Contacts of the helix formed by residues 65 - 79 (chain C) in PDB entry 4WMJ
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 65 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.0 17.0 + - - -
27C ILE* 5.3 5.8 - - + +
32C LEU* 4.2 21.1 - - + +
39C ARG* 4.5 4.0 - - - +
43C TYR* 3.2 12.4 + - - -
64C ILE* 1.3 74.2 - - - +
66C ASP* 1.3 64.7 + - - +
67C THR* 3.1 10.7 + - - -
68C THR* 2.9 26.6 + - - -
69C PHE* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LYS* 5.2 9.8 - - - +
43C TYR* 3.2 15.3 + - - +
65C ASP* 1.3 79.3 - - - +
67C THR* 1.3 58.2 + - - +
69C PHE* 3.6 11.6 + - - -
70C SER* 3.0 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.5 30.3 - - + -
65C ASP* 3.1 10.5 + - - -
66C ASP* 1.3 76.3 - - - +
68C THR* 1.3 65.6 + - - +
70C SER* 3.3 5.7 + - - -
71C LEU* 2.9 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 5.0 5.4 - - + -
19C TYR* 2.7 41.1 + - + -
27C ILE* 4.4 4.1 - - + +
63C ARG 4.3 4.5 - - - +
64C ILE* 3.7 23.5 - - + -
65C ASP* 2.9 24.7 + - - -
67C THR* 1.3 79.6 - - - +
69C PHE* 1.3 63.9 + - - +
71C LEU* 3.3 4.4 + - - +
72C LEU* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TYR* 4.0 20.0 - + + +
59C TYR* 3.6 34.3 - + - -
64C ILE* 4.2 19.0 - - + +
65C ASP 3.0 16.8 + - - +
66C ASP* 3.9 11.0 - - - +
68C THR* 1.3 75.9 - - - +
70C SER* 1.3 62.8 + - - +
72C LEU* 3.2 13.9 + - + +
73C LEU* 2.9 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 3.0 30.0 + - - -
67C THR* 3.6 7.6 - - - -
69C PHE* 1.3 76.4 - - - +
71C LEU* 1.3 60.0 + - - +
73C LEU* 3.3 11.1 + - - +
74C ASN* 3.0 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 4.8 3.5 - - - +
15C LYS* 3.5 42.8 - - + +
16C LEU* 3.5 23.1 - - + +
19C TYR* 3.5 46.0 - - + -
67C THR* 2.9 29.7 + - + +
68C THR 3.6 1.8 - - - +
70C SER* 1.3 75.1 - - - +
72C LEU* 1.3 64.6 + - - +
74C ASN* 3.3 17.4 + - + +
75C LEU* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.8 28.5 - - + -
64C ILE* 4.4 13.7 - - + -
68C THR* 2.9 36.0 + - + +
69C PHE* 3.2 12.5 + - + +
71C LEU* 1.3 71.0 - - - +
73C LEU* 1.3 66.6 + - + +
75C LEU* 3.0 20.3 + - + +
76C ALA* 3.2 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PHE* 2.9 57.9 + - + +
70C SER* 3.6 10.5 - - - +
72C LEU* 1.3 76.4 - - + +
74C ASN* 1.3 61.9 + - - +
76C ALA* 3.2 12.7 + - + +
77C LYS* 3.1 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 3.7 11.5 - - + +
70C SER* 3.0 23.9 + - - +
71C LEU* 3.6 20.5 - - + +
72C LEU 3.2 0.4 - - - -
73C LEU* 1.3 74.8 - - - +
75C LEU* 1.4 57.4 + - - +
77C LYS* 2.8 32.9 + - - +
78C SER* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.1 16.2 - - + -
10C ASP* 3.9 16.2 - - - +
12C ALA* 3.7 7.3 - - + +
13C TYR* 3.9 24.2 - - + +
16C LEU* 3.8 22.7 - - + -
71C LEU 3.1 11.9 + - - +
72C LEU* 3.0 16.6 + - + +
74C ASN* 1.4 74.7 - - - +
76C ALA* 1.3 65.0 + - - +
78C SER* 3.2 0.5 + - - -
79C ARG* 3.0 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU 3.2 9.9 + - - +
73C LEU* 3.2 15.7 + - + +
75C LEU* 1.3 76.1 - - - +
77C LYS* 1.3 61.8 + - + +
79C ARG* 3.5 0.6 + - - -
80C ASN 3.3 3.1 + - - -
81C VAL* 3.2 49.0 + - + +
82C GLU* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 3.1 25.8 + - - +
74C ASN* 2.8 35.9 + - - +
75C LEU 3.2 0.2 - - - -
76C ALA* 1.3 72.8 - - + +
78C SER* 1.3 65.1 + - - +
80C ASN* 3.0 21.9 + - - +
81C VAL 5.3 0.2 - - - +
82C GLU* 4.8 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LYS* 5.6 2.3 - - - +
10C ASP* 2.8 38.6 + - - +
11C PRO* 4.5 6.1 - - - +
12C ALA* 3.8 10.1 + - - +
74C ASN 2.9 18.0 + - - -
75C LEU 3.2 3.8 + - - -
77C LYS* 1.3 75.7 - - - +
79C ARG* 1.3 61.5 + - - +
80C ASN* 3.3 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LYS* 2.8 60.3 + - + +
5C VAL* 2.8 32.5 + - - +
7C LEU* 3.4 37.1 - - + +
10C ASP* 3.4 34.3 + - - +
75C LEU* 3.0 30.7 + - + +
76C ALA* 3.5 2.7 + - - +
78C SER* 1.3 77.0 - - - +
80C ASN* 1.3 63.1 + - - +
81C VAL* 3.3 11.6 + - + +
84C ALA* 5.3 0.3 - - - +
----------------------------------------------------------
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