Contacts of the helix formed by residues 56 - 79 (chain C) in PDB entry 5T5W
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 GLU 56 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 4.0 23.5 - - + +
53C GLN* 2.8 39.1 + - + +
55C ARG* 1.3 80.8 - - + +
57C ARG* 1.3 65.2 + - - +
58C PRO 3.4 0.7 - - - -
59C VAL* 3.1 21.0 + - + +
60C ALA 3.3 8.8 + - - -
118C LEU* 3.8 27.6 - - + +
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 3.1 32.0 + - + +
50C ARG* 3.2 17.3 + - - +
52C LEU* 2.9 32.3 + - + -
53C GLN* 3.0 9.8 + - - +
54C VAL* 3.3 32.8 - - - +
56C GLU* 1.3 76.3 - - - +
58C PRO* 1.3 69.1 - - + +
59C VAL 3.2 0.2 + - - -
60C ALA* 3.3 3.8 + - - +
61C LEU* 3.0 22.7 + - - +
155C CYS* 4.2 13.4 + - - -
156C VAL* 3.9 17.2 - - + +
159C GLY 3.7 6.7 + - - -
162C CYS* 3.0 28.8 + - - +
163C GLU* 3.1 25.3 + - - -
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Residues in contact with PRO 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 5.3 1.6 - - + -
54C VAL 3.1 19.3 - - - +
55C ARG* 3.6 9.4 - - - +
56C GLU 3.6 2.9 - - - -
57C ARG* 1.3 90.7 - - + +
59C VAL* 1.3 55.8 + - - +
61C LEU* 3.9 3.4 - - + +
62C GLU* 2.8 31.5 + - - +
100C LEU* 4.1 10.2 - - + +
103C CYS* 5.0 13.9 - - + +
104C ILE* 3.4 23.5 - - + +
156C VAL* 3.8 26.4 - - + -
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ARG 4.0 14.1 - - - +
56C GLU* 3.1 14.7 + - + +
58C PRO* 1.3 77.4 - - - +
60C ALA* 1.3 63.3 + - - +
62C GLU* 3.5 6.3 + - - +
63C ALA* 3.3 16.3 + - - +
104C ILE* 3.8 32.8 - - + -
118C LEU* 4.4 9.2 - - + -
122C LEU* 3.8 30.5 - - + +
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C TRP* 4.4 0.4 - - + -
49C LEU* 3.8 21.5 - - + -
52C LEU* 4.1 6.7 - - + -
56C GLU 3.3 2.2 + - - -
57C ARG 3.3 7.7 + - - +
59C VAL* 1.3 81.0 - - - +
61C LEU* 1.3 61.6 + - - +
63C ALA* 3.3 3.8 + - - +
64C GLU* 3.2 28.5 + - - +
118C LEU* 3.7 24.3 - - + +
121C TRP* 4.0 15.5 + - + +
122C LEU* 4.2 5.4 - - - -
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 4.5 4.2 - - + +
57C ARG 3.0 16.7 + - - +
58C PRO* 3.9 3.6 - - + +
60C ALA* 1.3 73.1 - - - +
62C GLU* 1.3 67.2 + - - +
64C GLU* 3.3 8.9 + - - +
65C LEU* 2.9 25.7 + - + +
100C LEU* 3.7 18.2 - - + -
148C LEU* 3.9 26.0 - - + -
152C ASP* 3.7 26.5 - - + -
153C LEU* 3.7 39.7 - - + +
156C VAL* 3.7 22.9 - - + -
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PRO 2.8 22.3 + - - +
59C VAL* 3.7 8.0 - - - +
60C ALA 3.3 0.2 - - - -
61C LEU* 1.3 73.0 - - - +
63C ALA* 1.3 72.3 + - - +
65C LEU* 3.8 0.9 - - - +
66C ALA* 2.8 34.5 + - - +
97C LEU* 3.7 16.2 - - + +
100C LEU* 3.6 13.2 - - + +
101C ARG* 3.6 39.6 + - + -
104C ILE* 4.0 15.0 - - + -
122C LEU* 5.8 0.2 - - - +
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL 3.3 4.2 + - - +
60C ALA 3.8 2.2 - - - +
61C LEU 3.3 0.2 - - - -
62C GLU* 1.3 87.6 + - - +
64C GLU* 1.3 60.9 + - - +
66C ALA* 4.1 4.0 - - - +
67C LEU* 3.2 23.7 + - - +
122C LEU* 3.5 32.8 - - + +
125C LEU* 3.6 22.8 - - + +
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PHE* 4.1 20.7 - - + -
45C ARG* 2.9 35.0 + - - -
49C LEU* 4.8 0.8 - - - +
60C ALA* 3.2 19.4 + - - +
61C LEU* 3.9 10.3 - - - +
63C ALA* 1.3 75.9 - - - +
65C LEU* 1.3 54.7 + - - +
67C LEU* 3.5 4.1 + - - +
68C THR* 2.7 37.6 + - - -
121C TRP* 2.8 44.2 + - + +
125C LEU* 3.6 6.5 - - + -
144C ASN* 4.5 4.7 + - - -
148C LEU* 4.1 8.6 - - + +
152C ASP* 3.4 10.2 - - - +
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 2.9 21.0 + - + +
62C GLU 3.9 2.7 - - - +
64C GLU* 1.3 74.9 - - - +
66C ALA* 1.3 61.8 + - - +
