Contacts of the helix formed by residues 164 - 178 (chain F) in PDB entry 2OV2
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 164 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F LEU* 6.1 0.2 - - - -
155F LEU* 5.8 0.3 - - - +
156F GLU 3.9 13.9 - - - +
157F CYS* 3.7 3.4 - - - +
162F GLN 3.2 1.8 + - - -
163F ARG* 1.3 75.4 - - - +
165F LEU* 1.3 62.0 + - - +
166F LYS 3.6 1.1 - - - -
167F THR* 3.5 16.3 + - - -
168F VAL* 3.3 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 3.2 46.9 - - + +
22F SER* 3.2 36.8 - - - +
23F TYR* 3.6 20.4 - - + +
157F CYS* 4.1 7.6 - - - -
158F SER 4.2 2.9 - - - +
159F ALA* 4.2 8.3 - - - -
162F GLN* 3.1 33.9 + - + +
163F ARG 3.2 1.2 + - - -
164F GLY* 1.3 74.3 - - - +
166F LYS* 1.3 67.9 + - - +
168F VAL* 3.1 20.3 + - - +
169F PHE* 3.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TYR* 4.4 20.9 - - + -
162F GLN 4.6 1.2 + - - -
165F LEU* 1.3 77.7 - - - +
167F THR* 1.3 57.9 + - - +
169F PHE* 3.2 3.6 + - - +
170F ASP* 2.9 55.4 + - - +
11N ILE 2.7 29.1 + - - -
12N SER* 3.8 18.8 - - - +
13N ALA* 4.0 12.1 - - + +
14N PRO* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F LEU* 4.2 15.9 - - + -
164F GLY* 3.5 17.7 + - - -
165F LEU 3.2 0.4 - - - -
166F LYS* 1.3 74.9 - - - +
168F VAL* 1.3 59.7 + - - +
170F ASP* 4.1 8.3 + - + -
171F GLU* 2.8 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 4.6 4.5 - - + -
79F LEU* 3.8 30.5 - - + -
111F LEU* 3.9 2.9 - - - +
113F VAL* 4.0 17.9 - - + -
155F LEU* 3.7 28.3 - - + -
157F CYS* 4.0 24.7 - - + -
164F GLY 3.3 15.0 + - - +
165F LEU 3.1 8.8 + - - +
167F THR* 1.3 76.1 - - - +
169F PHE* 1.3 68.5 + - + +
171F GLU* 3.4 2.8 + - - +
172F ALA* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F CYS* 4.9 2.2 - - - -
19F LEU* 3.9 31.9 - - + -
20F LEU* 3.6 33.2 - - + -
23F TYR* 3.3 66.0 - + + +
53F LEU* 4.9 6.1 - - + -
55F LEU* 3.8 17.5 - - + -
79F LEU* 4.0 17.0 - - + -
165F LEU* 3.6 15.5 - - + -
166F LYS 3.2 2.0 + - - +
168F VAL* 1.3 77.7 - - + +
170F ASP* 1.3 66.8 + - - +
172F ALA* 3.5 9.1 - - + +
173F ILE* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TYR* 4.9 3.5 + - - -
166F LYS* 2.9 54.6 + - - +
167F THR* 3.7 9.1 - - + +
169F PHE* 1.3 76.2 - - - +
171F GLU* 1.3 59.5 + - + +
173F ILE* 3.3 4.9 + - - +
174F ARG* 2.9 34.0 + - - +
11N ILE* 3.1 41.0 - - + +
12N SER 4.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F LEU* 3.8 7.1 - - + +
152F VAL* 6.1 1.0 - - - +
153F LYS* 4.1 21.0 - - + +
155F LEU* 3.7 28.7 - - + -
167F THR* 2.8 35.9 + - + +
170F ASP* 1.3 71.2 - - + +
172F ALA* 1.3 61.0 + - - +
174F ARG* 3.8 13.4 - - - +
175F ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 5.5 0.9 - - + -
6F CYS* 4.8 8.5 - - + -
53F LEU* 6.1 2.7 - - + -
77F VAL* 4.0 20.3 - - + +
79F LEU* 4.4 11.4 - - + -
111F LEU* 3.5 14.0 - - + +
168F VAL 2.9 18.3 + - - +
169F PHE* 3.5 13.7 - - + +
171F GLU* 1.3 75.0 - - - +
173F ILE* 1.3 64.7 + - + +
175F ALA* 3.2 18.0 - - - +
176F VAL* 3.5 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 3.9 19.7 - - + -
23F TYR* 4.5 2.5 - - - +
44F VAL* 4.0 16.2 - - + -
46F VAL* 4.0 17.0 - - + -
51F VAL* 5.7 1.8 - - + -
53F LEU* 4.3 27.4 - - + -
169F PHE 3.0 21.3 + - - +
170F ASP 3.5 4.3 - - - +
171F GLU 3.2 0.2 - - - -
172F ALA* 1.3 73.9 - - + +
174F ARG* 1.3 62.0 + - - +
176F VAL* 3.0 4.9 + - - +
177F LEU* 3.0 49.6 + - + +
11N ILE* 4.0 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F VAL* 3.6 15.0 - - - +
47F ASP* 3.4 36.2 + - - -
170F ASP 2.9 21.8 + - - +
171F GLU* 4.0 16.8 - - - +
173F ILE* 1.3 76.7 - - - +
175F ALA* 1.3 51.6 + - - +
177F LEU* 4.9 6.3 - - - +
178F GLY* 2.5 47.5 + - - +
10N GLU* 4.2 9.3 - - - +
11N ILE* 3.8 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F VAL* 4.3 7.6 - - + -
109F PRO* 4.3 18.1 - - + +
111F LEU* 4.0 21.5 - - + -
152F VAL* 4.7 14.3 - - + +
171F GLU 2.9 18.8 + - - +
172F ALA 3.2 10.3 - - - +
173F ILE 3.1 0.4 - - - -
174F ARG* 1.3 76.3 - - - +
176F VAL* 1.3 56.3 + - - +
178F GLY* 3.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F GLN* 4.7 5.2 - - - +
3F ALA 5.2 0.2 - - - +
4F ILE* 3.8 38.6 - - + -
76F ASP* 3.9 34.8 - - + +
77F VAL* 3.9 9.2 - - + -
109F PRO* 5.8 0.4 - - - -
172F ALA 3.6 13.5 - - - +
173F ILE 3.0 5.4 + - - +
175F ALA* 1.3 79.5 - - - +
177F LEU* 1.3 71.1 + - + +
178F GLY 3.4 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F GLN* 3.2 41.7 - - + +
4F ILE* 4.0 8.3 - - + -
46F VAL* 4.5 12.3 - - + -
51F VAL* 4.0 24.2 - - + -
173F ILE* 3.0 34.7 + - + +
174F ARG* 4.9 7.4 - - - +
176F VAL* 1.3 84.5 - - + +
178F GLY* 1.3 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F ARG* 2.5 28.7 + - - +
175F ALA* 3.5 17.5 - - - +
176F VAL 4.0 5.5 - - - +
177F LEU* 1.3 76.3 - - - +
----------------------------------------------------------
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