Contacts of the helix formed by residues 66 - 81 (chain C) in PDB entry 1ZZJ
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 66 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C MET* 3.6 47.3 - - + +
11C GLY 3.9 10.8 - - - +
12C PRO 3.4 10.8 - - - +
13C ILE* 4.6 9.2 - - + -
65C GLY* 1.3 76.1 - - - -
67C GLN* 1.3 58.9 + - - +
68C ASP* 3.6 7.4 + - - +
69C GLN* 2.9 37.7 + - - +
70C ILE* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 6.0 0.4 - - - -
19A THR* 2.8 42.3 + - - +
58A ASP* 4.9 3.0 + - - -
10C MET 4.4 9.7 + - - +
11C GLY* 5.2 1.2 - - - -
12C PRO* 4.3 15.2 + - - +
14C ILE* 3.9 21.9 - - + +
66C THR* 1.3 73.2 - - - +
68C ASP* 1.3 59.1 + - - +
70C ILE* 3.5 4.3 + - - +
71C GLN* 2.9 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C MET* 5.4 5.1 + - - -
66C THR* 3.3 7.9 + - - +
67C GLN* 1.3 76.4 - - - +
69C GLN* 1.3 61.4 + - + +
71C GLN* 3.3 12.7 + - - +
72C ASN* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C MET* 4.6 15.6 - - + +
13C ILE* 5.6 0.9 - - - +
43C SER* 3.2 23.5 + - - +
44C GLY* 3.7 22.0 + - - +
45C ALA* 3.9 14.1 - - + +
65C GLY* 3.3 8.1 - - - -
66C THR* 2.9 39.4 + - - +
68C ASP* 1.3 77.8 - - + +
70C ILE* 1.3 59.1 + - - +
72C ASN* 3.2 4.0 + - - +
73C ALA* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 3.4 51.8 - - + +
16C THR* 4.2 20.6 - - + +
63C ILE* 3.8 33.4 - - + +
65C GLY 3.7 11.9 - - - +
66C THR 2.8 13.5 + - - +
67C GLN* 3.7 5.4 - - - +
69C GLN* 1.3 76.6 - - - +
71C GLN* 1.3 58.3 + - + +
73C ALA* 3.4 1.7 + - - +
74C GLN* 2.9 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLN* 2.9 30.8 + - - +
68C ASP* 3.8 12.6 + - - +
70C ILE* 1.3 73.2 - - + +
72C ASN* 1.3 65.9 + - - +
74C GLN* 3.3 13.8 + - - +
75C TYR* 3.0 43.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 4.0 7.2 + - - +
43C SER* 3.7 22.4 - - - +
68C ASP 2.8 17.0 + - - +
69C GLN* 3.2 11.7 - - - +
71C GLN* 1.3 71.2 - - - +
73C ALA* 1.3 62.0 + - - +
75C TYR* 3.1 12.2 + - - +
76C LEU* 3.1 40.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
39C ILE* 4.2 6.2 - - - +
43C SER* 3.4 19.6 - - - +
45C ALA* 3.9 0.4 - - + -
47C ILE* 3.8 14.6 - - + -
63C ILE* 3.7 25.4 - - + -
69C GLN 2.8 18.7 + - - +
70C ILE 3.7 4.7 - - - +
72C ASN* 1.3 71.3 - - - +
74C GLN* 1.3 57.3 + - - +
76C LEU* 3.2 1.8 + - - +
77C LEU* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 4.2 17.8 - - - +
18C VAL* 4.7 14.6 - - + +
63C ILE* 3.7 22.9 - - + +
70C ILE* 2.9 34.3 + - - +
71C GLN* 3.7 13.0 - - - +
72C ASN 3.2 0.4 - - - -
73C ALA* 1.3 71.9 - - - +
75C TYR* 1.3 68.0 + - + +
77C LEU* 3.8 7.7 - - + +
78C GLN* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLN* 3.0 38.4 + - + -
72C ASN* 3.6 9.4 - - - +
74C GLN* 1.3 78.4 - - + +
76C LEU* 1.3 57.8 + - + +
78C GLN* 3.0 21.3 + - + +
79C ASN* 2.9 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 5.0 8.7 - - - +
39C ILE* 3.6 39.4 - - + +
42C GLU* 3.4 39.9 - - + -
43C SER* 3.9 5.6 - - - +
72C ASN* 3.1 31.8 + - - +
73C ALA 3.8 2.0 - - - +
75C TYR* 1.3 77.3 - - + +
77C LEU* 1.3 56.2 + - - +
79C ASN* 3.4 13.9 + - + +
80C SER* 2.9 30.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
18C VAL* 5.3 5.4 - - + -
28C ILE* 3.3 41.8 - - + +
36C ILE* 5.7 0.2 - - + -
39C ILE* 3.9 17.3 - - + -
47C ILE* 4.9 10.5 - - + -
61C ILE* 4.4 22.7 - - + -
63C ILE* 4.0 26.7 - - + -
73C ALA* 3.0 23.3 + - + +
74C GLN* 3.8 7.2 - - + +
76C LEU* 1.3 76.3 - - - +
78C GLN* 1.3 60.9 + - - +
80C SER* 3.2 16.7 - - - -
81C VAL* 3.4 12.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
74C GLN 3.1 10.9 + - - +
75C TYR* 3.0 32.7 + - - +
77C LEU* 1.3 80.2 - - - +
79C ASN* 1.3 66.3 + - - +
81C VAL* 3.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 2.9 33.0 + - - +
76C LEU* 3.7 15.8 - - + +
78C GLN* 1.3 76.8 + - - +
80C SER* 1.3 64.2 + - - +
81C VAL 3.4 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C SER* 3.6 33.1 + - - +
28C ILE* 4.0 12.9 + - - -
35C ARG* 4.4 6.2 - - - +
39C ILE* 3.5 22.3 - - - +
76C LEU 2.9 9.0 + - - -
77C LEU* 3.2 13.2 - - - -
78C GLN 3.2 0.2 - - - -
79C ASN* 1.3 75.3 - - - +
81C VAL* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 5.8 2.5 - - + -
24C LEU* 3.7 37.5 - - + -
27C SER* 4.3 11.1 + - - +
28C ILE* 4.0 21.1 - - + -
77C LEU 3.6 14.6 - - - +
78C GLN* 3.2 18.0 + - - +
79C ASN 4.2 4.5 - - - -
80C SER* 1.3 81.8 - - - +
----------------------------------------------------------
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