Contacts of the helix formed by residues 175 - 187 (chain A) in PDB entry 5OC9
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 175 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 3.7 35.5 - - + +
174A HIS* 1.3 69.2 - - - +
176A SER* 1.3 55.0 + - - +
177A GLU* 3.9 11.5 + - - +
178A ALA* 3.0 25.0 + - + +
179A LEU 2.8 31.2 + - - -
203A TYR* 2.8 13.8 + - + -
481A GLN* 5.0 0.2 - - - +
543A ARG* 3.7 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A HIS* 3.6 5.1 + - - +
175A ASP* 1.3 71.0 + - - +
177A GLU* 1.4 58.6 + - - +
179A LEU* 3.4 11.0 + - - +
180A LYS* 3.0 30.8 + - - +
481A GLN* 3.5 23.0 + - - +
485A GLU* 5.3 0.5 + - - -
539A ARG* 5.1 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP* 3.3 8.7 + - - +
176A SER* 1.4 79.3 - - - +
178A ALA* 1.4 61.5 + - - +
180A LYS* 3.6 6.7 + - - +
181A LYS* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP* 3.0 29.9 + - + +
177A GLU* 1.4 74.5 - - - +
179A LEU* 1.4 64.0 + - - +
181A LYS* 3.3 8.4 + - - +
182A LEU* 3.1 22.5 + - - +
203A TYR* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A HIS* 4.1 17.9 - - + +
175A ASP 2.8 13.9 + - - +
176A SER* 3.7 8.5 - - - +
178A ALA* 1.4 70.8 - - - +
180A LYS* 1.4 55.9 + - - +
182A LEU* 3.4 6.3 + - + +
183A GLU* 3.0 41.3 + - - +
203A TYR* 3.4 40.1 - - + +
204A PHE* 3.9 11.0 - - + -
538A CYS* 3.6 46.7 - - - +
539A ARG* 4.2 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER 3.0 17.7 + - - +
177A GLU* 3.8 7.4 - - - +
178A ALA 3.4 0.2 - - - -
179A LEU* 1.4 73.0 - - - +
181A LYS* 1.4 63.6 + - - +
183A GLU* 3.4 20.9 - - - +
184A ASP* 3.4 24.9 - - - +
539A ARG* 4.5 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU 3.3 11.5 + - - +
178A ALA* 3.6 11.0 - - - +
179A LEU 3.3 0.4 - - - -
180A LYS* 1.4 78.7 - - - +
182A LEU* 1.4 61.0 + - - +
184A ASP* 3.7 11.9 + - - +
185A THR* 3.6 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ALA 3.1 13.1 + - - +
179A LEU* 3.7 10.5 - - + +
180A LYS 3.4 0.2 - - - -
181A LYS* 1.4 74.8 - - - +
183A GLU* 1.4 53.0 + - - +
185A THR* 2.7 22.9 + - - +
186A TRP* 2.9 42.7 + - + +
196A PRO* 4.7 2.5 - - + -
199A SER* 3.7 38.1 - - - +
200A ILE* 4.0 13.0 - - + +
203A TYR* 3.9 22.7 - - + -
204A PHE* 3.7 31.6 - - + -
538A CYS* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 3.0 22.7 + - - +
180A LYS* 3.4 12.2 - - - +
182A LEU* 1.4 75.6 - - - +
184A ASP* 1.3 61.2 + - - +
186A TRP* 4.3 5.2 - - - -
187A TYR* 2.9 53.9 + - + +
538A CYS* 3.3 34.3 - - - +
539A ARG* 2.8 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 3.4 18.2 + - - +
181A LYS* 4.1 7.7 - - - +
182A LEU 3.3 0.6 - - - -
183A GLU* 1.3 80.4 - - - +
185A THR* 1.4 62.2 + - + +
187A TYR 4.4 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LYS 3.7 10.3 + - - +
182A LEU* 2.7 28.4 + - - +
184A ASP* 1.4 79.0 - - + +
186A TRP* 1.3 59.6 + - - +
194A TYR 5.6 0.5 - - - +
196A PRO* 3.4 28.9 - - - +
199A SER* 5.1 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 2.9 33.0 + - + +
183A GLU 3.8 4.0 - - - +
185A THR* 1.3 78.8 - - - +
187A TYR* 1.4 63.5 + + + +
195A GLN* 2.8 30.1 + - + +
196A PRO* 4.1 16.3 - - + +
200A ILE* 3.5 20.6 - - + +
204A PHE* 3.6 26.5 - + - -
212A PHE* 3.5 45.8 - + - -
530A VAL* 4.6 9.3 - - + +
531A ASN* 4.7 4.0 - - - +
534A ALA* 3.6 24.5 - - + +
537A MET* 4.2 4.9 - - + -
538A CYS* 3.6 32.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 2.9 50.7 + - + +
184A ASP* 4.4 10.3 - - - -
185A THR 3.9 0.4 - - - -
186A TRP* 1.4 77.6 - - + +
531A ASN* 3.8 33.7 - - + +
534A ALA* 3.6 34.5 - - + -
535A LEU* 3.5 39.8 - - + +
538A CYS* 3.8 16.2 - - - +
539A ARG* 4.2 4.2 - - - +
----------------------------------------------------------
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