Contacts of the helix formed by residues 160 - 174 (chain A) in PDB entry 2HSG
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 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 1.3 73.8 - - - +
161A TYR* 1.3 56.9 + - - +
162A GLU* 3.2 12.6 + - - +
163A GLN* 2.8 42.3 + - + +
164A ALA* 2.9 27.7 + - - +
320A GLN* 3.0 36.7 - - + +
321A LEU 3.8 6.3 + - - +
323A HIS* 3.9 7.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 3.4 31.2 + - - -
148A ILE* 3.8 29.6 - - + -
158A THR* 4.1 12.8 - - - -
159A ILE* 3.7 26.0 - - + -
160A ASP* 1.3 72.8 + - - +
162A GLU* 1.3 55.2 + - - +
164A ALA* 3.5 1.5 - - - +
165A ALA* 2.6 36.4 + - - +
191A ILE* 3.8 36.4 - - + +
195A LYS* 3.6 28.3 - - + +
196A LYS* 4.4 11.0 - - + +
274A PHE* 3.9 14.5 - + - -
292A GLN* 3.7 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 3.2 9.1 - - - +
161A TYR* 1.3 78.3 - - - +
163A GLN* 1.3 61.9 + - + +
165A ALA* 3.4 0.2 - - - +
166A PHE* 2.7 25.3 + - - +
194A ALA 5.1 0.7 - - - +
195A LYS* 3.5 33.2 - - + +
198A LYS* 3.1 16.0 - - + +
199A GLY* 2.8 37.7 + - - -
202A ARG* 2.2 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 2.8 30.2 + - + +
162A GLU* 1.3 83.5 - - + +
164A ALA* 1.3 51.9 + - - +
166A PHE* 3.3 14.9 - - - +
167A ASP* 2.6 74.7 + - - +
202A ARG* 2.8 29.2 + - - +
323A HIS* 4.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.8 5.2 - - + -
160A ASP 2.9 19.0 + - - +
161A TYR 3.2 4.7 + - - +
163A GLN* 1.3 72.4 - - - +
165A ALA* 1.3 53.4 + - - +
167A ASP* 3.1 2.4 + - - +
168A ALA* 2.7 35.9 + - - +
274A PHE* 3.7 24.9 - - + -
290A VAL* 4.2 7.5 - - + +
323A HIS* 3.4 32.7 - - + +
325A ILE* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR 2.6 20.5 + - - +
162A GLU 3.4 5.6 - - - +
164A ALA* 1.3 68.9 - - - +
166A PHE* 1.3 57.5 + - - +
168A ALA* 2.9 3.5 + - - +
169A VAL* 2.6 39.1 + - - +
196A LYS* 3.4 39.9 - - + +
199A GLY* 3.9 5.4 - - - -
200A TYR* 4.1 0.7 - - - +
244A PHE* 4.2 18.8 - - + -
274A PHE* 4.1 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU* 2.7 21.6 + - - +
163A GLN* 3.3 16.8 - - - +
165A ALA* 1.3 73.0 - - - +
167A ASP* 1.3 65.9 + - - +
169A VAL* 3.1 1.0 + - - -
170A GLN* 2.7 61.2 + - + -
199A GLY* 3.3 15.7 + - - +
202A ARG* 3.1 35.4 - - + +
203A ALA* 3.5 31.2 - - - +
206A GLU* 3.2 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN* 2.6 50.1 + - - +
164A ALA 3.5 4.5 - - - +
166A PHE* 1.3 74.3 - - - +
168A ALA* 1.3 67.6 + - - +
170A GLN* 3.3 5.9 + - - +
171A SER* 3.2 17.2 + - - -
323A HIS* 2.7 29.4 + - - +
325A ILE* 3.8 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA 2.7 17.5 + - - +
165A ALA 2.9 6.0 + - - +
167A ASP* 1.3 70.7 - - - +
169A VAL* 1.3 62.8 + - - +
171A SER* 2.7 25.6 + - - -
172A LEU* 3.7 3.5 + - - +
244A PHE* 3.3 38.8 - - + -
272A ILE* 3.7 19.4 - - + +
290A VAL* 4.3 6.5 - - + -
325A ILE* 3.9 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA 2.6 21.1 + - - +
168A ALA* 1.3 70.2 - - - +
170A GLN* 1.3 65.9 + - - +
172A LEU* 2.7 18.7 + - - +
173A ILE* 3.1 21.0 + - + +
180A ILE* 4.2 21.1 - - + -
200A TYR* 3.5 35.4 - - + -
203A ALA* 3.5 23.1 - - + -
204A LEU* 4.3 9.9 - - + -
244A PHE* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 2.7 49.4 + - + +
167A ASP* 3.7 9.2 - - - +
168A ALA 3.3 0.2 - - - -
169A VAL* 1.3 72.7 - - - +
171A SER* 1.3 57.5 + - - +
173A ILE* 3.0 27.4 + - - +
174A ASP* 2.6 64.8 + - - +
203A ALA* 4.3 2.2 - - - +
207A SER* 4.4 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASP 3.2 7.1 + - - -
168A ALA* 2.7 20.9 + - - -
170A GLN* 1.3 78.9 - - - +
172A LEU* 1.3 63.6 + - - +
174A ASP* 3.7 10.6 + - - +
175A SER* 3.4 18.2 + - - -
270A GLU* 5.0 0.9 - - - +
272A ILE* 2.9 22.2 - - - +
325A ILE* 5.2 0.3 - - - +
327A PHE* 3.8 27.2 - - - -
331A THR* 5.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA 3.9 10.8 - - - +
169A VAL* 2.7 13.9 + - - +
171A SER* 1.3 78.6 - - - +
173A ILE* 1.3 58.4 + - - +
175A SER* 2.9 18.0 + - - -
176A GLY 3.4 1.4 + - - -
177A HIS* 3.1 23.1 + - - +
180A ILE* 3.4 38.1 - - + -
242A ALA* 3.9 18.2 - - + -
243A ILE 4.2 16.8 - - - +
244A PHE* 4.3 7.4 - - + +
270A GLU* 3.8 27.6 - - + +
272A ILE* 3.9 22.0 - - + -
331A THR* 4.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A VAL* 3.7 19.7 - - + +
170A GLN* 3.0 19.2 + - - +
172A LEU* 1.3 71.5 - - - +
174A ASP* 1.3 55.4 + - - +
175A SER 2.5 16.0 + - - -
176A GLY* 2.8 14.7 + - - -
177A HIS 3.9 8.7 + - - +
180A ILE* 3.7 16.2 - - + -
203A ALA* 2.9 36.1 - - + +
204A LEU* 4.4 1.1 - - + -
207A SER* 3.9 23.6 - - - +
209A LEU* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLN* 2.6 59.9 + - - +
171A SER* 3.7 9.1 + - - +
172A LEU 3.3 0.4 - - - -
173A ILE* 1.3 71.7 - - - +
175A SER* 1.3 57.5 + - - +
176A GLY 3.5 0.2 - - - -
----------------------------------------------------------
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