Contacts of the helix formed by residues 170 - 194 (chain C) in PDB entry 5XVO
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 ASN 170 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C PHE* 4.1 11.1 - - - -
168C GLN* 3.2 26.1 + - - +
169C GLU* 1.3 76.6 - - - +
171C ASP* 1.3 64.7 + - - +
172C ILE* 2.9 12.6 + - + +
173C ASN* 2.6 49.9 + - - +
174C ALA* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ASN* 1.3 75.9 - - - +
172C ILE* 1.3 63.9 + - + +
174C ALA* 3.7 7.8 - - - +
175C GLY 3.0 18.2 + - - -
233C ARG 5.9 0.4 - - - +
235C GLU 4.1 3.3 - - - +
236C ALA* 4.0 8.0 - - - -
237C PHE* 3.6 30.6 + - + +
240C MET* 3.1 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C PHE* 3.7 47.3 - - + -
164C PHE* 3.8 19.7 - - + -
170C ASN* 2.9 11.6 + - + +
171C ASP* 1.3 78.2 - - + +
173C ASN* 1.3 59.5 + - - +
175C GLY* 3.4 1.7 + - - -
176C LEU* 2.9 33.6 + - + +
229C ILE* 3.9 9.4 - - + +
233C ARG* 4.0 31.9 - - + +
240C MET* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C PHE* 3.2 20.5 - - - -
165C THR 3.1 23.4 + - - -
166C ARG* 2.7 41.1 + - - +
168C GLN 2.8 27.1 + - - +
170C ASN* 2.6 23.1 + - - +
172C ILE* 1.3 72.2 - - - +
174C ALA* 1.3 55.7 + - - +
176C LEU* 3.1 3.5 + - - +
177C ASN* 2.7 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ASN 3.1 18.8 + - - +
171C ASP* 3.7 8.7 - - - +
172C ILE 3.4 0.2 - - - -
173C ASN* 1.3 76.2 - - - +
175C GLY* 1.3 57.7 - - - +
177C ASN* 3.7 8.6 - - - +
178C TYR* 2.9 30.5 + - - +
237C PHE* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASP 3.0 14.7 + - - -
172C ILE 3.7 2.7 - - - -
174C ALA* 1.3 74.9 - - - +
176C LEU* 1.3 63.3 + - - +
178C TYR* 3.4 1.4 + - - +
179C GLY* 3.0 19.2 + - - -
229C ILE* 3.6 23.1 - - - +
237C PHE* 3.7 13.4 - - - -
240C MET* 4.1 4.7 - - - -
244C LEU* 3.4 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PHE* 3.9 23.6 - - + -
160C PHE* 4.6 3.4 - - + -
164C PHE* 4.6 2.0 - - + -
166C ARG* 4.0 17.7 - - - +
172C ILE* 2.9 28.9 + - + +
173C ASN* 3.1 23.3 + - - +
175C GLY* 1.3 76.3 - - - +
177C ASN* 1.3 57.8 + - - +
179C GLY* 3.2 2.3 + - - -
180C TYR* 2.8 43.6 + - + +
225C VAL* 3.9 3.8 - - + +
226C ASP* 3.2 39.5 - - + +
229C ILE* 3.9 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 2.7 33.5 + - - +
173C ASN* 2.7 34.1 + - - +
174C ALA* 3.7 8.7 - - - +
176C LEU* 1.3 71.5 - - - +
178C TYR* 1.3 62.8 + - - +
180C TYR* 3.3 8.3 + - - +
181C THR* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ALA 2.9 17.3 + - - +
175C GLY 3.7 4.7 - - - +
176C LEU 3.3 0.2 - - - -
177C ASN* 1.3 77.6 - - - +
179C GLY* 1.3 64.4 + - - +
181C THR* 3.1 16.4 + - - -
182C LEU* 3.1 39.9 + - + +
237C PHE* 4.3 11.2 - + + -
241C LYS* 3.5 49.1 + - + +
244C LEU* 3.8 13.5 - - + -
245C PHE* 3.3 27.6 - + - -
24G G 5.5 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C GLY 3.0 10.1 + - - -
176C LEU 3.7 2.5 - - - -
