Contacts of the helix formed by residues 76 - 86 (chain C) in PDB entry 2VES
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 VAL 76 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 3.8 30.4 - - + -
64C THR* 3.4 32.3 - - + +
66C LEU* 4.1 14.6 - - + -
73C VAL* 3.7 37.5 - - + +
74C ASP 4.1 0.7 - - - +
75C THR* 1.3 79.1 - - - +
77C GLU* 1.3 68.9 + - - +
78C HIS 3.4 1.4 + - - -
79C LEU* 3.4 5.6 + - - +
80C LEU* 3.0 38.0 + - + +
100C VAL* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C SER* 3.1 16.8 - - - -
64C THR* 2.9 27.0 + - - +
75C THR* 4.5 3.3 - - - +
76C VAL* 1.3 86.3 + - - +
78C HIS* 1.3 68.7 + - + +
80C LEU* 4.3 6.3 - - - -
81C SER* 2.8 27.1 + - - -
240C LEU* 4.7 1.0 - - - +
241C ASP* 3.8 7.9 - - - +
244C GLY* 3.4 9.0 - - - -
245C ASP* 3.4 27.6 - - - +
264C HIS* 3.1 12.2 + - + -
1301C GVR 2.5 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C THR* 4.6 10.2 + - + +
76C VAL 3.4 0.8 - - - -
77C GLU* 1.3 81.9 - - + +
79C LEU* 1.3 62.8 + - - +
81C SER* 3.3 12.0 + - - -
82C ALA* 3.3 9.0 + - - +
102C ILE* 4.0 27.4 + - + +
105C GLY 3.5 25.0 + - - -
106C SER 3.9 19.2 + - - +
107C ALA* 3.4 9.5 - - - +
110C PHE* 4.0 9.0 - - + -
190C THR* 4.4 1.8 - - - -
237C HIS* 3.2 2.1 + + - -
240C LEU* 3.6 17.9 - - + -
241C ASP* 3.3 8.7 - - - -
1300C ZN 2.1 36.8 - - - -
1301C GVR 3.3 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.3 9.6 - - + -
28C LEU* 4.3 11.0 - - + -
39C PHE* 4.2 12.3 - - + -
75C THR 5.1 1.0 + - - -
76C VAL 3.4 7.8 + - - +
77C GLU 3.4 0.2 - - - -
78C HIS* 1.3 77.6 - - - +
80C LEU* 1.3 65.0 + - + +
82C ALA* 3.0 4.2 + - - +
83C MET* 3.0 43.0 + - + +
93C VAL* 3.5 38.6 - - + -
100C VAL* 4.4 11.4 - - + -
110C PHE* 3.7 44.8 - - + -
114C ILE* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.9 36.8 - - + -
39C PHE* 4.1 8.7 - - + -
52C ALA* 3.9 13.7 - - + -
76C VAL* 3.0 38.0 + - + +
77C GLU* 3.8 3.6 - - - +
79C LEU* 1.3 77.1 - - + +
81C SER* 1.3 56.4 + - - +
83C MET* 3.3 6.1 + - + +
84C ALA* 2.9 30.0 + - - +
244C GLY* 3.7 22.2 - - - +
247C TYR* 3.9 13.3 - - + +
248C LEU* 3.6 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU 2.8 14.0 + - - -
78C HIS 3.3 11.0 - - - -
79C LEU 3.2 0.2 - - - -
80C LEU* 1.3 77.2 - - - +
82C ALA* 1.3 56.4 + - - +
84C ALA* 3.4 2.6 + - - +
85C GLY 2.8 23.6 + - - -
107C ALA* 4.3 0.7 - - - -
181C PHE* 3.2 33.9 - - - -
240C LEU* 2.8 38.0 + - - +
243C ILE* 3.6 7.0 - - - +
244C GLY* 3.5 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C HIS 3.3 3.5 + - - +
79C LEU 3.0 9.7 + - - +
81C SER* 1.3 77.3 - - - +
83C MET* 1.3 65.6 + - - +
85C GLY* 3.8 0.2 - - - -
86C LEU* 3.0 30.3 + - - +
107C ALA* 4.0 4.5 - - + +
110C PHE* 3.6 26.5 - - + -
111C VAL* 3.7 21.3 - - + +
114C ILE* 3.8 8.4 - - + +
181C PHE* 4.0 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 5.1 2.7 - - + -
28C LEU* 4.2 18.4 - - + -
37C ILE* 3.9 18.8 - - + -
79C LEU* 3.0 40.5 + - + +
80C LEU* 3.6 9.9 - - - +
82C ALA* 1.3 75.8 - - - +
84C ALA* 1.3 60.5 + - - +
86C LEU 3.5 0.3 + - - -
87C GLY 3.0 3.8 + - - -
88C ILE* 2.8 57.2 + - + +
91C ALA* 4.1 18.4 - - + -
93C VAL* 4.2 16.6 - - + -
114C ILE* 3.9 14.1 - - + +
247C TYR* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU 2.9 15.9 + - - +
81C SER 3.6 4.5 - - - +
83C MET* 1.3 77.2 - - - +
85C GLY* 1.3 62.8 + - - +
87C GLY* 3.2 9.9 + - - -
152C PHE* 6.3 0.7 - - + -
176C PHE* 3.6 12.8 - - + -
243C ILE* 3.7 20.2 - - + +
247C TYR* 3.7 38.3 - - + -
296C TYR* 3.7 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C SER 2.8 20.8 + - - -
82C ALA 3.3 1.3 + - - -
84C ALA* 1.3 75.7 - - - +
86C LEU* 1.3 54.6 + - - +
87C GLY 3.7 0.2 + - - -
176C PHE* 3.8 16.3 - - - -
178C SER* 2.6 37.8 + - - -
181C PHE* 3.6 23.1 - - - -
296C TYR* 4.2 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 3.0 25.3 + - - -
82C ALA 3.0 12.1 + - - +
85C GLY* 1.3 78.8 - - - +
87C GLY* 1.3 60.9 + - - +
88C ILE* 3.4 12.6 + - + +
111C VAL* 3.7 31.2 - - + +
114C ILE* 3.5 35.2 - - + -
115C GLN* 4.3 3.6 - - + +
119C LEU* 3.9 2.3 - - - +
178C SER* 3.7 10.1 - - - +
182C VAL* 3.8 26.9 - - + -
297C MET* 3.4 35.8 - - + +
----------------------------------------------------------
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