Contacts of the helix formed by residues 166 - 180 (chain F) in PDB entry 5IRC
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 GLY 166 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F MET* 4.1 3.6 - - - +
158F GLU 3.9 12.6 - - - -
159F CYS* 3.7 4.6 - - - +
164F LYS 3.2 1.8 + - - -
165F ASP* 1.3 77.6 + - - +
167F VAL* 1.3 63.8 + - - +
169F GLU* 3.3 26.2 + - - +
170F VAL* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 3.9 20.9 - - + +
24F VAL* 3.8 21.5 - - + -
25F ASN* 4.4 8.3 - - - +
159F CYS* 4.1 10.1 - - + -
160F SER 3.6 25.8 - - - +
161F ALA* 4.1 8.3 - - - -
164F LYS* 3.2 21.5 + - + +
165F ASP 4.1 1.6 - - - +
166F GLY* 1.3 74.7 - - - +
168F ARG* 1.3 68.8 + - - +
170F VAL* 3.0 19.2 + - - +
171F PHE* 3.4 18.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ASN* 5.1 6.5 - - - +
46F ILE* 5.0 3.8 - - + +
164F LYS 4.7 1.2 + - - -
166F GLY 3.5 0.2 - - - -
167F VAL* 1.3 81.3 - - - +
169F GLU* 1.3 90.2 + - - +
171F PHE* 3.2 3.6 + - - +
172F GLU* 3.1 53.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F MET* 3.7 23.0 - - + +
166F GLY* 3.3 29.8 + - - +
167F VAL 3.2 0.2 - - - -
168F ARG* 1.3 109.7 + - - +
170F VAL* 1.3 61.4 + - - +
172F GLU* 4.0 12.8 - - - +
173F MET* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 4.5 8.7 - - + -
81F LEU* 4.0 32.2 - - + +
113F ILE* 5.0 2.7 - - + +
115F VAL* 4.1 15.0 - - + -
157F MET* 3.7 28.3 - - + -
159F CYS* 4.0 23.8 - - + -
166F GLY 3.2 15.8 + - - +
167F VAL* 3.0 9.7 + - - +
169F GLU* 1.3 77.2 - - - +
171F PHE* 1.3 64.2 + - + +
173F MET* 3.3 4.0 + - - +
174F ALA* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F LEU* 4.2 13.2 - - + -
21F LEU* 3.7 38.4 - - + -
22F LEU* 4.0 16.4 - - + -
25F ASN* 3.4 46.4 - - + +
46F ILE* 4.1 12.8 - - + -
55F LEU* 4.5 11.1 - - + +
57F LEU* 4.1 21.8 - - + -
81F LEU* 3.9 17.9 - - + -
167F VAL* 3.4 12.7 + - + -
168F ARG* 3.2 6.2 + - - +
170F VAL* 1.3 76.5 - - + +
172F GLU* 1.3 57.8 + - - +
174F ALA* 3.8 3.1 - - - +
175F THR* 2.6 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ILE* 3.7 17.5 - - + +
47F GLU 4.8 5.1 - - - +
48F VAL* 3.8 15.2 - - + +
168F ARG* 3.1 49.1 + - + +
169F GLU* 4.0 12.2 - - - +
171F PHE* 1.3 78.3 - - - +
173F MET* 1.3 56.9 + - - +
175F THR* 3.3 2.3 + - - -
176F ARG* 2.9 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 173 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ILE* 3.7 20.2 - - + -
154F PHE* 3.9 13.5 - - + -
155F GLY* 3.9 27.6 - - - -
156F TYR 4.4 4.7 - - - +
157F MET* 3.6 37.7 - - + -
169F GLU 3.1 17.0 + - - +
170F VAL 3.6 3.8 - - - +
172F GLU* 1.3 74.7 - - - +
174F ALA* 1.3 60.5 + - - +
176F ARG* 3.3 9.9 + - - +
177F ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F LEU* 3.8 19.7 - - + -
55F LEU* 5.3 0.9 - - + -
79F VAL* 3.6 12.7 - - + +
81F LEU* 3.8 24.2 - - + -
113F ILE* 4.0 10.7 - - - +
170F VAL 2.9 17.8 + - - +
171F PHE* 3.8 7.9 - - - +
173F MET* 1.3 76.3 - - - +
175F THR* 1.3 55.9 + - - +
177F ALA* 3.4 3.6 + - - +
178F ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ILE* 3.2 37.6 - - + +
48F VAL* 3.6 21.8 - - + -
53F VAL* 3.6 24.2 - - + -
55F LEU* 3.5 12.6 - - + +
171F PHE 2.6 23.5 + - - -
172F GLU 3.6 4.5 - - - -
174F ALA* 1.3 73.6 - - - +
176F ARG* 1.3 60.4 + - - +
178F ALA* 3.1 8.3 + - + +
179F LEU* 2.9 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F VAL* 3.9 21.8 - - + +
49F ASP* 2.9 43.6 + - - +
154F PHE* 4.5 8.3 - - + -
172F GLU* 2.9 54.0 + - - +
173F MET* 3.7 8.2 - - - +
175F THR* 1.3 75.4 - - - +
177F ALA* 1.3 62.6 + - - +
179F LEU* 3.3 7.1 + - - +
180F GLN* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ASP 4.6 0.2 - - - +
79F VAL* 4.0 8.3 - - + -
111F PRO* 3.7 32.2 - - + +
113F ILE* 4.2 2.2 - - + -
154F PHE* 3.7 33.3 - - + -
173F MET 2.9 17.8 + - - +
174F ALA 3.5 5.4 - - - +
176F ARG* 1.3 76.3 - - - +
178F ALA* 1.3 62.0 + - - +
180F GLN* 3.4 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LYS* 3.7 41.6 + - + +
55F LEU* 5.2 0.7 - - + -
78F ASP* 3.8 27.1 - - + +
79F VAL* 4.0 11.4 - - + +
174F ALA 3.0 13.4 + - - +
175F THR* 3.1 11.2 + - - +
177F ALA* 1.3 77.6 - - - +
179F LEU* 1.3 61.7 + - - +
180F GLN 3.4 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 3.8 38.4 - - + -
6F LYS* 4.3 11.3 + - + +
48F VAL* 3.9 25.4 - - + +
49F ASP* 6.0 1.3 - - + +
51F LYS* 3.9 18.4 - - + -
53F VAL* 3.7 23.1 - - + -
175F THR* 2.9 15.3 + - + +
176F ARG* 3.9 6.5 - - + +
177F ALA 3.3 0.2 - - - -
178F ALA* 1.3 76.2 - - - +
180F GLN* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 180 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F PHE* 3.4 35.5 - - - -
176F ARG 3.0 15.6 + - - +
177F ALA 3.9 9.1 - - - +
178F ALA 3.3 8.0 - - - +
179F LEU* 1.3 82.4 - - - +
----------------------------------------------------------
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