Contacts of the helix formed by residues 187 - 194 (chain B) in PDB entry 3HW4
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 187 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B LEU* 5.2 0.9 - - + +
-1B GLY 3.5 31.0 - - - +
0B SER 3.9 5.2 - - - +
1B MET* 4.2 26.2 - - + +
4B PHE* 3.7 33.7 - - + -
33B ASN* 4.8 0.3 - - - +
182B MET* 2.8 17.5 + - + +
185B ARG* 3.3 39.0 - - + +
186B GLY* 1.3 80.1 - - - +
188B TRP* 1.3 65.8 + - - +
189B ASP 3.3 1.8 - - - -
190B SER* 3.7 5.4 + - - -
191B PHE* 3.3 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG* 3.7 32.1 - - + -
150B PHE* 3.6 31.2 - + + -
151B THR* 5.6 3.4 - - + -
179B ARG* 3.5 53.8 - - + +
182B MET* 3.5 11.3 + - - -
183B ALA* 3.6 30.2 - - + +
186B GLY 3.5 1.4 - - - -
187B LEU* 1.3 78.8 - - - +
189B ASP* 1.3 55.6 + - - +
191B PHE* 3.2 30.3 + + - +
192B ARG* 2.7 75.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY 4.6 7.1 + - - +
187B LEU 3.3 0.4 - - - -
188B TRP* 1.3 81.2 - - - +
190B SER* 1.3 58.7 + - - +
192B ARG* 2.9 26.6 + - - +
193B GLN* 2.8 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 3.0 20.5 + - - -
186B GLY 5.2 1.7 + - - -
187B LEU* 3.7 6.8 + - - -
188B TRP 3.4 0.4 - - - -
189B ASP* 1.3 77.9 - - - +
191B PHE* 1.3 61.3 + - - +
193B GLN* 4.3 6.1 - - - +
194B SER* 2.8 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.9 10.3 - - + -
33B ASN* 3.5 44.9 + - + +
36B ALA* 3.9 4.7 - - + -
37B ALA* 3.6 22.2 - - - -
40B THR* 4.7 0.2 - - - -
124B ARG* 2.7 51.5 + - - -
150B PHE* 3.5 36.3 - + - -
182B MET* 3.3 30.1 - - + -
187B LEU 3.3 19.2 + - - +
188B TRP* 3.2 18.5 + + - +
190B SER* 1.3 77.0 - - - +
192B ARG* 1.3 54.3 + - - +
194B SER* 3.1 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG* 3.5 37.6 - - + +
125B ARG* 4.2 15.0 - - + -
179B ARG* 5.9 0.6 - - - +
188B TRP* 2.7 62.1 + - + +
189B ASP* 2.9 37.3 + - - +
191B PHE* 1.3 71.6 - - - +
193B GLN* 1.3 77.0 + - - +
194B SER 3.3 0.3 + - - -
195B GLU* 3.4 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG* 5.9 0.6 - - - +
189B ASP* 2.8 51.0 + - - +
190B SER* 3.9 5.8 - - - +
192B ARG* 1.3 99.5 - - - +
194B SER* 1.3 61.9 + - - +
195B GLU 3.3 6.6 + - - +
196B ARG* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 3.5 28.5 - - - +
124B ARG* 3.1 10.6 + - - -
190B SER* 2.8 15.9 + - - -
191B PHE 3.1 14.9 + - - -
192B ARG 3.2 0.2 - - - -
193B GLN* 1.3 75.5 - - - +
195B GLU* 1.3 61.6 + - - +
196B ARG* 3.3 15.1 + - - +
----------------------------------------------------------
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