Contacts of the strand formed by residues 79 - 85 (chain C) in PDB entry 4JZJ
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 THR 79 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LYS* 3.6 25.1 - - + -
55C ASP* 3.5 19.1 + - - +
74C SER* 3.7 11.8 + - - -
77C GLU* 3.2 13.7 + - - +
78C VAL* 1.3 79.1 + - - +
80C ASN* 1.5 61.6 + - - +
81C TYR* 3.5 38.9 + - + +
94C ILE 3.7 1.0 - - - +
95C LEU* 3.2 4.7 - - - -
96C PHE 2.9 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C VAL 3.8 0.5 - - - +
55C ASP* 2.8 48.1 + - - +
79C THR* 1.5 56.3 - - - +
81C TYR* 1.3 63.7 + - - +
82C THR* 3.8 10.0 + - - -
93C TRP* 3.8 22.8 - - - +
94C ILE 3.6 9.5 - - - +
95C LEU* 3.8 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 4.4 1.9 - - - +
32C MET* 3.7 18.6 - - + -
39C LEU* 3.8 22.4 - - + -
53C VAL 3.4 4.5 - - - +
54C LYS* 3.8 17.4 - - + +
70C PHE* 3.6 40.6 - + - -
73C ILE* 3.6 30.1 - - - +
74C SER 4.8 0.7 + - - -
79C THR* 3.5 37.3 + - + +
80C ASN* 1.3 74.2 - - - +
82C THR* 1.3 59.4 + - - +
83C VAL 4.3 0.2 + - - -
93C TRP* 3.1 5.9 - - - +
94C ILE* 3.0 42.5 + - + +
96C PHE* 4.0 28.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C CYS* 3.3 2.3 - - - +
53C VAL* 2.6 56.8 + - + +
55C ASP 5.7 0.2 + - - -
80C ASN* 3.8 15.6 + - - -
81C TYR* 1.3 74.3 + - - +
83C VAL* 1.3 69.4 + - - +
91C SER* 4.7 4.9 - - - +
92C THR 3.4 12.8 - - - +
93C TRP* 3.9 8.0 - - + +
59H PHE* 4.2 26.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
27C ILE* 4.4 19.5 - - + -
30C LEU* 3.8 22.0 - - + -
39C LEU* 3.6 31.0 - - + -
41C TRP* 3.8 7.6 - - + -
50C ILE* 3.4 26.9 - - + -
51C GLU 3.3 2.9 - - - -
52C CYS* 3.7 14.8 - - - -
82C THR* 1.3 74.8 - - - +
84C ARG* 1.3 65.3 + - - +
90C PHE* 5.2 0.9 - - + -
91C SER* 3.3 2.6 - - - -
92C THR* 2.9 36.6 + - + +
93C TRP* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASP 3.9 0.9 - - - +
50C ILE* 3.6 4.7 - - - -
51C GLU* 3.0 69.8 + - + +
53C VAL* 5.1 7.3 - - + +
82C THR* 5.1 0.7 - - + -
83C VAL* 1.3 78.0 - - - +
85C VAL* 1.3 65.5 + - - +
86C ALA 4.0 0.3 + - - -
90C PHE* 3.3 7.9 - - - +
91C SER* 3.7 10.3 - - - -
33H TYR* 3.7 29.7 - - + +
47H TRP* 5.5 0.6 - - - -
50H ASP* 2.8 35.9 + - - +
59H PHE* 3.6 31.9 - - + +
104H ALA* 3.7 16.3 - - + +
105H SER* 4.2 6.3 - - - -
102L TYR* 3.1 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PRO* 4.8 3.8 - - + -
27C ILE* 3.6 31.2 - - + -
47C VAL* 3.5 22.7 - - + -
48C THR* 4.6 1.1 - - - +
49C ASP 3.8 2.7 - - - +
50C ILE* 4.1 10.8 - - + -
84C ARG* 1.3 77.8 - - - +
86C ALA* 1.3 63.0 + - - +
87C ASN 3.2 19.1 - - - +
88C PRO* 3.2 23.3 - - + +
89C PRO* 3.5 5.5 - - - +
90C PHE* 2.7 24.6 + - + +
33H TYR* 2.6 26.4 + - - -
----------------------------------------------------------
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