Contacts of the strand formed by residues 74 - 82 (chain C) in PDB entry 4ICX
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 PRO 74 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS 4.1 5.2 - - - +
34C PHE* 3.9 11.1 - - - -
35C ASP 5.4 0.5 + - - -
72C ARG 3.1 9.8 - - - +
73C THR* 1.3 94.6 - - + +
75C ILE* 1.3 62.2 + - - +
76C LYS* 3.8 8.4 + - + +
96C VAL* 3.7 23.1 - - + -
97C LEU 3.5 7.2 - - - +
98C ASP* 4.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.2 9.6 - - + -
12C VAL* 4.4 5.8 - - + -
32C ALA* 4.5 10.3 - - + -
33C LYS 4.2 3.1 - - - +
34C PHE* 3.5 31.6 - - + -
58C TRP* 4.2 24.9 - - + -
73C THR 4.8 1.8 - - - +
74C PRO* 1.3 70.1 - - - +
76C LYS* 1.3 59.2 + - - +
77C LEU* 3.4 7.8 + - + -
95C ILE 3.7 0.3 - - - +
96C VAL* 3.5 1.8 - - - -
97C LEU* 2.8 60.3 + - + +
99C LEU* 3.9 16.8 - - + -
130C ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLU 3.5 2.1 - - - +
32C ALA* 3.2 21.1 - - - -
33C LYS* 3.2 21.0 + - + +
74C PRO* 3.7 9.9 - - + +
75C ILE* 1.3 70.6 - - - +
77C LEU* 1.3 64.0 + - - +
78C GLN* 3.7 23.2 + - - +
94C TYR* 4.0 36.8 - - + -
95C ILE 3.8 2.0 - - - +
96C VAL* 4.7 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 4.7 6.7 - - + -
14C ILE* 3.9 19.1 - - + -
30C VAL* 3.8 20.9 - - + -
31C GLU 3.6 2.5 - - - -
32C ALA* 3.6 22.0 - - + -
56C LEU* 4.1 3.4 - - + -
75C ILE* 3.4 5.5 + - + +
76C LYS* 1.3 71.4 - - - +
78C GLN* 1.3 59.8 + - - +
79C CYS 4.1 0.2 - - - -
94C TYR* 3.3 5.8 - - - +
95C ILE* 2.8 55.3 + - + +
97C LEU* 3.8 24.0 - - + -
126C ILE* 6.4 0.2 - - + -
128C ILE* 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.3 5.2 - - - -
31C GLU* 2.7 41.1 + - + +
76C LYS* 3.7 26.6 + - + +
77C LEU* 1.3 73.2 - - - +
79C CYS* 1.3 62.3 + - - +
80C PHE* 3.6 31.7 - - + -
91C THR* 3.2 24.3 + - - +
93C GLY 3.8 11.4 - - - +
94C TYR* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 4.8 4.0 - - - -
28C LEU* 3.9 24.7 - - - -
29C VAL 3.8 5.6 - - - -
30C VAL* 4.4 6.7 - - + -
52C PHE* 4.6 10.3 - - - -
77C LEU 4.1 1.6 + - - -
78C GLN* 1.3 71.2 - - - +
80C PHE* 1.3 63.9 + - - +
91C THR* 3.9 2.3 + - - -
92C ILE* 2.9 30.1 + - + +
93C GLY 3.1 11.8 + - - +
94C TYR* 4.6 0.2 - - - +
114C LEU* 3.8 31.9 - - + -
126C ILE* 4.4 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C MSE 3.5 0.9 - - - +
28C LEU* 3.4 14.0 - - - +
29C VAL* 2.7 45.4 + - + +
31C GLU* 3.3 34.1 - - + -
78C GLN* 3.6 48.9 - - + -
79C CYS* 1.3 75.1 - - - +
81C ALA* 1.3 60.3 + - - +
82C LEU* 5.1 0.7 - - + +
89C LYS* 3.9 39.7 - - + -
90C GLU 3.7 1.3 - - - -
91C THR* 3.7 31.6 - - - -
92C ILE* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ARG* 3.7 27.4 - - - +
26C HIS* 5.0 6.1 - - + -
27C MSE 3.5 5.2 - - - +
28C LEU* 4.5 1.3 - - - -
46C HIS* 4.7 4.7 - - + -
80C PHE* 1.3 72.9 - - - +
82C LEU* 1.3 60.7 + - - +
83C ASP 4.1 0.2 + - - -
88C ALA 3.8 1.4 - - - +
89C LYS* 3.6 2.1 - - - -
90C GLU* 2.8 52.5 + - + +
92C ILE* 3.7 16.4 - - + +
119C TYR* 3.9 2.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
66B HIS* 3.6 48.7 - - + +
26C HIS* 3.4 6.3 - - - -
27C MSE 2.7 50.3 + - + +
29C VAL* 4.0 21.8 - - + -
43C PRO* 4.3 8.5 - - + -
80C PHE 4.9 1.3 - - - +
81C ALA* 1.3 72.8 - - - +
83C ASP* 1.3 63.3 + - - +
84C PRO* 3.3 12.9 - - + +
87C SER* 3.4 29.4 - - - +
88C ALA 3.6 3.1 - - - +
89C LYS* 3.7 18.8 - - + -
----------------------------------------------------------
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