Contacts of the helix formed by residues 176 - 188 (chain C) in PDB entry 4FJV
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 ASP 176 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PHE* 6.0 0.9 - - + -
174C GLU 5.3 0.4 - - - +
175C CYS* 1.3 74.6 - - - +
177C HIS* 1.3 78.8 + - - +
178C ILE* 3.2 4.1 + - + +
179C GLN* 3.2 19.4 + - - +
180C ILE* 3.0 27.9 + - - +
42D ARG* 4.6 13.7 + - - -
70D VAL* 6.6 0.2 - - - -
71D LEU 3.5 8.8 - - - +
72D ARG* 4.2 0.7 - - - -
73D LEU 3.1 29.5 + - - -
74D ARG* 3.7 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ASP* 1.3 80.2 + - - +
178C ILE* 1.3 63.3 + - + +
180C ILE* 3.3 2.7 + - - +
181C THR* 2.9 25.2 + - + +
208C PHE* 3.6 32.8 - + - -
7D THR* 6.4 0.4 - - - -
8D LEU* 3.5 38.5 - - + +
9D THR* 6.1 2.5 - - + +
69D LEU 5.2 0.9 - - - -
70D VAL* 3.9 7.1 - - + -
71D LEU* 3.0 61.7 + - + +
73D LEU* 4.0 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 3.6 24.5 - - + -
150C PHE* 3.9 24.0 - - + +
153C PHE* 3.8 14.6 - - + +
154C ILE* 3.6 30.7 - - + -
163C PHE* 4.0 18.8 - - + -
176C ASP* 3.2 2.6 + - + +
177C HIS* 1.3 76.5 - - + +
179C GLN* 1.3 64.0 + - - +
181C THR* 3.5 3.6 - - - +
182C ALA* 2.8 32.9 + - - +
8D LEU* 4.1 24.5 - - + -
70D VAL* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PHE* 4.9 1.6 - - - -
53C TYR* 3.5 26.7 - - + +
139C THR* 3.5 15.9 - - + +
143C ILE* 4.7 0.2 - - - -
163C PHE* 3.7 23.9 - - + -
167C GLU* 3.2 21.8 + - - +
168C VAL* 3.8 21.3 - - + -
174C GLU 3.9 8.3 + - - -
175C CYS* 4.1 3.1 - - + -
176C ASP* 3.3 38.0 + - - +
178C ILE* 1.3 81.2 - - - +
180C ILE* 1.3 56.4 + - - +
182C ALA* 3.3 0.7 + - - -
183C LEU* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PHE* 3.8 26.9 - - + -
175C CYS* 4.2 8.7 - - + -
176C ASP 3.0 29.4 + - - +
177C HIS* 3.6 4.0 - - - +
178C ILE 3.3 0.2 - - - -
179C GLN* 1.3 76.7 - - - +
181C THR* 1.3 61.3 + - - +
183C LEU* 3.5 1.7 + - - +
184C SER* 3.1 22.7 + - - -
191C LEU* 3.6 28.9 - - + -
193C VAL* 5.1 2.0 - - + -
208C PHE* 4.1 18.2 - - + -
225C TYR* 3.3 35.0 - - + +
73D LEU* 4.1 14.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
150C PHE* 4.8 7.0 - - + -
177C HIS* 2.9 23.2 + - + +
178C ILE* 3.5 4.9 - - - +
180C ILE* 1.3 75.0 - - - +
182C ALA* 1.3 64.4 + - - +
184C SER* 3.7 3.3 - - - -
185C GLN* 3.0 53.0 + - - +
208C PHE* 3.7 31.0 - - - +
209C PRO* 6.0 0.7 - - - +
8D LEU* 4.2 28.0 + - + +
9D THR* 6.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C THR* 4.0 10.1 - - + +
142C PHE* 3.7 29.9 - - + -
143C ILE* 3.8 22.2 - - + -
150C PHE* 4.6 4.5 - - + -
178C ILE 2.8 19.0 + - - +
179C GLN 3.6 3.6 - - - +
181C THR* 1.3 79.7 - - - +
183C LEU* 1.3 56.1 + - - +
185C GLN* 3.3 2.1 + - - +
186C ALA* 2.8 30.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
52C PHE* 4.1 6.7 - - + -
53C TYR* 3.8 30.1 - - + -
56C LEU* 3.7 28.2 - - + +
135C LEU* 4.0 26.5 - - + +
138C LEU* 4.7 3.6 - - + -
139C THR* 3.5 22.8 - - - +
179C GLN 2.9 17.4 + - - +
180C ILE 4.0 2.7 - - - +
182C ALA* 1.3 69.3 - - - +
184C SER* 1.3 67.4 + - - +
186C ALA* 3.1 8.1 + - + -
187C LEU* 3.1 46.2 + - + +
189C ILE* 5.4 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
56C LEU* 5.0 5.1 - - - +
180C ILE 3.1 17.8 + - - -
181C THR 3.7 5.6 - - - -
183C LEU* 1.3 77.6 - - - +
185C GLN* 1.3 59.0 + - - +
188C SER* 2.9 9.0 + - - -
189C ILE* 2.8 55.2 + - - +
191C LEU* 5.0 6.5 - - - -
208C PHE* 3.3 30.9 + - - +
209C PRO* 4.2 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 4.5 3.3 + - - -
142C PHE* 3.4 35.5 - - + -
150C PHE* 4.8 6.2 - - - -
181C THR* 3.0 49.9 + - - +
182C ALA 3.8 0.8 - - - +
184C SER* 1.3 76.9 - - - +
186C ALA* 1.3 65.9 + - - +
187C LEU 3.2 0.7 + - - -
188C SER* 3.3 14.2 + - - +
209C PRO* 5.9 7.6 - - + -
8D LEU 5.0 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 4.1 14.0 + - - +
81C THR* 5.3 2.9 - - - +
84C ASP* 5.6 1.6 - - - +
138C LEU* 4.2 26.9 - - + +
142C PHE* 3.7 28.2 - - + -
182C ALA 2.8 21.0 + - - +
183C LEU* 3.1 11.0 + - + +
185C GLN* 1.3 74.3 - - - +
187C LEU* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 5.7 0.2 - - + -
60C TYR* 5.1 1.0 + - - -
74C PHE* 3.9 34.5 - - + -
77C ARG* 3.6 18.5 - - - +
78C VAL* 5.0 4.3 - - + -
81C THR* 4.5 10.3 - - + -
102C PHE* 4.6 7.2 - - + -
134C PHE* 5.4 0.2 - - + -
135C LEU* 3.7 29.8 - - + -
138C LEU* 3.5 26.7 - - + -
183C LEU* 3.1 20.1 + - + +
186C ALA* 1.3 78.7 - - - +
188C SER* 1.3 69.5 + - - +
189C ILE* 3.3 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 5.3 3.6 + - - -
77C ARG* 3.0 34.5 + - - -
184C SER 2.9 9.4 + - - -
185C GLN* 3.3 10.2 + - - +
187C LEU* 1.3 79.4 - - - +
189C ILE* 1.3 59.9 + - - +
190C ALA* 3.6 3.3 + - - +
209C PRO* 6.2 1.6 - - - -
----------------------------------------------------------
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