Contacts of the strand formed by residues 179 - 186 (chain D) in PDB entry 6D6Q
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 ALA 179 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D ALA* 3.5 0.3 - - - -
159D LEU* 2.8 45.7 + - + +
177D ALA* 4.0 1.7 - - - +
178D ARG* 1.3 81.5 - - + +
180D VAL* 1.3 71.6 + - - +
181D LEU* 5.3 2.2 - - + -
198D LYS 3.4 9.6 - - - +
199D GLY 4.8 0.2 - - - -
200D LEU 3.9 16.4 - - - +
201D TYR* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ALA* 5.1 5.6 - - + -
157D CYS 3.5 14.8 - - - +
158D ALA* 4.2 13.5 - - + -
169D PRO* 5.1 0.9 - - + -
174D GLU* 4.4 42.4 - - + +
177D ALA* 4.7 1.8 - - + -
178D ARG 5.8 0.2 - - - -
179D ALA* 1.3 81.4 - - - +
181D LEU* 1.3 69.8 + - - +
182D THR* 4.3 6.5 - - - +
196D SER 4.7 0.4 - - - -
197D THR* 3.2 5.7 + - - -
198D LYS* 2.8 54.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D VAL 3.9 0.2 - - - +
156D ALA* 3.4 2.0 - - - -
157D CYS* 2.9 51.4 + - - +
159D LEU* 4.6 14.8 - - + -
179D ALA* 5.3 0.4 - - + -
180D VAL* 1.3 80.9 - - - +
182D THR* 1.3 62.6 + - - +
183D PHE* 3.5 18.5 + - + -
195D SER* 4.8 5.2 - - - +
196D SER 3.7 1.6 - - - -
197D THR* 2.8 36.1 - - - +
201D TYR* 3.8 28.7 - - + +
206D LEU* 4.3 8.3 - - + -
209D CYS* 3.6 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D LEU* 3.6 32.8 + - + +
131D ALA* 4.3 8.9 + - - +
134D LEU* 4.9 2.9 - - + -
155D VAL 3.3 12.1 - - - +
156D ALA* 4.1 11.0 - - - +
180D VAL* 5.0 5.5 - - - +
181D LEU* 1.3 73.8 - - - +
183D PHE* 1.3 64.7 + - - +
194D MET* 3.8 10.7 - - + +
195D SER* 3.2 7.6 + - - -
196D SER* 2.9 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 4.9 0.2 - - + -
154D GLY* 3.3 2.8 - - - -
155D VAL* 2.9 39.8 + - + +
157D CYS* 3.5 33.0 - - - -
181D LEU* 3.5 15.9 - - + -
182D THR* 1.3 75.1 - - - +
184D ALA* 1.3 60.2 + - - +
185D LEU* 3.7 19.8 - - + +
192D LEU* 3.5 31.6 - - + -
194D MET 3.4 1.1 - - - +
195D SER* 3.4 24.7 - - - -
206D LEU* 3.7 30.3 - - + -
209D CYS* 3.7 12.8 - - + -
210D LEU* 4.3 11.0 - - + -
213D ALA* 4.4 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D THR* 4.7 9.9 - - + +
134D LEU* 3.7 23.8 - - + -
152D PHE* 5.4 1.1 - - + -
153D CYS 3.1 7.9 - - - +
183D PHE* 1.3 71.8 - - - +
185D LEU* 1.3 57.1 + - - +
192D LEU* 3.5 1.6 - - - -
193D LEU* 2.5 40.0 + - + +
194D MET* 2.8 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D PHE* 3.2 8.7 - - - +
153D CYS* 2.9 34.2 + - + +
155D VAL* 4.3 5.6 - - + +
183D PHE* 3.7 33.0 - - + +
184D ALA* 1.3 74.9 - - - +
186D ASP* 1.3 64.5 + - - +
190D ARG* 4.8 7.0 - - + +
191D LYS 3.2 17.5 - - - +
192D LEU* 5.1 1.6 - - - -
193D LEU* 4.0 4.3 - - - -
210D LEU* 5.2 6.7 - - + +
213D ALA* 3.9 11.7 - - + +
214D GLN* 3.7 30.3 - - + +
217D SER* 3.4 33.7 - - - +
221D PHE* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D VAL* 5.0 3.8 - - - +
150D ALA* 3.2 21.5 - - - +
151D LEU 2.7 16.9 - - - +
185D LEU* 1.3 77.8 - - - +
187D SER* 1.3 80.9 + - - +
188D VAL* 3.9 13.2 + - - +
189D GLU* 4.9 1.6 + - + +
190D ARG* 3.3 22.4 - - - +
191D LYS* 3.5 19.5 + - + +
193D LEU* 3.9 26.3 - - + +
221D PHE* 3.7 12.0 - - - -
----------------------------------------------------------
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