Contacts of the helix formed by residues 182 - 190 (chain A) in PDB entry 1H5R
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 182 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASP* 2.9 17.2 + - - +
181A ASN* 1.3 81.3 + - - +
183A VAL* 1.3 64.0 + - - +
184A VAL 3.1 1.4 + - - -
185A GLN* 3.3 10.0 + - + +
186A MET* 3.2 28.4 + - + +
207A TYR* 3.8 5.4 - - - +
212A ARG* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.6 43.5 - - + -
100A ILE* 5.1 3.4 - - + -
105A CYS* 5.2 4.0 - - + -
179A TYR* 3.6 38.8 - - + -
180A ASP 3.6 12.8 - - - +
181A ASN* 3.2 1.3 - - - -
182A ASP* 1.3 77.2 - - - +
184A VAL* 1.3 67.1 + - + +
186A MET* 3.8 7.7 - - - +
187A ALA* 2.9 27.9 + - - +
203A ILE* 3.9 16.2 - - + -
207A TYR* 3.3 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.1 15.7 - - + +
97A GLU* 3.9 33.7 - - + +
100A ILE* 3.8 44.4 - - + -
101A GLY 5.3 1.8 - - - +
181A ASN* 3.8 11.4 + - - +
182A ASP 3.2 0.6 - - - -
183A VAL* 1.3 82.0 - - + +
185A GLN* 1.3 69.7 + - + +
187A ALA* 3.1 3.6 + - - +
188A LYS* 3.0 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 4.4 3.0 + - - -
181A ASN 5.5 2.9 - - - +
182A ASP* 3.3 10.3 + - + +
184A VAL* 1.3 83.1 - - + +
186A MET* 1.3 62.6 + - + +
188A LYS* 3.4 32.1 + - - +
189A ASN* 2.8 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ASP* 3.2 17.9 + - + +
183A VAL* 3.8 6.7 - - - +
185A GLN* 1.3 78.5 - - + +
187A ALA* 1.3 63.0 + - - +
189A ASN* 3.2 14.2 + - - +
190A LEU* 3.4 18.2 + - - +
203A ILE* 4.1 17.0 - - + -
206A ILE* 3.8 38.1 - - + +
207A TYR* 3.3 50.0 - - + +
210A GLN* 3.6 27.6 - - - +
212A ARG* 3.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA* 3.6 24.0 - - + +
93A PHE* 3.8 13.2 - - + -
94A ILE* 3.4 18.9 - - + +
183A VAL 2.9 18.1 + - - +
184A VAL* 3.1 4.5 + - - +
186A MET* 1.3 76.9 - - - +
188A LYS* 1.3 62.9 + - - +
189A ASN 3.0 1.1 + - - -
190A LEU* 3.2 30.0 + - - +
198A LEU* 4.9 1.0 - - - +
203A ILE* 4.0 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 4.0 28.9 - - + -
97A GLU* 3.1 37.4 + - + +
184A VAL* 3.0 31.8 + - + +
185A GLN* 3.9 24.8 + - - +
186A MET 3.3 0.2 - - - -
187A ALA* 1.3 76.0 - - - +
189A ASN* 1.3 62.9 + - - +
190A LEU 3.6 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLN* 2.8 37.6 + - - +
186A MET* 3.2 6.7 + - - +
187A ALA 3.0 0.8 - - - -
188A LYS* 1.3 81.3 - - - +
190A LEU* 1.3 59.4 + - - +
191A LYS* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA* 3.3 34.3 - - + -
186A MET 3.4 14.1 - - - +
187A ALA* 3.2 19.9 + - - +
188A LYS 4.4 4.2 - - - +
189A ASN* 1.3 81.0 - - - +
191A LYS* 1.3 68.3 + - - +
192A PRO* 4.8 0.2 - - - +
198A LEU* 3.9 21.0 - - + +
199A GLU 3.7 15.7 - - - +
202A ASP* 3.6 31.4 - - + +
203A ILE* 3.9 10.8 - - + +
206A ILE* 5.0 9.2 - - + -
----------------------------------------------------------
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