Contacts of the helix formed by residues 170 - 185 (chain D) in PDB entry 4WLU
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 THR 170 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D VAL* 4.9 1.1 - - + -
168D GLY 3.1 13.2 + - - +
169D VAL* 1.3 73.9 - - - +
171D THR* 1.3 65.6 + - - +
172D LEU* 3.1 3.8 - - - -
173D ASP* 2.9 34.8 + - - +
174D ILE* 3.6 10.0 - - - +
196D VAL* 5.9 1.1 - - - -
199D GLY 4.8 5.4 - - - +
200D HIS* 4.2 23.1 - - + -
275D CYS 3.5 19.7 + - - -
276D SER* 3.6 1.0 - - - -
277D PHE* 3.8 22.0 - - + +
289D SER* 3.6 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D VAL* 3.4 8.7 - - - +
170D THR* 1.3 78.6 + - - +
172D LEU* 1.3 61.6 + - - +
174D ILE* 3.0 21.6 + - + +
175D VAL* 3.0 13.7 + - + +
254D ALA* 3.4 30.5 - - + +
257D ARG* 3.9 32.5 - - + +
258D PHE* 3.4 32.3 - - + +
274D GLU* 4.4 7.1 + - - +
275D CYS 4.3 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C HIS* 5.1 0.9 - - + -
170D THR 3.0 1.6 + - - -
171D THR* 1.3 78.4 - - - +
173D ASP* 1.3 58.2 + - - +
175D VAL* 4.3 12.6 - - + -
176D ARG* 2.9 79.6 + - + +
200D HIS* 5.1 0.4 - - + -
247D ALA* 4.2 2.0 - - + -
250D SER* 3.6 42.6 - - - +
251D MET* 3.9 31.5 - - + +
254D ALA* 3.6 14.9 - - + +
401D LMR 3.9 9.2 - - - +
402D NAD 4.8 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D THR* 2.9 16.6 + - - +
172D LEU* 1.3 76.7 - - - +
174D ILE* 1.3 57.4 + - + +
176D ARG* 3.7 16.0 + - - +
177D ALA* 3.0 28.2 + - - +
196D VAL* 3.9 22.7 - - + +
199D GLY 3.9 6.8 - - - +
200D HIS* 2.8 38.8 + - - -
205D ILE* 3.8 31.6 - - + +
230D ILE* 4.2 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D THR* 3.6 23.1 - - - +
171D THR* 3.0 11.5 + - + +
173D ASP* 1.3 73.8 - - + +
175D VAL* 1.3 61.7 + - - +
177D ALA* 3.3 1.6 + - - +
178D ASN* 2.9 49.5 + - - +
193D ASN* 4.6 7.9 - - - +
194D VAL 3.6 21.3 - - - +
196D VAL* 3.7 30.5 - - + +
257D ARG* 3.9 22.0 - - - +
274D GLU* 5.9 1.3 - - - +
275D CYS* 3.7 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C HIS 3.4 17.3 - - - +
71C ILE* 3.9 5.4 - - + -
72C GLU* 3.6 46.6 - - + +
171D THR* 3.0 23.1 + - + +
172D LEU* 3.7 15.9 - - + +
174D ILE* 1.3 76.3 - - - +
176D ARG* 1.3 61.0 - - - +
178D ASN* 3.4 3.8 + - - +
179D THR* 3.0 26.2 + - - -
253D TYR* 3.8 20.0 - - + -
254D ALA* 4.4 4.0 - - + -
257D ARG* 4.1 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C HIS* 3.3 41.6 + - + +
110D ARG* 4.2 1.8 - - - +
172D LEU* 2.9 44.4 + - + +
173D ASP* 3.7 20.3 + - - +
175D VAL* 1.3 72.8 - - - +
177D ALA* 1.3 66.2 + - - +
179D THR* 3.0 3.6 + - - -
180D PHE* 2.9 42.1 + - + -
205D ILE* 5.9 0.6 - - - +
230D ILE* 4.9 6.8 + - + -
233D ALA* 3.5 17.9 + - + +
234D GLY* 3.5 25.6 - - - +
237D VAL* 4.5 1.2 - - - +
247D ALA* 3.9 9.9 - - - +
250D SER* 5.0 0.2 + - - -
401D LMR 2.5 44.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ASP 3.0 18.4 + - - +
174D ILE 3.6 4.5 - - - +
