Contacts of the strand formed by residues 77 - 84 (chain C) in PDB entry 2ZOT
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 SER 77 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLY 3.4 3.0 + - - -
76C THR* 1.3 85.4 - - - +
78C TYR* 1.3 60.3 + - - +
115C GLN* 6.0 1.8 - - - -
146C PHE* 4.4 23.9 - - - -
147C TRP 3.5 5.4 - - - -
148C ILE* 4.1 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 3.9 16.4 - - + -
66C GLU 5.4 2.2 - - - -
69C PRO* 3.9 31.2 - - + -
72C TYR* 3.4 10.5 - - + -
73C LYS* 2.8 55.8 + - - +
76C THR* 3.3 37.5 - - + -
77C SER* 1.3 75.0 - - - +
79C ARG* 1.3 62.5 + - - +
80C VAL* 3.5 1.2 + - + -
146C PHE* 3.4 7.1 - - - -
147C TRP* 2.8 59.6 + + + +
149C ALA* 4.0 7.6 - - + -
181C LEU* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 3.5 5.6 - - - +
66C GLU* 3.0 64.5 + - + +
78C TYR* 1.3 71.8 - - - +
80C VAL* 1.3 63.9 + - - +
81C THR* 4.9 0.2 - - + -
117C ILE* 3.8 34.7 - - + +
144C GLN* 2.6 42.0 + - + +
145C VAL 3.8 2.0 - - - +
146C PHE* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 3.5 26.2 - - + -
64C ARG 3.4 13.0 - - - +
65C VAL* 4.4 6.5 - - + +
78C TYR* 4.2 2.5 - - + +
79C ARG* 1.3 73.5 - - - +
81C THR* 1.3 64.4 + - - +
95C LEU* 4.2 11.7 - - + -
114C PHE* 4.4 3.4 - - + -
143C ILE* 5.3 1.1 - - - +
144C GLN* 3.2 4.2 - - - +
145C VAL* 2.7 50.4 + - + +
147C TRP* 3.6 32.3 - - + -
159C LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C SER 3.7 0.9 - - - +
63C LEU* 3.5 6.7 - - - +
64C ARG* 2.9 47.9 + - - +
66C GLU* 3.8 25.2 - - + +
79C ARG* 4.4 1.3 - - + +
80C VAL* 1.3 78.4 - - - +
82C LEU* 1.3 62.6 + - - +
83C SER* 4.2 8.0 + - - -
95C LEU* 6.3 0.2 - - - -
142C ARG* 3.5 34.5 - - - +
143C ILE* 3.3 8.5 - - - -
144C GLN* 4.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C SER 3.4 23.8 - - - +
63C LEU* 3.8 20.2 - - + +
81C THR* 1.3 74.5 - - - +
83C SER* 1.3 62.8 + - - +
90C PHE* 4.2 5.1 - - + -
93C PHE* 3.7 41.5 - - + -
95C LEU* 5.5 2.5 - - + -
142C ARG* 3.3 2.3 - - - -
143C ILE* 2.8 53.5 + - + +
161C ALA* 3.8 23.3 - - + -
163C ILE* 3.8 15.5 - - + -
177C LEU* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLU 4.1 0.5 - - - +
61C PHE* 3.6 6.1 - - - -
62C SER* 3.0 37.6 + - - -
64C ARG* 4.2 17.0 + - - -
81C THR* 4.6 7.8 + - - -
82C LEU* 1.3 78.7 - - - +
84C ALA* 1.3 61.8 - - - +
85C ALA 4.3 0.3 + - - -
90C PHE* 4.6 3.4 - - - -
141C THR 3.2 14.1 - - - -
142C ARG* 4.2 13.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
60C GLU 3.7 4.7 - - - -
61C PHE* 3.6 26.7 - - + -
83C SER* 1.3 74.3 - - - +
85C ALA* 1.3 66.9 + - - +
86C PRO* 3.7 1.0 - - - +
88C SER* 3.4 24.3 - - - +
89C TYR* 3.8 7.6 - - - -
90C PHE* 4.3 3.4 - - + -
141C THR* 2.8 27.1 + - - +
----------------------------------------------------------
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