Contacts of the helix formed by residues 164 - 178 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E LEU* 5.9 0.2 - - - -
155E LEU* 5.7 0.3 - - - +
156E GLU 3.8 13.8 - - - +
157E CYS* 3.7 4.7 - - - +
162E GLN 3.1 2.2 + - - -
163E ARG* 1.3 76.4 - - - +
165E LEU* 1.3 61.3 - - - +
166E LYS 3.5 1.8 - - - -
167E THR* 3.3 17.7 + - - -
168E VAL* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU* 3.7 31.4 - - + +
22E SER* 3.2 31.2 - - - +
23E TYR* 3.5 25.8 - - + +
157E CYS* 4.1 13.7 - - - -
158E SER 4.2 3.1 - - - +
159E ALA* 4.4 6.3 - - - -
162E GLN* 3.1 35.4 + - + +
163E ARG 3.1 1.6 - - - -
164E GLY* 1.3 74.9 - - - +
166E LYS* 1.3 67.5 + - - +
168E VAL* 3.2 12.5 + - + +
169E PHE* 3.4 31.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E TYR* 4.4 18.8 - - + -
162E GLN 4.5 1.8 + - - -
165E LEU* 1.3 79.9 - - - +
167E THR* 1.3 58.3 + - - +
169E PHE* 3.2 3.6 + - - +
170E ASP* 2.7 67.2 + - - +
11M ILE* 2.8 28.4 + - - +
12M SER 3.9 16.2 - - - -
13M ALA* 4.2 9.4 - - + +
14M PRO* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 3.9 23.1 - - + -
164E GLY* 3.3 19.0 + - - -
165E LEU 3.1 0.6 - - - -
166E LYS* 1.3 76.8 - - - +
168E VAL* 1.3 65.0 + - - +
170E ASP* 4.2 8.5 + - + -
171E GLU* 3.0 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU* 5.1 2.7 - - + -
79E LEU* 4.0 22.4 - - + -
111E LEU* 3.9 2.9 - - - +
113E VAL* 3.9 28.3 - - + -
155E LEU* 3.8 28.0 - - + -
156E GLU 4.9 0.2 - - - +
157E CYS* 4.1 24.7 - - + -
164E GLY 3.2 15.1 + - - +
165E LEU* 3.2 9.5 + - + +
167E THR* 1.3 77.8 - - - +
169E PHE* 1.3 66.7 + - + +
171E GLU* 3.8 2.1 - - - +
172E ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E CYS* 5.0 0.9 - - - -
19E LEU* 3.3 34.5 - - + -
20E LEU* 3.8 22.2 - - + -
23E TYR* 3.4 67.5 - + + +
53E LEU* 4.5 5.4 - - + -
55E LEU* 4.0 16.2 - - + -
79E LEU* 4.0 18.2 - - + -
165E LEU* 3.4 21.3 - - + -
166E LYS 3.2 2.7 + - - +
168E VAL* 1.3 79.3 - - + +
170E ASP* 1.3 61.6 + - - +
172E ALA* 3.5 7.9 - - + +
173E ILE* 2.9 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E TYR* 4.8 4.7 + - - -
166E LYS* 2.7 61.5 + - - +
167E THR* 3.9 9.0 + - - +
169E PHE* 1.3 77.1 - - - +
171E GLU* 1.3 57.5 + - + +
173E ILE* 4.4 0.7 - - - -
174E ARG* 2.9 36.1 + - + +
11M ILE* 3.4 33.6 - - + +
12M SER 4.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E LEU* 3.7 17.0 - - + +
152E VAL* 5.9 0.9 - - - +
153E LYS* 4.0 23.6 - - + +
155E LEU* 3.8 18.1 - - + +
167E THR* 3.0 36.0 + - + +
168E VAL 3.8 0.2 - - - +
170E ASP* 1.3 75.8 - - + +
172E ALA* 1.3 55.1 + - - +
