Contacts of the helix formed by residues 74 - 89 (chain C) in PDB entry 3IEW
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 74 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C SER* 5.2 4.7 - - - -
38C ASP* 3.7 23.6 - - + +
75C SER* 1.3 63.2 + - - +
76C ARG* 3.7 24.4 + - - +
77C ALA* 3.3 25.3 + - - +
78C LEU* 3.2 27.1 + - - +
80C ARG* 5.0 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C SER* 3.7 2.9 + - - -
38C ASP* 2.3 31.7 + - - -
40C ASP* 3.6 19.7 - - - +
43C LEU* 4.1 11.6 - - - +
44C HIS* 2.9 31.9 + - - -
47C THR* 5.1 0.9 + - - -
74C ASP* 1.3 73.0 - - - +
76C ARG* 1.3 60.8 + - - +
78C LEU* 3.5 11.7 + - - +
79C LEU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLY* 4.1 20.5 + - - -
38C ASP* 5.7 1.6 - - - +
43C LEU* 3.6 18.4 - - + -
74C ASP* 3.3 14.4 + - - +
75C SER* 1.3 74.5 - - - +
77C ALA* 1.3 55.6 + - - +
79C LEU* 3.2 2.5 + - - +
80C ARG* 2.8 57.3 + - - +
117C ASN* 3.4 48.6 + - - +
120C ALA* 4.3 8.5 - - - +
121C ASP* 2.8 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASP* 3.3 27.9 + - - +
76C ARG* 1.3 78.4 - - - +
78C LEU* 1.3 59.9 + - + +
80C ARG* 3.3 18.8 + - - +
81C GLU* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C SER* 5.0 10.3 - - - -
44C HIS* 5.0 14.4 - - + +
47C THR* 4.9 3.6 - - + +
59C ILE* 5.5 5.2 - - + -
63C PHE* 3.6 53.5 - - + -
74C ASP 3.2 16.4 + - - +
75C SER* 3.7 13.9 - - - +
76C ARG 3.3 0.4 - - - -
77C ALA* 1.3 80.7 - - + +
79C LEU* 1.3 56.5 + - - +
81C GLU* 3.2 6.6 + - + +
82C CYS* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.9 26.7 - - + +
46C ILE* 4.1 11.0 - - + -
47C THR* 3.6 24.2 + - - +
50C LEU* 3.9 16.4 - - + -
75C SER 2.9 19.0 + - - +
76C ARG* 3.2 4.5 + - - +
78C LEU* 1.3 76.1 - - - +
80C ARG* 1.3 58.1 + - - +
82C CYS* 3.3 4.6 + - + +
83C ALA* 2.9 27.2 + - - +
118C ILE* 4.5 10.3 - - + -
121C ASP* 3.6 29.2 - - + +
122C LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASP* 5.0 3.6 + - - -
76C ARG* 2.8 40.0 + - - +
77C ALA* 3.6 24.3 - - - +
79C LEU* 1.3 76.4 - - - +
81C GLU* 1.3 62.0 + - - +
83C ALA* 3.2 5.7 + - - +
84C SER* 3.0 20.4 + - - -
121C ASP* 2.4 66.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C PHE* 3.6 26.7 - - + -
77C ALA 2.9 16.8 + - - +
78C LEU* 3.5 7.2 - - + +
80C ARG* 1.3 74.5 - - - +
82C CYS* 1.3 65.8 + - - +
84C SER* 2.9 17.6 + - - -
85C ARG* 2.9 55.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.6 41.5 - - + +
50C LEU* 3.6 28.0 - - - -
51C PHE* 3.8 28.4 - - + -
63C PHE* 4.0 0.6 - - - -
78C LEU 2.8 14.2 + - - +
79C LEU* 3.4 11.0 - - + +
81C GLU* 1.3 75.4 - - - +
83C ALA* 1.3 64.2 + - - +
85C ARG* 3.0 3.9 + - - +
86C VAL* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU 2.9 13.1 + - - +
80C ARG 3.3 10.3 - - - +
82C CYS* 1.3 76.3 - - - +
84C SER* 1.3 62.7 + - - +
86C VAL* 3.4 7.4 + - - +
87C ALA* 3.1 23.9 + - - +
93C ILE* 4.7 9.6 - - + +
121C ASP 4.2 9.2 - - - +
122C LEU* 3.8 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ARG 3.0 11.7 + - - -
81C GLU* 2.9 24.9 + - - -
83C ALA* 1.3 77.4 - - - +
85C ARG* 1.3 58.7 + - - +
87C ALA* 3.3 7.0 + - - +
88C GLN* 2.8 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE* 4.2 15.5 - - + -
56C LEU* 3.6 9.9 - - + +
62C HIS* 2.9 55.8 + - + +
63C PHE* 3.6 13.5 - - - -
81C GLU* 2.9 45.8 + - - +
82C CYS 3.7 5.8 - - - +
84C SER* 1.3 73.3 - - - +
86C VAL* 1.3 60.8 + - - +
88C GLN* 3.3 13.2 + - + +
89C ALA* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 3.9 36.1 - - + +
51C PHE* 4.6 0.9 - - + +
54C ALA* 4.2 10.3 - - + -
56C LEU* 4.2 10.8 - - + -
82C CYS* 2.9 23.5 + - - +
83C ALA* 3.8 7.9 - - - +
85C ARG* 1.3 78.6 - - - +
87C ALA* 1.3 60.4 + - - +
89C ALA* 3.3 8.8 + - - +
90C GLY 3.4 0.5 + - - -
91C PHE* 3.1 47.9 + - + +
93C ILE* 4.3 19.1 - - + -
156C VAL* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ALA 3.1 13.8 + - - +
84C SER* 3.6 9.6 - - - +
86C VAL* 1.3 75.5 - - - +
88C GLN* 1.3 64.2 + - - +
90C GLY* 2.9 16.3 + - - -
91C PHE 3.4 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C SER* 2.8 24.7 + - - +
85C ARG* 3.3 19.7 + - + +
87C ALA* 1.3 71.7 - - - +
89C ALA* 1.3 59.6 + - - +
90C GLY 3.5 1.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
56C LEU* 4.0 26.2 - - + -
85C ARG 3.0 15.7 + - - +
86C VAL 3.7 5.4 - - - +
87C ALA 3.1 0.4 - - - -
88C GLN* 1.3 74.4 - - - +
90C GLY* 1.3 54.6 + - - +
91C PHE* 3.6 16.5 - - + -
158C ARG* 2.7 33.8 + - - +
----------------------------------------------------------
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