Contacts of the strand formed by residues 78 - 84 (chain C) in PDB entry 2VWI
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 TYR 78 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 3.6 11.1 - - + +
67C MET* 3.3 61.7 - - + +
68C SER* 3.4 27.7 + - - -
70C CYS 6.0 0.7 - - - +
71C HIS* 3.9 20.2 + + + -
76C VAL 3.2 7.4 + - - +
77C SER* 1.3 73.1 - - - +
79C TYR* 1.3 68.7 + - - +
80C THR* 3.4 28.7 - - - -
81C SER* 2.8 34.1 + - - -
90C LEU* 4.7 4.5 - - + -
91C VAL 3.9 8.5 - - - -
92C MET* 4.5 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 3.4 65.3 - + + +
41C GLU* 2.7 30.4 + - - -
43C VAL* 3.8 6.1 - - + -
77C SER* 4.0 15.4 - - - -
78C TYR* 1.3 87.5 - - - +
80C THR* 1.3 63.6 + - - +
91C VAL* 2.8 18.5 + - + +
92C MET* 3.5 19.7 - - - -
93C LYS* 3.4 39.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 3.8 17.2 + - + +
11C SER 3.6 23.3 - - - +
12C ILE* 3.5 17.8 - - - +
17C TYR* 3.8 10.8 - - - +
78C TYR* 3.3 19.0 - - - -
79C TYR* 1.3 81.8 - - - +
81C SER* 1.3 67.5 + - - +
82C PHE* 4.4 4.9 - - + -
91C VAL* 2.8 39.7 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
12C ILE* 4.0 4.9 - - - +
57C MET* 5.6 1.5 - - - +
64C ILE* 3.5 19.6 - - - +
78C TYR* 2.8 19.5 + - - -
80C THR* 1.3 86.4 + - - +
82C PHE* 1.3 68.9 + - - +
88C LEU* 4.0 8.0 - - - +
89C TRP 3.2 15.0 - - - -
90C LEU* 3.9 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C SER 3.8 16.6 - - - -
12C ILE* 3.6 40.4 - - + +
14C ARG* 4.1 15.5 - - + -
17C TYR* 3.8 25.4 - + - -
57C MET* 5.9 1.8 - - - -
80C THR* 4.4 1.6 - - + -
81C SER* 1.3 80.5 - - - +
83C VAL* 1.3 67.4 + - - +
84C VAL* 3.6 28.0 - - + -
88C LEU* 4.1 4.9 - - - +
89C TRP* 2.9 52.6 + + + +
91C VAL* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.7 9.2 - - + -
57C MET* 3.8 41.3 - - + -
82C PHE* 1.3 78.6 - - - +
84C VAL* 1.3 66.9 + - - +
85C LYS 3.6 23.6 + - - +
87C GLU 3.3 12.8 - - - +
88C LEU* 4.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ARG* 4.0 24.0 - - + +
47C ARG* 6.0 0.4 - - - +
82C PHE* 3.6 33.5 + - + -
83C VAL* 1.3 73.0 - - - +
85C LYS* 1.3 72.9 + - + +
86C ASP 3.0 0.9 + - - -
87C GLU* 2.8 36.5 + - - +
89C TRP* 3.6 39.9 - - + +
----------------------------------------------------------
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