176D ARG* 1.3 74.6 - - - +
178D ASN* 1.3 57.5 + - - +
180D PHE* 3.4 0.7 + - - +
181D VAL* 2.9 36.4 + - + +
194D VAL* 3.7 27.6 - - + -
196D VAL* 4.1 8.5 - - + -
230D ILE* 3.7 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLU* 2.8 28.2 + - + +
174D ILE* 2.9 29.8 + - - +
175D VAL 3.5 7.4 - - - +
177D ALA* 1.3 75.1 - - - +
179D THR* 1.3 56.7 + - - +
182D ALA* 3.0 31.2 + - - +
189D PRO* 4.2 8.7 - - - +
192D VAL* 3.1 36.0 + - + +
193D ASN* 3.5 4.3 - - - +
194D VAL* 2.8 28.9 + - - +
257D ARG* 4.1 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 6.0 0.4 - - - +
69C SER 3.4 24.2 - - - +
70C HIS* 2.8 23.8 + - - +
71C ILE 3.3 17.9 - - - +
72C GLU* 3.3 4.2 - - - -
73C THR 5.6 2.0 - - - +
175D VAL 3.0 8.5 + - - -
176D ARG* 3.0 7.4 + - - -
178D ASN* 1.3 75.5 - - - +
180D PHE* 1.3 62.9 + - + +
182D ALA* 3.4 2.3 + - - +
183D GLU* 2.9 46.0 + - + +
189D PRO* 4.3 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C SER 5.4 0.2 - - - -
70C HIS* 3.7 42.0 - + - -
176D ARG* 2.9 32.3 + - + +
177D ALA 4.0 1.8 - - - +
179D THR* 1.3 78.0 - - + +
181D VAL* 1.3 65.2 + - - +
183D GLU* 3.4 19.9 + - - +
184D LEU* 3.1 30.0 + - + +
226D LEU* 3.6 19.1 - - + -
229D ARG* 3.7 53.4 - - + +
230D ILE* 3.7 19.5 - - + -
233D ALA* 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ALA 2.9 19.7 + - - +
178D ASN 4.0 2.7 - - - +
180D PHE* 1.3 75.0 - - - +
182D ALA* 1.3 64.4 + - - +
184D LEU* 3.3 2.6 + - - +
185D LYS* 3.0 25.3 + - + +
187D LEU* 4.8 4.3 - - + -
192D VAL* 4.0 17.9 - - + -
194D VAL* 3.8 14.8 - - + -
209D ILE* 4.0 11.0 - - + -
212D CYS* 4.1 13.2 - - - -
216D VAL* 4.3 20.4 - - + -
218D PHE* 4.6 12.3 - - + -
226D LEU* 3.9 24.2 - - + -
230D ILE* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ASN 3.0 20.2 + - - +
179D THR 3.7 3.8 - - - +
181D VAL* 1.3 76.1 - - - +
183D GLU* 1.3 57.6 + - - +
186D GLY* 2.9 11.3 + - - -
187D LEU* 2.9 46.7 + - - +
189D PRO* 3.5 30.3 - - + -
192D VAL* 4.0 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C SER* 4.7 4.9 - - - +
179D THR* 2.9 38.0 + - + +
180D PHE* 3.5 22.1 - - - +
181D VAL 3.3 0.2 - - - -
182D ALA* 1.3 78.7 - - - +
184D LEU* 1.3 64.9 + - + +
185D LYS 3.3 0.2 + - - -
186D GLY* 3.4 8.4 + - - -
229D ARG* 5.2 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D PHE* 3.1 18.8 + - + +
181D VAL 3.3 3.8 + - - +
183D GLU* 1.3 82.9 - - + +
185D LYS* 1.3 62.8 + - - +
186D GLY 3.5 0.7 + - - -
218D PHE* 3.9 29.4 - - + -
222D GLN* 4.2 22.0 - - + +
226D LEU* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D VAL* 3.0 16.7 + - + +
184D LEU* 1.3 80.1 - - - +
186D GLY* 1.3 64.8 + - - +
187D LEU* 3.2 28.5 + - + +
216D VAL* 3.9 26.5 - - + +
217D ASP* 2.8 32.1 + - - +
218D PHE* 3.8 32.0 - - + +
219D PRO* 5.7 1.2 - - - +
222D GLN* 5.7 1.0 + - - -
----------------------------------------------------------
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