178C TYR* 1.3 79.1 - - - +
180C TYR* 1.3 62.0 + - - +
182C LEU* 3.1 18.7 + - - +
183C LEU* 3.2 9.9 + - - +
225C VAL* 3.7 24.5 - - - +
244C LEU* 3.6 22.4 - - - -
247C LEU* 4.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PHE* 3.7 14.8 - + - -
166C ARG* 3.4 34.1 - - - -
176C LEU* 2.8 26.6 + - + +
177C ASN* 3.6 7.2 - - - +
179C GLY* 1.3 76.5 - - - +
181C THR* 1.3 56.0 + - - +
183C LEU* 3.4 4.4 + - - +
184C LEU* 2.9 27.5 + - - +
218C MET* 3.5 14.4 - - + +
222C ARG* 3.4 64.4 + - + +
225C VAL* 4.0 12.3 - - + -
226C ASP* 2.5 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS* 5.3 15.3 - - + -
72C LEU* 5.7 8.1 - - + -
177C ASN 2.9 17.4 + - - -
178C TYR* 3.1 11.7 + - - -
180C TYR* 1.3 73.4 - - - +
182C LEU* 1.3 69.2 + - + +
184C LEU* 3.2 15.4 + - + +
185C SER* 3.0 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 3.1 46.6 + - + +
179C GLY* 3.1 12.7 + - - +
181C THR* 1.3 76.9 - - + +
183C LEU* 1.3 64.0 + - + +
185C SER* 2.8 24.9 + - - +
186C ILE* 3.2 13.1 + - + +
244C LEU* 4.4 11.0 - - + +
245C PHE* 4.5 12.3 - - + -
247C LEU* 4.4 16.6 - - + -
248C PHE* 4.1 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C GLY 3.2 10.0 + - - +
180C TYR* 3.5 8.5 - - + +
182C LEU* 1.3 77.2 - - - +
184C LEU* 1.3 66.6 + - - +
186C ILE* 3.1 18.3 + - + +
187C PHE* 3.2 26.5 + - + -
218C MET* 3.8 19.7 - - + -
221C PHE* 3.7 43.3 - - + +
222C ARG* 4.1 6.3 - - - +
224C LEU* 5.5 1.3 - - + -
225C VAL* 3.7 21.3 - - + -
247C LEU* 4.8 10.8 - - + -
261C LEU* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 4.8 8.7 - - + -
180C TYR 2.9 15.3 + - - +
181C THR* 3.4 18.6 - - + +
183C LEU* 1.3 76.6 - - - +
185C SER* 1.3 59.5 + - - +
187C PHE* 3.2 1.0 + - - -
188C ALA* 2.8 29.9 + - - +
209C ASN* 5.2 4.7 - - - +
211C PHE* 4.0 29.6 - - + +
214C ALA* 3.6 27.6 - - + +
215C SER* 3.6 26.0 - - - +
218C MET* 3.8 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS* 6.0 0.9 - - - -
71C ARG* 4.1 14.7 + - - +
72C LEU* 3.4 29.4 - - - -
181C THR* 3.0 12.4 + - - -
182C LEU* 2.8 19.2 + - - +
183C LEU 3.1 0.2 - - - -
184C LEU* 1.3 74.1 - - - +
186C ILE* 1.3 65.8 + - - +
188C ALA* 3.7 1.1 - - - +
189C ARG* 3.1 43.9 + - - +
248C PHE* 5.9 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LEU 3.2 13.4 + - - +
183C LEU* 3.1 15.8 + - + +
185C SER* 1.3 85.6 + - - +
187C PHE* 1.3 59.9 + - + +
189C ARG* 3.5 26.7 + - - +
190C GLU* 3.2 30.2 + - + +
247C LEU* 6.5 0.2 - - + -
248C PHE* 3.7 29.2 - - + -
261C LEU* 4.1 26.0 - - + -
262C THR* 4.5 15.0 - - + -
265C ALA* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LEU* 3.2 30.2 + - + +
184C LEU 4.0 4.3 - - - +
186C ILE* 1.3 82.6 - - + +
188C ALA* 1.3 66.7 + - - +
189C ARG 3.2 0.2 - - - -
190C GLU* 3.8 3.7 - - - +
191C LEU* 3.0 28.6 + - - +
214C ALA* 4.2 19.7 - - + +
217C LEU* 4.1 18.2 - - + -
218C MET* 3.8 22.2 - - + -
221C PHE* 3.4 45.8 - + + -
