Contacts of the helix formed by residues 61 - 80 (chain C) in PDB entry 3E20
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 SER 61 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 2.8 23.7 + - - +
60C LYS* 1.3 75.2 - - - +
62C ARG* 1.3 58.9 + - - +
63C VAL* 3.1 3.4 - - - -
64C ASN* 2.6 24.5 + - - +
65C ARG* 2.5 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LYS 3.3 9.0 + - - +
61C SER* 1.3 73.1 - - - +
63C VAL* 1.3 75.5 + - + +
65C ARG* 4.5 10.5 - - - +
66C LEU* 3.1 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C SER 2.9 2.6 + - - -
62C ARG* 1.3 90.0 - - + +
64C ASN* 1.3 60.0 + - - +
66C LEU* 4.4 2.9 - - - +
67C SER* 3.6 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASN 4.3 2.1 - - - +
28C GLY* 3.3 36.6 - - - +
29C THR* 4.1 12.7 + - - +
59C ILE* 4.2 19.4 - - - +
61C SER* 2.6 26.6 + - - -
63C VAL* 1.3 73.4 - - - +
65C ARG* 1.3 66.9 + - - +
67C SER* 2.9 17.7 + - - -
68C VAL* 3.0 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ALA 3.5 18.2 - - - +
57C SER* 2.7 45.7 + - - -
59C ILE* 3.6 30.3 - - + +
60C LYS 4.4 5.6 - - - +
61C SER 2.5 20.1 + - - +
62C ARG* 4.1 8.8 + - - +
64C ASN* 1.3 71.7 - - - +
66C LEU* 1.3 78.3 + - - +
68C VAL* 2.8 16.1 + - - +
69C LEU* 2.9 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 3.1 45.7 + - - +
63C VAL* 4.4 3.4 - - - +
65C ARG* 1.3 95.8 - - - +
67C SER* 1.3 61.4 + - - +
69C LEU* 3.5 12.7 + - + +
70C SER* 3.2 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASN 5.1 3.2 + - - -
30C SER* 3.0 26.8 + - - -
63C VAL 3.6 13.3 + - - -
64C ASN* 2.9 16.9 + - - -
65C ARG 2.8 1.4 + - - -
66C LEU* 1.3 77.3 - - - +
68C VAL* 1.3 62.1 + - - -
69C LEU 3.4 0.2 + - - -
70C SER* 3.4 5.7 + - - -
71C ALA* 3.1 22.0 + - - +
96C GLU* 4.4 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 3.3 22.7 - - - +
30C SER* 4.2 6.3 - - - -
32C ILE* 5.5 0.2 - - + -
56C ALA* 3.9 13.2 - - + -
59C ILE* 3.7 22.9 - - + -
64C ASN* 3.0 20.2 + - - +
65C ARG 2.8 9.5 + - - +
67C SER* 1.3 73.0 - - - +
69C LEU* 1.3 61.2 + - - +
71C ALA* 3.2 3.5 + - + +
72C ILE* 2.9 49.7 + - + +
124C CYS* 4.0 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TYR* 3.8 54.2 - - + +
56C ALA* 4.2 20.2 - - + -
57C SER* 4.3 4.9 - - - +
65C ARG* 2.9 50.7 + - + +
66C LEU* 3.6 17.7 - - + +
68C VAL* 1.3 77.8 - - - +
70C SER* 1.3 58.2 + - - +
72C ILE* 3.3 3.1 + - - +
73C THR* 3.0 33.0 + - - -
----------------------------------------------------------
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 LEU 3.2 14.0 + - - -
67C SER* 4.0 4.3 - - - -
68C VAL 3.4 0.2 - - - -
69C LEU* 1.3 78.6 - - - +
71C ALA* 1.3 54.4 + - - +
73C THR* 4.0 7.8 - - - +
74C SER* 3.1 16.7 + - - -
96C GLU* 6.1 0.9 - - - -
106C LYS* 2.7 45.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER* 3.8 24.7 - - - +
32C ILE* 4.1 13.0 - - + -
67C SER 3.1 16.0 + - - +
68C VAL* 3.6 5.6 - - + +
69C LEU 3.1 0.6 - - - -
70C SER* 1.3 78.2 - - - +
72C ILE* 1.3 64.0 + - - +
74C SER* 3.2 5.9 + - - -
