - - + +
176C LEU 3.3 0.2 - - - -
177C PHE* 1.3 76.8 - - - +
179C LYS* 1.3 63.3 + - - +
182C LEU* 3.6 4.3 - - - +
183C GLY 3.4 5.5 + - - -
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Residues in contact with LYS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A HIS* 2.5 51.7 + - + +
181A THR* 3.7 11.0 - - - -
184A ASP 4.9 4.6 - - - -
49C LYS* 2.9 36.7 - - - +
50C ASN* 4.1 6.2 - - - +
175C TYR* 3.2 28.0 + - + +
176C LEU* 3.7 6.3 - - - +
177C PHE 3.1 0.2 - - - -
178C ASP* 1.3 84.2 - - - +
180C HIS* 1.3 78.2 + - + +
181C THR 3.4 0.2 - - - -
183C GLY* 3.3 21.8 + - - -
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Residues in contact with HIS 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A HIS* 3.1 43.5 + + - -
176C LEU* 2.8 43.2 + - + +
179C LYS* 1.3 78.6 - - + +
181C THR* 1.3 58.9 + - - +
184C ASP* 3.0 20.6 - - - +
175F TYR* 3.3 14.7 - + + +
176F LEU* 4.4 8.8 - - + +
179F LYS* 3.1 31.9 + - + +
180F HIS* 3.1 34.0 - + - -
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Residues in contact with THR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C HIS* 3.7 20.6 - - + +
161C ASN* 5.7 1.2 - - - +
177C PHE* 3.1 40.1 + - + -
180C HIS* 1.3 77.0 - - - +
182C LEU* 1.3 60.7 + - - +
183C GLY 3.1 7.6 + - - -
184C ASP* 3.3 19.1 + - - +
175F TYR* 2.6 33.5 + - - -
179F LYS* 3.6 13.2 + - - +
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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