Contacts of the helix formed by residues 177 - 190 (chain M) in PDB entry 5PRC
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 ILE 177 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174L MET* 5.9 0.2 - - + -
73M MET* 6.2 0.4 - - + +
88M PHE* 4.4 12.1 - - + +
89M PHE* 3.8 52.7 + - + +
91M LEU 4.2 1.0 + - - -
176M GLY* 1.3 70.7 - - - -
178M TRP* 1.3 61.7 + - + +
179M PRO* 3.6 1.8 - - - +
180M HIS* 2.9 25.4 + - - -
181M ILE* 3.4 9.4 - - - +
600M NS5 3.7 28.0 - - + -
805M BCB 3.6 47.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 178 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ALA* 3.6 13.5 - - + -
168L HIS 4.4 2.9 - - - -
169L TYR* 3.4 49.2 - + - +
174L MET* 3.7 31.2 - - + -
263L TRP* 3.9 23.8 - + - -
89M PHE* 2.9 42.1 + + + +
90M TRP* 3.4 50.0 - + - -
177M ILE* 1.3 74.5 - - + +
179M PRO* 1.4 65.3 - - + +
181M ILE* 3.0 9.6 + - + +
182M ASP* 2.9 30.4 + - - +
805M BCB 3.6 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 179 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ALA* 4.5 2.0 - - + -
227C TYR* 4.9 1.0 - - - -
89M PHE 3.3 12.6 - - - +
90M TRP 3.8 8.1 - - - +
91M LEU 3.6 14.8 - - - +
92M GLY* 3.8 4.0 - - - -
94M TYR* 3.3 39.3 - - + +
174M PRO* 3.9 16.3 - - + +
175M PHE 4.3 5.4 - - - +
176M GLY 3.5 12.1 - - - +
178M TRP* 1.4 91.6 - - + +
180M HIS* 1.3 62.1 + - - +
181M ILE 3.0 1.0 + - - -
182M ASP* 3.1 18.5 + - + +
183M TRP* 3.2 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 180 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173M VAL* 4.1 8.4 - - + +
174M PRO* 3.5 22.5 + - - +
176M GLY 3.0 15.8 + - - +
177M ILE 2.9 26.8 + - - -
179M PRO* 1.3 74.4 - - - +
181M ILE* 1.3 70.3 + - + +
183M TRP* 3.4 19.2 - - - +
184M LEU* 3.7 9.5 - - - +
600M NS5 3.6 22.8 - - + +
805M BCB 2.1 93.1 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L ASN* 4.8 0.8 + - - +
168L HIS* 3.2 37.5 + - + +
169L TYR* 4.2 15.0 - - + -
177M ILE 3.4 16.2 - - - +
178M TRP* 3.0 12.9 + - + +
180M HIS* 1.3 80.4 - - + +
182M ASP* 1.3 66.5 + - - +
183M TRP 3.2 1.6 - - - -
184M LEU* 3.1 25.2 + - + +
185M THR* 3.9 2.1 + - - -
805M BCB 3.4 68.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 182 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C SER* 4.7 1.4 - - - -
184C ALA* 3.5 29.8 + - - +
185C LEU* 3.7 25.8 + - + +
227C TYR* 4.3 7.4 - - + -
230C PHE* 4.8 5.1 - - + -
166L ASN* 3.9 11.7 + - - +
169L TYR* 2.5 39.4 + - - -
178M TRP 2.9 12.3 + - - +
179M PRO* 3.1 9.1 + - + +
181M ILE* 1.3 76.1 - - - +
183M TRP* 1.3 62.4 + - - +
185M THR* 3.1 7.2 + - - -
186M ALA* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 183 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C LEU* 3.7 14.7 - - + +
227C TYR* 3.2 33.3 - - - +
158M ILE* 4.0 24.5 - - + -
171M GLU 3.0 20.9 + - - -
172M GLY 3.4 12.6 + - - -
173M VAL* 3.7 24.9 - - + -
174M PRO* 3.7 13.7 - - + -
