Contacts of the helix formed by residues 69 - 80 (chain C) in PDB entry 3L9J
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 69 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LYS* 1.3 75.9 - - - +
70C PHE* 1.3 64.5 + - - +
71C HIS* 3.7 7.3 + - - +
72C GLU* 3.1 37.9 + - - +
73C ALA* 3.0 20.6 + - - +
111C TRP* 3.5 0.7 - - - -
168C CYS 3.6 8.5 - - - -
169C ARG* 3.6 28.9 - - + +
170C ASP 3.2 10.3 - - - +
171C GLN* 4.3 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C THR* 1.3 72.1 - - - +
71C HIS* 1.3 70.4 + - + +
73C ALA* 3.3 2.1 + - - +
74C SER* 2.9 25.7 + - - -
84C LEU* 3.5 22.2 - - + -
111C TRP* 3.4 28.7 - + + +
112C LEU 3.4 23.6 - - - -
114C LEU 3.7 16.8 - - - -
115C ASN* 4.4 13.9 - - + -
126C MET* 3.8 28.9 - - + -
152C CYS* 3.4 32.1 - - - -
168C CYS* 3.1 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C THR* 3.2 7.5 + - - +
70C PHE* 1.3 89.6 - - + +
72C GLU* 1.3 63.9 + - + +
74C SER* 3.7 4.1 - - - -
75C GLU* 3.1 57.3 + - + +
168C CYS* 4.8 0.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LYS* 3.5 30.6 - - + +
69C THR* 3.1 40.6 + - - +
71C HIS* 1.3 85.6 - - + +
73C ALA* 1.3 60.5 + - - +
75C GLU* 3.3 5.6 + - - +
76C ASP* 2.8 30.4 + - - +
171C GLN* 4.9 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LYS* 4.1 1.3 - - + +
69C THR 3.0 17.1 + - - +
70C PHE 3.6 2.7 - - - +
72C GLU* 1.3 78.4 - - - +
74C SER* 1.3 61.7 + - - +
76C ASP* 3.3 4.2 + - - +
77C CYS* 3.0 26.3 + - - -
84C LEU* 4.4 6.5 - - + -
111C TRP* 3.5 25.4 - - + -
174C TYR* 3.5 36.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PHE* 2.9 21.3 + - - -
71C HIS* 3.7 6.5 - - - -
73C ALA* 1.3 77.4 - - - +
75C GLU* 1.3 58.4 + - - +
77C CYS* 3.2 4.5 + - - +
78C ILE* 2.9 40.8 + - - +
84C LEU* 3.8 25.4 + - - +
126C MET* 3.2 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C HIS* 3.1 46.2 + - + +
72C GLU* 3.8 5.8 - - - +
74C SER* 1.3 75.2 - - - +
76C ASP* 1.3 58.9 + - - +
78C ILE* 3.8 23.4 - - - +
79C SER* 2.9 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 3.9 10.3 - - - -
72C GLU 2.8 15.1 + - - +
73C ALA 3.3 10.1 - - - +
75C GLU* 1.3 75.4 - - - +
77C CYS* 1.3 62.0 + - - +
79C SER* 2.7 25.4 + - - -
80C ARG* 3.0 39.4 + - - +
174C TYR* 2.3 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ALA 3.0 19.7 + - - -
74C SER 3.2 5.4 + - - +
76C ASP* 1.3 74.6 - - - +
78C ILE* 1.3 61.7 + - - +
80C ARG* 3.1 11.4 + - - +
81C GLY 3.2 0.2 + - - -
82C GLY* 2.8 25.4 + - - -
83C THR* 3.6 21.5 - - - +
84C LEU* 3.7 24.9 - - - +
174C TYR* 4.1 1.6 - - - -
176C CYS* 2.0 56.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER* 2.9 33.7 + - - +
75C GLU* 3.8 24.5 - - - +
76C ASP 3.3 0.2 - - - -
77C CYS* 1.3 76.2 - - - +
79C SER* 1.3 57.5 + - - +
81C GLY* 2.9 20.6 + - - -
82C GLY 3.5 15.0 - - - +
83C THR* 5.2 4.9 - - - +
126C MET* 5.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLU 2.9 15.7 + - - -
76C ASP* 2.7 25.9 + - - -
78C ILE* 1.3 75.7 - - - +
80C ARG* 1.3 63.3 + - - +
81C GLY 3.3 1.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
62C LEU* 5.0 6.8 - - - +
64C PHE* 3.4 42.9 - - - -
76C ASP* 3.0 34.2 + - - +
77C CYS* 3.1 9.2 + - - +
78C ILE 3.1 1.2 - - - -
79C SER* 1.3 81.2 - - - +
81C GLY* 1.3 58.1 + - - +
82C GLY 3.4 0.4 - - - -
178C PHE* 3.3 28.6 - - + -
----------------------------------------------------------
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