Contacts of the helix formed by residues 170 - 188 (chain C) in PDB entry 1Z10
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 PRO 170 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ILE* 3.3 18.6 - - + +
169C ASP* 1.3 89.8 - - - +
171C THR* 1.3 64.7 + - - +
172C PHE 3.4 0.7 - - - -
173C PHE* 2.9 20.2 + - + +
174C LEU* 3.0 29.4 + - + +
311C ARG* 4.8 3.6 - - + -
487C TYR* 3.5 46.7 - - + +
489C MET* 4.0 16.6 - - + -
491C PHE* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ASP* 2.7 29.6 + - - -
170C PRO* 1.3 77.9 - - - +
172C PHE* 1.3 78.9 + - + +
174C LEU* 3.6 4.5 + - - +
175C SER* 3.0 28.2 + - - +
206C LEU* 4.4 18.4 - - + -
307C SER* 4.3 2.3 + - - +
311C ARG* 3.3 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ASP* 4.5 9.7 + - - -
170C PRO 3.4 0.4 - - - -
171C THR* 1.3 87.9 - - + +
173C PHE* 1.3 67.6 + - + +
174C LEU 3.1 1.3 - - - -
175C SER* 3.5 15.9 - - - -
176C ARG* 3.0 40.4 + - + +
199C LEU* 3.6 24.5 - - + -
202C LEU* 3.8 28.3 - - + -
203C ARG* 3.6 30.7 - - + -
206C LEU* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 3.7 9.6 - - + +
159C ALA* 4.0 16.8 - - + -
160C LEU* 4.0 24.9 - - + -
163C THR* 3.8 26.5 - - + -
168C ILE* 3.7 28.5 - - + -
169C ASP 3.5 22.0 - - - -
170C PRO* 2.9 7.5 + - + +
172C PHE* 1.3 81.0 - - + +
174C LEU* 1.3 63.3 + - + +
176C ARG* 3.5 29.4 + - - +
177C THR* 3.0 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 4.2 22.9 - - + -
160C LEU* 5.6 1.1 - - + -
170C PRO* 3.0 35.9 + - + +
171C THR* 3.7 3.4 - - - +
173C PHE* 1.3 79.6 - - + +
175C SER* 1.3 67.4 + - - +
177C THR* 3.2 6.9 + - - -
178C VAL* 3.0 26.3 + - - +
307C SER* 4.4 6.5 - - - +
310C LEU* 4.1 22.1 - - + +
311C ARG* 3.9 30.3 - - + +
314C PHE* 3.9 28.5 - - + -
456C VAL* 5.6 1.1 - - + -
491C PHE* 5.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C THR* 3.0 19.9 + - - -
172C PHE* 3.5 24.1 - - - -
173C PHE 3.6 0.2 - - - -
174C LEU* 1.3 73.4 - - - +
176C ARG* 1.3 68.4 + - - +
178C VAL* 4.5 0.7 - - - -
179C SER* 2.8 28.9 + - - -
202C LEU* 3.6 17.0 - - - +
303C THR* 4.4 4.6 - - - +
304C GLU* 5.0 4.7 - - - -
307C SER* 3.2 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 5.8 0.2 - - - +
159C ALA* 4.0 8.9 - - - +
172C PHE* 3.0 30.6 + - + +
173C PHE* 3.5 38.8 + - - +
175C SER* 1.3 78.0 + - - +
177C THR* 1.3 63.3 + - - +
180C ASN* 3.2 23.4 + - - +
193C TYR* 3.3 68.8 + - + +
194C LYS* 5.2 8.1 - - - +
198C PHE* 3.4 29.6 - - + -
199C LEU* 5.8 6.7 - - + -
202C LEU* 3.4 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C GLU* 3.2 33.0 - - + +
156C LEU* 3.5 24.7 - - + +
173C PHE 3.0 14.9 + - - -
174C LEU 3.2 8.4 + - - -
175C SER 3.1 0.6 - - - -
176C ARG* 1.3 79.6 - - - +
178C VAL* 1.3 63.0 + - + +
180C ASN* 3.4 6.2 + - - +
181C VAL* 3.8 4.9 + - - +
193C TYR* 2.9 21.0 + - - -
310C LEU* 6.4 0.4 - - + -
452C PHE* 3.4 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU 3.0 16.4 + - - +
175C SER* 4.0 4.9 - - - +
177C THR* 1.3 73.3 - - - +
179C SER* 1.3 67.1 + - - +
181C VAL* 2.9 21.7 + - - +
182C ILE 3.8 2.9 + - - -
302C GLY 3.6 15.1 - - - +
303C THR* 3.5 25.8 - - - +
306C VAL* 3.7 17.0 - - + -
307C SER* 4.3 5.4 - - - +
310C LEU* 3.4 33.7 - - + -
448C GLU* 3.5 16.4 - - - +
452C PHE* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C SER 2.8 22.8 + - - -
178C VAL* 1.3 75.1 - - - +
180C ASN* 1.3 54.3 + - - +
