Contacts of the strand formed by residues 67 - 72 (chain C) in PDB entry 2V76
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 MET 67 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLN* 6.1 0.2 - - - +
63C ARG* 3.4 11.2 - - - +
64C ASP* 2.9 62.7 + - + +
66C VAL* 1.4 85.8 - - + +
68C PHE* 1.3 73.0 + - - +
69C SER* 3.9 16.4 - - - -
84C THR* 4.2 13.5 - - + -
85C PHE 3.1 14.6 - - - +
86C GLN* 3.9 13.9 - - - +
87C THR* 3.3 7.9 + - - -
90C GLY* 3.9 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.8 17.7 - - + -
35C LEU* 4.3 7.6 - - + -
61C TYR* 4.1 17.9 - + + -
62C GLY 3.2 24.5 - - - -
63C ARG* 3.9 1.6 - - + -
67C MET* 1.3 75.9 - - - +
69C SER* 1.3 63.4 + - - +
70C PHE* 3.9 24.2 - + + -
84C THR* 3.6 0.7 - - - +
85C PHE* 2.8 35.9 + + + +
87C THR* 3.7 5.5 - - + +
90C GLY* 3.9 14.4 - - - -
93C ILE* 3.7 48.7 - - + -
94C PHE* 3.9 22.9 - + + -
97C VAL* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TYR* 3.2 3.7 - - - +
62C GLY 2.8 37.5 + - - +
67C MET* 3.9 18.1 - - - -
68C PHE* 1.3 78.2 - - - +
70C PHE* 1.3 65.7 + - - +
82C THR* 3.4 12.5 - - - +
83C PHE 3.2 6.1 + - - -
84C THR* 2.7 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 4.6 4.0 - - + -
35C LEU* 3.6 25.4 - - + -
53C TRP* 3.5 57.2 - + - -
58C LEU* 3.7 18.2 - - + -
60C ARG 3.4 13.2 - - - +
61C TYR* 3.7 10.8 - - + +
68C PHE* 3.9 13.0 - + + -
69C SER* 1.3 76.9 + - - +
71C GLU* 1.3 66.1 + - - +
72C ALA* 4.8 0.4 - - + -
82C THR* 3.5 3.8 - - - +
83C PHE* 2.8 58.7 + + + +
85C PHE* 3.6 22.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C LEU* 3.5 6.6 - - - +
59C ARG* 2.8 62.0 + - + +
60C ARG* 2.9 55.1 + - + -
70C PHE* 1.3 77.6 - - - +
72C ALA* 1.3 58.3 + - - +
81C GLY* 3.3 19.9 - - - +
82C THR* 4.1 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TRP* 3.6 33.0 - - + +
57C LEU 4.1 3.4 - - - -
58C LEU* 4.3 4.3 - - + -
59C ARG* 3.6 9.8 + - - -
70C PHE* 4.2 1.6 - - + -
71C GLU* 1.3 73.9 - - - +
73C GLY* 1.3 59.7 + - - +
76C CYS* 3.7 8.5 - - - -
78C SER* 4.1 0.2 - - - +
79C GLY 3.7 17.9 - - - +
80C PRO* 3.3 2.9 - - - +
81C GLY 2.8 32.0 + - - +
83C PHE* 4.3 4.0 - - + -
----------------------------------------------------------
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