Contacts of the helix formed by residues 185 - 199 (chain B) in PDB entry 2DH3
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 SER 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.9 2.1 - - - +
179B ILE* 3.8 9.1 - - - +
184B GLY* 1.3 74.0 - - - -
186B LYS* 1.3 63.5 + - - +
187B GLU* 2.8 22.3 + - - +
188B ASP* 3.2 29.0 + - - +
189B PHE* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU 6.2 0.2 - - - +
179B ILE* 3.7 20.9 - - + +
185B SER* 1.3 73.0 - - - +
187B GLU* 1.3 67.5 + - - +
189B PHE* 3.5 2.4 + - + +
190B ASP* 3.0 58.4 + - - +
235B PHE* 4.6 17.8 - - + -
236B TRP* 4.1 21.2 - - + -
239B ALA* 3.4 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER* 2.8 23.1 + - - +
186B LYS* 1.3 82.9 + - - +
188B ASP* 1.3 65.2 + - - +
190B ASP* 3.4 11.9 + - - +
191B SER* 3.2 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASN* 6.0 0.7 - - - +
140B LEU* 4.2 17.6 - - + +
141B ALA* 4.1 24.8 + - + +
144B LYS* 5.0 3.7 - - - +
184B GLY* 3.9 5.7 - - - -
185B SER* 3.2 35.0 + - - +
187B GLU* 1.3 79.8 - - - +
189B PHE* 1.3 63.0 + - - +
191B SER* 3.1 10.1 + - - -
192B LEU* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.0 23.2 - - + +
160B LEU* 4.5 15.9 - - + -
163B ILE* 4.1 21.8 - - + -
179B ILE* 4.0 11.7 - - + -
185B SER 3.1 10.8 + - - +
186B LYS* 3.5 10.3 - - + +
188B ASP* 1.3 77.7 - - - +
190B ASP* 1.3 69.9 + - - +
192B LEU* 3.0 22.9 + - + +
193B LEU* 3.2 40.9 + - + +
203B VAL* 5.3 5.4 - - + -
205B LEU* 4.8 9.2 - - + -
236B TRP* 3.6 33.0 - + - -
239B ALA* 5.2 2.0 - - + -
241B VAL* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LYS* 3.0 52.8 + - - +
187B GLU* 3.6 13.7 - - - +
189B PHE* 1.3 79.6 - - - +
191B SER* 1.3 62.1 + - - +
193B LEU* 3.3 11.6 + - - +
194B GLN* 3.1 22.8 + - - +
239B ALA* 5.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS* 3.9 22.5 + - - +
187B GLU 3.2 8.8 + - - -
188B ASP* 3.1 11.9 + - - -
190B ASP* 1.3 76.2 - - - +
192B LEU* 1.3 62.1 + - - +
194B GLN* 3.6 14.8 + - - +
195B SER* 3.0 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.1 32.1 - - + +
143B LEU* 4.0 26.9 - - + +
144B LYS* 3.8 39.6 - - + +
147B LEU* 4.2 13.2 - - + -
158B LEU* 6.1 2.5 - - + -
160B LEU* 4.4 10.3 - - + -
188B ASP 3.1 9.9 + - - +
189B PHE* 3.0 17.3 + - + +
191B SER* 1.3 77.2 - - - +
193B LEU* 1.3 58.5 + - + +
195B SER* 3.4 2.9 + - - -
196B ALA* 2.9 32.0 + - + +
203B VAL* 5.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE* 3.2 44.1 + - + +
190B ASP* 3.3 12.8 + - - +
192B LEU* 1.3 79.8 - - + +
194B GLN* 1.3 64.0 + - - +
196B ALA* 3.7 3.7 - - + +
197B LYS* 3.1 40.7 + - + +
203B VAL* 3.6 37.7 - - + -
239B ALA* 4.5 11.4 - - + +
240B GLY* 4.1 30.5 - - - +
241B VAL* 4.4 4.7 - - + +
242B ASP* 5.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP 3.1 14.6 + - - +
191B SER* 3.9 15.9 + - - +
192B LEU 3.4 0.2 - - - -
193B LEU* 1.3 76.2 - - - +
195B SER* 1.3 62.5 + - - +
197B LYS* 3.5 5.1 + - - +
198B LYS* 3.2 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS* 3.9 15.4 - - - +
147B LEU* 4.1 15.5 - - - -
191B SER* 3.0 19.0 + - - -
192B LEU 3.7 3.8 - - - -
194B GLN* 1.3 76.1 + - - +
196B ALA* 1.3 64.4 + - - +
198B LYS* 3.5 6.7 + - - +
199B LYS* 3.1 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 4.1 15.7 - - + +
192B LEU* 2.9 20.5 + - + +
193B LEU* 3.7 6.5 - - + +
194B GLN 3.3 0.2 - - - -
195B SER* 1.3 76.6 - - - +
197B LYS* 1.3 60.0 + - + +
199B LYS* 3.3 4.0 + - - -
200B SER 3.1 4.0 + - - -
201B ILE* 2.8 47.4 + - + +
203B VAL* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.1 32.3 + - + +
194B GLN* 3.9 4.7 - - - +
196B ALA* 1.3 75.4 - - + +
198B LYS* 1.3 59.6 + - - +
200B SER* 2.9 22.8 + - - +
201B ILE 4.3 7.0 - - - +
202B ARG* 5.7 7.0 - - - +
239B ALA 5.3 1.2 + - - -
240B GLY* 3.5 31.3 + - - -
242B ASP* 4.7 14.1 - - - +
273B ARG* 5.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLN* 3.2 17.6 + - + +
195B SER* 3.8 7.6 - - - +
197B LYS* 1.3 77.5 - - - +
199B LYS* 1.3 62.2 + - + +
200B SER* 3.4 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS 5.3 3.1 - - - -
147B LEU* 3.9 28.3 - - + +
148B ASP* 2.7 34.4 + - - +
151B SER* 4.9 9.9 + - - -
195B SER* 3.1 24.2 + - - +
196B ALA* 3.3 3.3 + - - +
197B LYS 3.1 0.8 - - - -
198B LYS* 1.3 80.9 - - + +
200B SER* 1.3 71.1 + - - +
201B ILE* 3.4 17.2 + - + +
----------------------------------------------------------
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