Contacts of the helix formed by residues 172 - 181 (chain A) 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 LEU 172 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLY* 1.3 70.2 - - - +
173A ALA* 1.3 56.5 + - - +
174A GLU 3.7 0.4 - - - -
175A TYR* 3.9 11.0 - - + +
176A LEU* 3.2 42.6 + - + +
172C LEU* 5.1 12.8 - - + -
164H LYS* 4.3 1.0 - - - +
165H MET* 3.8 58.9 - - + +
170H SER* 5.4 5.2 - - - +
172H LEU* 4.5 20.6 - - + -
173H ALA* 4.4 8.1 - - - -
176H LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 4.8 1.8 - - - -
165A MET* 3.2 55.1 - - + +
167A ALA* 4.1 8.3 - - + +
170A SER* 3.4 19.9 + - - +
171A GLY 2.8 5.3 + - - -
172A LEU* 1.3 76.1 - - - +
174A GLU* 1.3 59.9 + - - +
175A TYR 3.2 0.9 - - - -
176A LEU 3.4 0.5 + - - -
177A PHE* 3.0 24.5 + - - +
172C LEU* 5.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.0 20.7 - - + +
51A PHE* 3.7 7.6 - - + -
95A SER* 3.9 3.9 - - - -
96A GLY* 2.9 34.5 + - - -
97A LEU 3.2 10.0 + - - -
162A LEU* 4.0 14.1 - - + -
167A ALA* 3.8 26.0 - - + +
168A PRO* 3.9 16.1 - - - +
170A SER 4.0 6.5 + - - +
171A GLY* 5.7 3.1 - - - -
172A LEU 4.5 0.8 - - - +
173A ALA* 1.3 75.3 - - - +
175A TYR* 1.3 63.9 + - - +
177A PHE* 4.3 0.2 - - - -
178A ASP* 3.1 23.6 + - - +
164H LYS* 6.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.5 9.4 - - + +
172A LEU* 3.9 11.6 - - + +
173A ALA 3.2 0.6 - - - -
174A GLU* 1.3 77.7 - - - +
176A LEU* 1.3 81.2 + - + +
178A ASP* 3.3 5.4 + - - +
179A LYS* 3.1 37.8 + - + +
161H ASN* 3.7 25.1 - - - +
164H LYS* 5.4 4.2 - - - +
165H MET* 3.4 44.2 - - + -
176H LEU* 4.6 6.3 - - + -
177H PHE* 3.4 17.5 - + - -
180H HIS* 3.4 18.1 - + + +
181H THR* 2.4 43.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A MET* 4.4 7.6 - - + -
172A LEU* 3.2 25.8 + - + +
173A ALA 3.4 2.4 + - - +
175A TYR* 1.3 92.6 - - + +
177A PHE* 1.3 61.4 + - - +
179A LYS* 4.4 1.8 - - - +
180A HIS* 2.9 63.2 + - + +
172C LEU* 4.0 15.7 - - + -
175C TYR* 4.2 3.4 - - + -
176C LEU* 4.0 23.8 - - + -
176H LEU* 4.1 30.3 - - + -
180H HIS* 4.4 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.7 20.0 - + - -
100A MET* 5.4 0.4 - - - -
158A HIS* 3.5 48.2 - + + -
161A ASN* 3.7 22.9 - - + -
162A LEU* 3.6 26.7 - - + -
165A MET* 3.9 17.8 - - + +
173A ALA 3.0 18.1 + - - +
174A GLU 4.0 2.5 - - - +
176A LEU* 1.3 75.2 - - - +
178A ASP* 1.3 65.0 + - - +
181A THR* 3.0 46.9 + - + -
182A LEU* 3.1 22.8 + - + -
175C TYR* 3.5 8.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.3 17.1 - - + -
49A LYS 4.1 4.6 + - - -
50A ASN* 2.7 66.7 + - - +
51A PHE* 2.9 25.6 + - + -
174A GLU 3.1 19.6 + - - +
175A TYR* 3.4 6.1 - - + +
177A PHE* 1.3 78.2 - - - +
179A LYS* 1.3 73.6 + - + +
182A LEU* 4.3 4.9 - - - -
183A GLY 3.0 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 5.8 1.4 + - - -
49A LYS* 4.9 12.5 - - - +
50A ASN* 4.1 8.6 - - - +
175A TYR* 3.1 33.0 + - + +
176A LEU* 4.0 5.2 - - - +
178A ASP* 1.3 98.1 + - + +
180A HIS* 1.3 62.7 + - - +
183A GLY* 3.6 14.1 - - - -
184A ASP* 4.2 2.4 + - - +
161H ASN* 6.1 1.4 - - - +
180H HIS* 3.8 48.2 - - + +
181H THR* 3.4 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 2.9 46.6 + - + +
179A LYS* 1.3 82.7 - - - +
181A THR* 1.3 55.5 + - - +
183A GLY 4.4 0.7 - - - -
184A ASP 3.9 12.4 - - - -
175C TYR* 3.3 11.1 - - - +
176C LEU* 4.2 7.7 - - + +
179C LYS* 2.5 44.2 + - + +
180C HIS* 3.1 32.9 + + - -
180H HIS* 3.0 35.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A HIS* 3.9 21.8 - - + +
161A ASN* 5.6 0.2 - - - -
177A PHE* 3.0 39.5 + - + -
180A HIS* 1.3 76.3 - - - +
182A LEU* 1.3 65.2 + - - +
183A GLY 3.2 1.6 + - - -
184A ASP* 3.8 12.8 + - - -
49C LYS* 3.8 17.5 + - - +
175C TYR* 2.7 30.8 + - - -
179C LYS* 3.7 10.3 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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