261C LEU* 5.8 1.6 - - + -
265C ALA* 3.6 31.6 - - + -
268C TYR* 4.4 7.2 - + - -
269C THR* 3.4 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 4.1 6.7 - - + -
73C PRO* 3.9 14.6 - - + -
184C LEU 2.8 17.9 + - - +
185C SER 3.7 4.9 - - - +
187C PHE* 1.3 78.5 - - - +
189C ARG* 1.3 62.0 + - - +
191C LEU* 3.4 1.9 + - - +
192C VAL* 3.2 28.6 + - - +
198C THR* 3.9 5.6 - - + +
211C PHE* 3.8 29.2 - - + -
214C ALA* 3.8 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 3.9 27.4 - - + +
43C GLU* 2.7 42.4 + - - -
65C LEU* 4.9 0.5 - - - +
67C CYS* 4.0 9.6 - - - -
71C ARG* 3.1 43.5 + - - +
73C PRO* 4.1 4.7 - - + +
185C SER* 3.1 33.3 + - - +
186C ILE* 3.5 29.4 + - - +
188C ALA* 1.3 79.6 - - - +
190C GLU* 1.3 66.5 + - + +
192C VAL* 3.0 24.3 - - + +
193C GLN* 3.1 14.4 + - - +
248C PHE* 5.4 4.0 - - - -
262C THR* 4.5 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 5.5 1.6 - - - +
186C ILE* 3.2 21.4 + - + +
187C PHE* 3.8 3.1 - - - +
188C ALA 3.3 0.2 - - - -
189C ARG* 1.3 82.9 + - - +
191C LEU* 1.3 61.5 + - - +
193C GLN* 3.3 33.2 + - - +
194C THR* 3.2 20.8 - - - +
262C THR* 4.3 5.4 - - - +
265C ALA* 4.0 18.4 - - + +
266C THR* 3.1 43.0 + - - +
269C THR* 3.7 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE 3.0 19.6 + - - +
188C ALA 3.7 4.0 - - - +
189C ARG 3.3 0.2 - - - -
190C GLU* 1.3 74.9 - - - +
192C VAL* 1.3 66.8 + - - +
194C THR* 2.7 23.7 + - - -
196C CYS* 3.2 18.7 + - + +
198C THR* 4.0 13.5 - - + -
213C LEU* 3.7 33.2 - - + +
214C ALA* 3.6 35.2 - - + +
217C LEU* 3.8 22.0 - - + -
269C THR* 3.8 12.3 - - + -
273C VAL* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 5.9 0.2 - - + -
63C LEU* 4.5 2.6 - - - +
65C LEU* 4.1 16.0 - - + +
73C PRO* 3.8 31.0 - - + -
76C LYS* 4.2 12.2 + - - +
86C SER* 4.2 1.2 + - - -
188C ALA 3.2 12.5 + - - +
189C ARG* 3.0 26.0 - - + +
191C LEU* 1.3 78.9 - - - +
193C GLN* 1.3 62.3 + - - +
195C GLY* 3.0 13.3 + - - -
196C CYS 3.7 16.2 - - - +
197C PHE* 5.6 0.4 - - - -
198C THR* 4.0 13.2 - - + +
80D PHE* 4.1 26.7 - - + -
81D TYR* 4.2 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 3.2 31.2 + - - +
7C VAL* 5.4 1.2 - - - +
39C VAL* 4.2 17.4 - - + +
41C LEU* 3.5 26.7 - - + +
63C LEU* 3.9 15.5 - - - +
65C LEU* 3.9 21.8 - - + -
84C HIS* 5.3 1.4 - - - -
86C SER* 4.2 2.4 + - - -
189C ARG 3.1 11.8 + - - +
190C GLU* 3.3 42.3 + - - +
192C VAL* 1.3 79.0 - - - +
194C THR* 1.3 61.2 + - + +
195C GLY 3.5 0.2 + - - -
266C THR* 5.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C SER* 3.9 7.1 + - - +
89C GLN* 3.4 19.2 - - - +
190C GLU 3.2 17.7 - - - +
191C LEU 2.7 14.7 + - - -
193C GLN* 1.3 78.3 - - + +
195C GLY* 1.3 57.2 + - - +
196C CYS* 3.3 19.9 - - - -
269C THR* 4.3 14.4 - - + -
270C LYS* 4.5 26.5 - - + +
273C VAL* 4.1 13.7 - - + +
----------------------------------------------------------
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