75C THR* 2.9 30.2 + - - -
94C CYS* 4.0 2.5 - - - -
95C GLY* 4.6 10.1 - - - +
106C LYS* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE* 4.1 19.5 - - + -
49C LEU* 3.4 38.7 - - + +
52C GLU* 3.6 34.1 - - + +
53C TYR* 4.0 15.0 - - + -
56C ALA* 3.7 15.9 - - + -
68C VAL* 2.9 27.7 + - + +
69C LEU* 3.7 4.3 - - - +
71C ALA* 1.3 74.3 - - - +
73C THR* 1.3 63.5 + - - +
75C THR* 3.4 7.3 + - - -
76C ARG* 3.0 24.4 + - + +
122C TYR* 4.2 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TYR* 3.2 21.9 + - - -
69C LEU 3.0 18.3 + - - -
70C SER* 4.0 9.4 - - - +
72C ILE* 1.3 77.8 - - - +
74C SER* 1.3 63.6 + - - +
76C ARG* 3.1 17.2 + - - +
77C GLU* 3.2 25.5 + - + +
----------------------------------------------------------
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 SER 3.1 19.2 + - - -
71C ALA 3.2 5.1 + - - -
73C THR* 1.3 82.2 - - - +
75C THR* 1.3 60.3 + - - +
77C GLU* 4.6 0.6 - - - +
78C ARG* 3.3 20.6 + - - +
94C CYS* 3.8 10.0 - - - -
106C LYS* 3.3 25.8 + - - +
108C ASN* 3.3 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE* 3.4 32.1 - - + +
34C LEU* 4.0 17.9 - - + -
49C LEU* 3.7 17.7 - - + -
71C ALA 2.9 16.3 + - - -
72C ILE* 3.6 5.8 - - - -
74C SER* 1.3 77.3 - - - +
76C ARG* 1.3 55.5 + - - +
78C ARG* 3.0 8.5 + - - +
79C LEU* 2.8 32.4 + - + +
92C ILE* 4.1 15.0 - - + -
94C CYS* 3.4 14.9 - - - +
108C ASN* 4.7 0.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
46C SER* 3.3 48.0 + - - +
47C ASN* 3.9 5.7 - - - +
49C LEU* 3.5 16.6 - - + -
50C ALA* 3.6 29.3 - - - +
53C TYR* 6.4 1.6 - - - -
72C ILE* 3.0 18.6 + - - +
73C THR* 3.6 6.7 - - - +
75C THR* 1.3 75.5 - - - +
77C GLU* 1.3 62.1 + - + +
79C LEU* 3.0 6.9 + - - +
80C LYS* 2.8 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 3.2 19.5 + - + +
74C SER* 5.5 0.7 - - - +
76C ARG* 1.3 80.2 + - + +
78C ARG* 1.3 61.2 + - - +
80C LYS* 2.9 50.8 + - + +
81C LEU* 3.9 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER 3.3 17.3 + - - +
75C THR 3.0 10.0 + - - +
77C GLU* 1.3 76.6 - - - +
79C LEU* 1.3 66.4 + - - +
80C LYS 3.1 1.1 - - - -
81C LEU* 3.0 39.8 + - - +
82C TYR* 4.2 4.3 + - - -
92C ILE* 4.1 16.2 - - + -
108C ASN* 3.2 54.6 + - - +
110C ASP* 3.2 39.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
34C LEU* 4.3 4.9 - - + -
36C ILE* 3.7 23.3 - - + -
42C ILE* 4.0 21.5 - - + +
45C TYR* 4.0 13.2 - - + -
46C SER* 3.6 37.0 - - - +
49C LEU* 4.3 12.1 - - + -
75C THR 2.8 11.5 + - - +
76C ARG* 3.2 8.1 - - - +
78C ARG* 1.3 77.3 - - - +
80C LYS* 1.3 62.2 + - - +
82C TYR* 3.1 26.7 + - + +
90C LEU* 4.1 9.0 - - + -
92C ILE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 5.1 4.7 - - - -
46C SER* 4.2 13.5 - - - +
76C ARG* 2.8 53.1 + - - +
77C GLU* 2.9 49.0 + - + +
78C ARG 3.1 0.2 - - - -
79C LEU* 1.3 77.6 - - - +
81C LEU* 1.3 61.3 + - - +
82C TYR 3.0 10.8 + - - +
83C ASN* 4.5 4.3 - - - +
----------------------------------------------------------
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