Contacts of the helix formed by residues 85 - 95 (chain C) in PDB entry 2WJZ
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 ASP 85 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 4.5 3.6 + - - -
83C ILE* 3.7 3.0 - - - +
84C HIS* 1.3 84.4 - - - +
86C PHE* 1.3 66.5 + - - +
87C GLU* 3.2 23.4 - - - +
88C THR* 2.5 45.6 + - - -
89C ALA* 3.2 19.6 + - - +
112C LEU* 3.9 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASP* 1.3 71.4 - - - +
87C GLU* 1.3 71.6 + - + +
89C ALA* 3.9 3.5 - - - +
90C SER* 2.8 46.2 + - - -
112C LEU* 3.6 11.9 - - + +
115C GLN* 3.1 72.2 + - + +
116C ILE* 3.8 12.6 - - + -
119C THR* 3.2 34.8 - - + -
120C PHE* 3.9 8.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 4.1 12.3 - - - +
85C ASP* 3.1 30.7 - - - +
86C PHE* 1.3 94.6 + - + +
88C THR* 1.3 60.3 + - - +
90C SER* 3.7 3.5 - - - -
91C GLU* 2.8 28.0 + - - +
115C GLN* 5.2 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 3.5 29.3 + - + +
62C MET* 5.5 2.9 - - + -
82C GLY 4.8 4.3 - - - +
83C ILE* 4.1 20.0 - - + -
84C HIS* 4.4 5.1 + - - +
85C ASP* 2.5 34.7 + - - -
87C GLU* 1.3 72.2 - - - +
89C ALA* 1.3 61.0 + - - +
91C GLU* 3.2 26.9 - - - +
92C LEU* 3.3 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 3.9 16.4 - - + -
85C ASP 3.2 13.1 + - - +
86C PHE 3.9 2.5 - - - +
88C THR* 1.3 78.4 - - - +
90C SER* 1.3 67.1 + - - +
92C LEU* 3.1 5.8 + - - +
93C ILE* 2.9 29.8 + - - +
100C VAL* 4.1 12.6 - - + -
116C ILE* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 2.8 43.0 + - - -
87C GLU* 3.7 5.2 - - - -
89C ALA* 1.3 74.4 - - - +
91C GLU* 1.3 56.7 + - - +
93C ILE 3.3 0.3 + - - -
94C LEU* 2.9 46.4 + - - +
120C PHE* 3.3 27.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 2.9 39.2 + - - +
63C LEU* 3.3 34.9 - - + +
87C GLU 2.8 19.5 + - - +
88C THR* 3.2 20.2 - - - +
90C SER* 1.3 75.7 + - - +
92C LEU* 1.3 57.4 + - - +
94C LEU* 3.9 10.3 - - - +
95C ARG* 3.1 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C MET* 3.6 34.5 - - + +
63C LEU* 3.5 22.0 - - + +
66C VAL* 3.5 32.9 - - + +
79C VAL* 4.6 5.8 - - + -
83C ILE* 3.6 32.8 - - + -
88C THR* 3.3 26.5 + - + +
89C ALA 3.1 5.2 + - - +
91C GLU* 1.3 78.2 - - - +
93C ILE* 1.3 64.9 + - - +
95C ARG 3.3 7.8 + - - -
96C GLY 3.5 1.0 + - - -
97C ALA* 3.3 19.0 + - - +
100C VAL* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ALA 2.9 19.7 + - - +
90C SER 3.8 3.1 - - - +
92C LEU* 1.3 74.7 - - - +
94C LEU* 1.3 64.1 + - + +
96C GLY* 3.1 12.1 + - - -
97C ALA* 3.4 24.2 + - - +
98C ASP 5.2 1.6 - - - +
99C LYS 5.0 0.2 - - - -
100C VAL* 3.8 24.2 - - + +
116C ILE* 4.1 11.7 - - + -
120C PHE* 3.5 54.5 - - + -
124C ALA* 4.0 18.4 - - + -
12D ASN* 5.9 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C SER* 2.9 42.2 + - - +
91C GLU* 4.0 8.3 - - - +
93C ILE* 1.3 76.8 - - + +
95C ARG* 1.3 60.3 + - - +
96C GLY* 3.1 2.3 + - - -
120C PHE* 3.7 22.0 - - + -
12D ASN* 5.1 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 3.7 56.9 + - + +
66C VAL* 3.6 12.0 - - + +
67C GLU* 3.8 46.8 + - + +
70C ALA* 4.2 2.8 - - - +
91C GLU* 3.1 24.2 + - - +
92C LEU 3.6 6.5 - - - +
93C ILE 3.2 0.8 - - - -
94C LEU* 1.3 76.7 - - - +
96C GLY* 1.3 56.9 + - - +
12D ASN* 5.7 0.2 - - - -
18D ARG* 5.9 1.2 + - - -
----------------------------------------------------------
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