174E ARG* 3.6 12.1 - - - +
175E ALA* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ILE* 5.5 0.9 - - + -
6E CYS* 4.9 7.6 - - + -
53E LEU* 6.0 2.9 - - + -
77E VAL* 4.2 19.2 - - + +
79E LEU* 4.5 11.2 - - + -
111E LEU* 3.4 13.6 - - + +
168E VAL 3.0 19.1 + - - +
169E PHE* 3.4 13.7 + - + +
171E GLU* 1.3 73.8 - - - +
173E ILE* 1.3 65.4 + - + +
175E ALA* 3.2 17.6 + - - +
176E VAL* 3.4 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ILE* 3.9 19.3 - - + -
23E TYR* 4.3 4.9 - - - +
44E VAL* 4.1 24.7 - - + -
46E VAL* 3.8 27.1 - - + -
51E VAL* 5.5 1.6 - - + -
53E LEU* 4.2 26.7 - - + -
169E PHE 2.9 26.9 + - - +
170E ASP 3.7 3.8 - - - +
172E ALA* 1.3 77.5 - - + +
174E ARG* 1.3 57.7 + - - +
176E VAL* 3.1 3.8 + - - +
177E LEU* 2.8 42.6 + - + +
11M ILE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN* 5.6 3.1 + - - -
46E VAL* 3.6 15.2 - - - +
47E ASP* 2.9 38.6 + - - -
170E ASP* 2.9 30.8 + - + +
171E GLU* 3.9 14.6 - - - +
173E ILE* 1.3 75.7 - - - +
175E ALA* 1.3 58.8 + - - +
177E LEU* 4.9 3.3 - - - +
178E GLY* 2.8 56.1 + - - +
10M GLU* 4.8 4.9 - - - +
11M ILE* 3.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR 5.1 5.9 - - - +
25A THR* 4.8 7.6 - - - +
26A ASN* 6.1 3.1 - - - +
77E VAL* 4.5 6.1 - - + -
109E PRO* 4.3 18.9 - - + +
111E LEU* 4.1 20.9 - - + -
152E VAL* 4.7 14.6 - - + -
171E GLU 2.7 19.0 + - - +
172E ALA 3.3 8.1 - - - +
173E ILE 3.2 0.4 - - - -
174E ARG* 1.3 78.2 - - - +
176E VAL* 1.3 60.6 + - - +
178E GLY 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ALA 5.5 0.4 - - - +
4E ILE* 4.1 17.9 - - + -
76E ASP* 3.7 41.5 - - + +
77E VAL* 3.7 20.4 - - + -
109E PRO* 5.3 0.9 - - + -
172E ALA 3.6 13.0 - - - +
173E ILE 3.1 6.1 + - - +
175E ALA* 1.3 81.0 - - - +
177E LEU* 1.3 68.5 + - + +
178E GLY 3.6 0.4 - - - -
15I SER* 3.6 3.5 - - - -
16I ASN* 3.0 50.2 + - - +
17I PHE 4.9 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E GLN* 6.1 4.0 - - + -
3E ALA 5.6 1.3 - - - +
4E ILE* 3.9 14.6 - - + -
46E VAL* 4.4 12.1 - - + -
51E VAL* 3.9 28.5 - - + -
173E ILE* 2.8 37.7 + - + +
174E ARG* 5.0 3.4 - - - +
176E VAL* 1.3 86.7 - - + +
178E GLY* 1.3 63.0 + - - +
13I ALA 5.5 0.9 - - - +
15I SER* 3.5 18.7 - - - -
16I ASN* 4.2 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN* 5.9 4.3 - - - -
174E ARG* 2.8 60.8 + - - +
175E ALA 4.7 0.4 - - - -
176E VAL 3.6 2.0 + - - -
177E LEU* 1.3 76.2 - - - +
13I ALA* 4.5 17.3 - - - +
14I PRO 4.1 15.0 + - - -
----------------------------------------------------------
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