Contacts of the helix formed by residues 63 - 68 (chain C) in PDB entry 3EVS
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 63 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 6.4 0.2 - - - -
61C LEU 3.3 0.4 + - - -
62C GLU* 1.3 77.7 - - - +
64C SER* 1.3 58.1 + - - +
65C ASP 3.4 2.9 - - - -
66C PHE* 3.0 24.6 + - - +
67C GLN* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 3.4 33.2 - - - -
59C LEU* 5.1 2.7 - - - -
60C GLY 3.4 15.2 + - - -
61C LEU* 2.6 24.5 + - - +
62C GLU 3.3 1.4 + - - -
63C GLY* 1.3 73.8 - - - +
65C ASP* 1.3 67.6 + - - +
66C PHE 3.0 1.6 - - - -
67C GLN* 4.2 6.9 - - - +
68C CYS* 2.8 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 4.2 11.2 - - + -
97B PHE* 4.6 5.9 - - - -
107B LYS* 3.9 12.1 + - - -
109B TYR* 2.5 47.4 + - + +
39C TYR* 5.6 1.9 + - - -
63C GLY 5.1 0.2 - - - -
64C SER* 1.3 81.5 + - - +
66C PHE* 1.3 60.5 + - + +
68C CYS* 4.3 2.4 + - - +
69C ARG* 3.1 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 4.9 3.6 - + - -
33B TRP* 3.4 52.7 - + + -
36B TRP* 3.9 21.3 - + - -
95B ILE* 4.1 12.8 - - + -
109B TYR* 3.7 35.2 - + - -
112B MET* 4.0 31.2 - - + -
63C GLY* 3.0 20.9 + - - +
65C ASP* 1.3 80.8 - - + +
67C GLN* 1.3 63.4 + - + +
69C ARG* 3.8 11.8 - - - +
71C THR* 4.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 3.9 37.3 - - + +
60C GLY 5.5 3.0 + - - +
62C GLU 5.0 3.4 + - - -
63C GLY* 3.0 25.3 + - - +
64C SER* 4.3 2.4 - - - +
66C PHE* 1.3 77.4 - - + +
68C CYS* 1.3 58.6 + - - +
69C ARG 3.0 13.0 + - - +
80C ILE* 3.2 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 4.3 9.4 - - - -
59C LEU* 3.8 11.4 - - - -
64C SER* 2.8 31.7 + - - +
65C ASP* 4.8 1.1 - - - +
66C PHE 3.5 0.4 - - - -
67C GLN* 1.3 75.7 - - - +
69C ARG* 1.3 63.3 + - - +
80C ILE* 4.4 10.1 - - - +
81C GLU* 5.3 0.5 - - - -
82C CYS* 2.0 57.6 + - + +
----------------------------------------------------------
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