179M PRO 3.2 4.8 + - - +
180M HIS 3.4 13.9 - - - +
182M ASP* 1.3 76.2 - - - +
184M LEU* 1.3 88.2 + - + +
186M ALA* 3.0 2.2 + - - +
187M PHE* 2.7 61.9 + + + +
805M BCB 4.0 17.0 - - + -
806M BCB 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168L HIS* 3.6 31.6 - - + +
302L BCB 4.0 3.6 - - - +
180M HIS 3.7 7.2 - - - +
181M ILE* 3.1 22.0 + - + +
183M TRP* 1.3 106.5 - - + +
185M THR* 1.3 57.6 + - - +
188M SER* 3.2 27.7 + - - -
805M BCB 3.6 54.1 - - + -
806M BCB 3.5 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 3.8 30.6 - - + -
162L TYR* 3.1 28.8 + - + +
166L ASN* 4.0 15.6 + - - -
168L HIS* 4.1 9.5 + - - -
302L BCB 5.7 0.3 - - - +
181M ILE 4.7 0.9 + - - -
182M ASP 3.1 4.8 + - - -
184M LEU* 1.3 76.4 - - - +
186M ALA* 1.3 67.4 + - - +
187M PHE 3.2 0.4 - - - -
189M ILE* 3.0 38.2 + - + +
806M BCB 4.0 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C LEU* 4.4 4.5 - - + -
226C ALA* 3.7 12.9 - - + +
227C TYR* 3.6 50.9 - - + +
230C PHE* 5.0 3.9 - - + -
182M ASP 3.0 11.5 + - - +
183M TRP 3.0 7.7 + - - +
185M THR* 1.3 77.6 - - - +
187M PHE* 1.3 62.6 + - - +
189M ILE* 3.6 4.5 - - - +
190M ARG* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C LEU* 4.1 14.5 - - + +
162M HIS* 3.4 39.5 - + - -
171M GLU* 4.1 5.6 - - - -
183M TRP* 2.7 54.6 + + + +
184M LEU 4.0 3.4 - - - +
186M ALA* 1.3 73.8 - - - +
188M SER* 1.3 62.7 + - - +
189M ILE 3.4 0.2 + - - -
190M ARG* 3.4 1.4 + - - +
191M TYR* 3.1 48.6 + + - +
194M PHE* 3.4 35.0 - + - -
282M ILE* 3.7 19.5 - - + -
285M THR* 4.0 7.0 - - + -
806M BCB 3.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162L TYR* 5.0 1.7 + - - -
184M LEU 3.2 18.0 + - - -
185M THR 4.2 0.7 - - - -
187M PHE* 1.3 79.6 - - - +
189M ILE* 1.3 61.7 + - - +
191M TYR 3.3 1.7 + - - -
192M GLY 3.0 5.5 + - - -
193M ASN* 2.8 30.2 + - - -
194M PHE* 3.4 36.8 + - - +
806M BCB 3.7 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 4.3 11.0 - - + -
204C VAL* 3.4 22.1 - - + +
226C ALA* 4.6 7.6 - - + +
229C THR* 5.8 0.4 - - + -
230C PHE* 4.4 23.3 - - + -
253C PHE* 4.5 11.0 - - + -
254C GLU* 5.3 0.2 - - - +
339C HEM 3.7 40.2 - - + -
162L TYR* 4.3 8.3 - - - +
185M THR* 3.0 44.7 + - + +
186M ALA* 3.6 4.5 - - - +
188M SER* 1.3 76.6 - - - +
190M ARG* 1.3 64.4 + - - +
192M GLY* 3.1 11.8 + - - -
193M ASN* 4.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 3.6 23.3 + - - -
204C VAL* 4.9 0.4 - - - -
205C PRO* 3.0 31.6 - - - +
214C VAL 5.9 0.6 + - - -
215C SER* 5.9 2.6 + - - +
220C ARG* 3.0 33.7 - - - +
221C ARG* 5.3 6.7 + - - +
223C LEU* 3.9 24.9 - - + +
226C ALA* 4.1 9.9 - - + -
171M GLU* 5.0 1.7 + - - +
186M ALA 3.1 14.4 + - - +
187M PHE 3.9 2.2 - - - +
189M ILE* 1.3 80.7 - - - +
191M TYR* 1.3 85.4 + - + +
192M GLY 3.5 0.2 + - - -
290M ASP* 3.1 28.7 + - - -
----------------------------------------------------------
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