182C ILE* 3.6 3.5 - - - +
183C SER* 2.5 38.6 + - - -
198C PHE* 3.7 13.4 - - - -
202C LEU* 3.6 18.2 - - - +
299C PHE* 3.3 19.1 - - - -
303C THR* 3.1 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ARG* 4.6 3.0 + - - -
152C GLU* 3.0 38.8 + - - +
176C ARG 3.2 12.5 + - - +
177C THR 3.6 0.9 - - - +
178C VAL 3.0 1.2 + - - -
179C SER* 1.3 75.2 - - - +
181C VAL* 1.3 64.7 + - - +
183C SER* 3.9 2.6 - - - -
184C SER* 3.1 23.6 + - - -
190C ARG* 3.5 21.1 - - + +
191C PHE* 2.7 54.7 + - - +
193C TYR* 3.5 11.7 - - - -
198C PHE* 3.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 4.2 12.3 - - + -
148C ARG* 5.0 4.9 - - + +
149C ILE* 4.0 22.2 - - + +
152C GLU* 4.4 10.8 - - + -
177C THR 4.0 3.8 - - - +
178C VAL 2.9 13.9 + - - +
180C ASN* 1.3 76.2 - - - +
182C ILE* 1.3 67.5 + - - +
184C SER* 2.9 23.0 + - - -
185C ILE* 3.4 5.9 + - + +
444C LEU* 3.9 19.3 - - + -
448C GLU* 3.4 23.6 - - - +
452C PHE* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU* 4.4 9.4 - - + -
178C VAL 3.8 1.4 + - - -
179C SER* 3.6 10.3 - - - +
181C VAL* 1.3 81.7 - - - +
183C SER* 1.3 66.3 + - - +
185C ILE* 3.1 22.4 + - + +
186C VAL* 3.0 40.1 + - + +
298C LEU* 3.7 22.4 - - + +
299C PHE* 4.2 8.7 - - + +
302C GLY* 4.0 20.6 - - - +
303C THR* 3.8 18.6 - - - +
444C LEU* 4.2 6.5 - - + -
448C GLU* 4.7 0.8 + - - +
500C HEM 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C SER* 2.5 26.9 + - - -
180C ASN* 4.0 8.5 - - - -
182C ILE* 1.3 75.9 - - - +
184C SER* 1.3 66.3 + - - +
186C VAL* 4.6 0.9 - - - +
187C PHE* 2.9 39.5 + - - +
189C ASP 3.6 5.5 - - - +
191C PHE* 3.4 25.4 - - - -
299C PHE* 3.3 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C PHE* 6.1 0.3 - - - -
145C ILE* 4.6 1.0 - - - +
148C ARG* 3.0 36.6 - - - +
180C ASN 3.1 13.6 + - - -
181C VAL 2.9 14.9 + - - -
183C SER* 1.3 75.8 - - - +
185C ILE* 1.3 62.2 + - - +
188C GLY* 2.8 30.0 + - - -
189C ASP* 3.6 22.9 + - - +
190C ARG* 4.2 2.5 - - - -
265C ARG 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU* 3.9 20.9 - - + -
138C PHE* 4.2 30.2 - - + +
140C VAL* 3.6 29.6 - - + -
145C ILE* 3.6 27.1 - - + -
181C VAL 3.4 10.7 + - - +
182C ILE* 3.1 21.9 + - + +
184C SER* 1.3 83.6 + - - +
186C VAL* 1.3 64.8 + - + +
266C ASP* 3.3 9.4 - - - +
267C PHE* 2.9 25.8 + - + -
444C LEU* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ILE* 3.0 30.6 + - + +
183C SER* 4.5 0.7 - - - +
185C ILE* 1.3 80.9 - - + +
187C PHE* 1.3 77.4 + - + +
188C GLY 3.6 0.4 - - - -
266C ASP* 3.3 15.8 - - - +
267C PHE* 3.7 18.8 - - + -
268C ILE* 3.4 18.2 + - + +
295C THR* 3.2 35.7 - - + +
298C LEU* 4.1 26.0 - - + -
299C PHE* 5.3 2.7 - - + +
----------------------------------------------------------
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 SER* 2.9 31.7 + - - +
186C VAL* 1.3 97.0 - - + +
188C GLY* 1.3 60.4 + - - +
189C ASP* 3.4 8.4 + - - +
191C PHE* 4.1 18.8 - + + -
247C PHE* 3.9 7.4 - + - -
248C ILE* 3.5 32.8 - - + -
251C LYS* 4.1 32.8 + - + +
255C ASN* 5.2 2.1 - - - +
266C ASP* 3.1 15.9 - - - +
268C ILE* 3.9 16.2 - - + -
299C PHE* 3.8 34.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C SER* 2.8 18.5 + - - -
187C PHE* 1.3 78.3 - - - +
189C ASP* 1.3 62.1 + - - +
265C ARG* 3.8 14.4 - - - +
266C ASP* 3.3 17.3 - - - +
----------------------------------------------------------
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