Contacts of the strand formed by residues 88 - 93 (chain C) in PDB entry 3ZXT
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 88 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PHE* 4.3 15.8 - - - +
44C ILE 3.2 20.3 - - - +
45C LYS* 3.4 25.1 + - - +
46C LYS* 3.6 9.2 - - - +
84C GLU* 3.5 3.8 - - - -
85C ASN* 2.8 45.3 + - - +
87C THR* 1.3 98.3 + - - +
89C VAL* 1.3 61.3 + - - +
90C ILE* 3.8 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LYS 3.6 1.4 - - - +
44C ILE* 2.8 39.3 + - + +
46C LYS* 4.3 7.9 - - - +
58C ARG* 6.1 2.0 - - - +
61C ILE* 3.8 37.5 - - + -
82C VAL* 5.3 3.1 - - + -
83C TYR 3.5 10.5 - - - +
84C GLU* 4.5 4.3 - - + +
88C ASP* 1.3 71.7 - - - +
90C ILE* 1.3 57.7 + - - +
91C LEU* 4.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.8 28.5 - - + -
41C ALA* 4.2 24.5 - - + -
42C LYS 3.5 7.2 - - - +
43C PHE* 3.6 35.0 - - + -
82C VAL* 3.5 2.9 - - - -
83C TYR* 2.8 50.7 + - + +
84C GLU 4.3 1.8 - - - +
85C ASN* 4.0 13.5 - - - +
88C ASP* 3.8 24.9 - - + +
89C VAL* 1.3 74.3 - - - +
91C LEU* 1.3 65.6 + - - +
92C ILE* 3.9 10.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA 3.5 0.9 - - - +
41C ALA* 3.5 3.1 - - - -
42C LYS* 2.9 44.1 + - + +
44C ILE* 4.0 22.7 - - + -
64C GLU* 4.0 19.1 - - + +
65C VAL* 4.1 17.5 - - + -
68C LEU* 4.2 18.6 - - + -
79C LEU* 4.3 11.0 - - + -
81C GLU 3.7 2.5 - - - -
82C VAL* 3.9 29.2 - - + -
89C VAL* 4.8 7.6 - - + -
90C ILE* 1.3 82.5 - - - +
92C ILE* 1.3 63.7 + - - +
93C LEU* 3.7 10.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 4.6 5.2 - - + -
13C TYR* 3.5 43.5 - - + +
30C CYS* 4.6 1.1 - - - -
39C TYR* 3.6 37.7 - - + -
40C ALA 3.5 1.6 - - - -
41C ALA* 4.1 23.8 - - + -
79C LEU* 3.2 9.4 - - - +
80C HIS* 2.9 35.3 + - + -
81C GLU* 2.7 28.7 + - + +
83C TYR* 4.1 5.4 - - + -
90C ILE* 3.9 10.1 + - + -
91C LEU* 1.3 72.6 - - - +
93C LEU* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 5.8 0.2 - - + -
39C TYR* 3.4 12.0 - - - +
40C ALA* 2.8 33.6 + - + +
42C LYS* 4.0 33.7 - - + -
64C GLU* 6.0 0.2 - - - +
68C LEU* 4.1 19.7 - - + -
77C ILE* 4.6 14.4 - - + -
78C THR 3.6 11.4 - - - +
79C LEU* 3.7 26.5 - - + -
80C HIS* 5.1 1.3 - - - -
91C LEU* 4.0 11.7 - - + +
92C ILE* 1.3 74.8 - - - +
94C GLU* 1.3 72.6 + - - +
1278C ACP 4.6 16.4 - - - +
----------------------------------------------------------
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