68C THR* 3.3 3.4 + - - -
69C LEU* 2.8 29.7 + - + +
93C LEU* 3.7 41.7 - - + +
96C ILE* 3.7 18.4 - - + -
97C LEU* 3.6 44.4 - - + +
100C LEU* 4.3 9.2 - - + -
148C LEU* 3.8 27.8 - - + +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU* 2.8 32.5 + - - +
63C ALA* 4.1 4.5 - - - +
65C LEU* 1.3 77.9 - - - +
67C LEU* 1.3 56.8 + - - +
69C LEU* 3.8 1.7 - - - +
70C LYS* 2.8 31.3 + - - +
97C LEU* 3.9 19.9 - - + +
101C ARG* 4.2 7.0 - - - +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 4.2 22.0 - - + -
43C PHE* 4.5 9.2 - - + -
63C ALA 3.2 17.6 + - - +
64C GLU* 3.6 4.5 - - - +
66C ALA* 1.3 78.7 - - - +
68C THR* 1.3 58.1 + - - +
70C LYS* 3.1 10.2 + - + +
71C VAL* 2.8 45.8 + - + +
125C LEU* 3.8 38.1 - - + +
128C ALA* 5.2 0.4 - - + -
129C PRO* 3.5 33.0 - - + -
137C LEU* 5.1 5.8 - - + -
141C VAL* 4.7 5.6 - - + -
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Residues in contact with THR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PHE* 4.6 4.5 - - - -
64C GLU 2.7 23.4 + - - -
65C LEU* 3.5 9.4 - - - -
67C LEU* 1.3 76.9 - - - +
69C LEU* 1.3 63.5 + - - +
71C VAL* 3.1 1.6 + - - +
72C LEU* 2.9 36.5 + - + +
93C LEU* 4.1 8.3 - - + -
141C VAL* 4.1 33.7 - - + +
144C ASN* 5.0 1.2 + - - -
145C LEU* 4.1 26.2 - - + -
148C LEU* 3.8 13.5 - - + +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 4.6 7.6 - - - +
65C LEU* 2.8 20.1 + - + +
66C ALA* 3.8 5.2 - - - +
68C THR* 1.3 71.9 - - - +
70C LYS* 1.3 58.2 + - - +
72C LEU* 5.0 0.7 - - - -
73C ASP* 2.9 34.6 + - + +
90C LEU* 3.5 45.8 - - + +
93C LEU* 3.7 21.7 - - + +
94C HIS* 3.7 34.8 - - + +
97C LEU* 3.8 20.6 - - + -
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Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ALA 2.8 18.3 + - - +
67C LEU* 3.1 10.3 + - + +
69C LEU* 1.3 76.6 - - - +
71C VAL* 1.3 63.7 + - + +
73C ASP* 4.0 4.7 - - - +
74C ALA* 3.2 21.8 + - - +
129C PRO* 5.1 22.2 - - + -
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 2.8 30.2 + - + +
68C THR 3.8 2.5 - - - +
70C LYS* 1.3 76.5 - - + +
72C LEU* 1.3 61.9 - - + +
74C ALA* 3.1 8.9 + - - +
75C THR* 2.8 29.3 + - - +
129C PRO* 6.0 0.7 - - + -
137C LEU* 3.9 29.6 - - + +
138C GLU* 3.7 42.0 - - + +
141C VAL* 3.9 16.8 - - + -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 3.8 36.1 - - + -
68C THR* 2.9 34.5 + - + +
71C VAL* 1.3 75.7 - - + +
73C ASP* 1.3 60.8 + - - +
75C THR* 3.5 11.7 - - - +
76C ALA* 2.8 31.5 + - - +
86C LEU* 4.3 9.5 - - + +
89C PRO* 6.0 2.5 - - + -
90C LEU* 3.7 25.1 - - + +
93C LEU* 4.4 14.1 - - + -
138C GLU* 5.2 2.0 - - + +
141C VAL* 4.0 19.3 - - + -
142C THR* 4.7 1.8 - - - +
145C LEU* 4.6 12.1 - - + -
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 2.5 38.1 + - - +
69C LEU* 2.9 20.8 + - + +
70C LYS* 4.0 5.2 - - - +
72C LEU* 1.3 77.1 - - - +
74C ALA* 1.3 60.8 + - - +
76C ALA* 3.4 3.5 + - - +
77C ASP* 2.8 47.1 + - - +
90C LEU* 3.6 11.0 - - + +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS 3.2 12.6 + - - +
71C VAL* 3.1 11.0 + - - +
73C ASP* 1.3 77.8 - - - +
75C THR* 1.3 53.9 + - - +
77C ASP* 3.9 6.6 - - - +
78C THR* 2.7 35.2 + - - -
138C GLU* 5.1 1.6 - - - +
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Residues in contact with THR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.1 24.7 - - + -
71C VAL* 2.8 15.4 + - - +
72C LEU* 3.0 14.5 + - - +
74C ALA* 1.3 75.9 - - - +
76C ALA* 1.3 60.0 + - - +
77C ASP 3.2 0.4 - - - -
78C THR* 3.3 4.5 + - - -
79C ASP* 3.0 29.5 + - + +
82C LEU* 4.3 11.8 - - + +
86C LEU* 4.2 6.1 - - + -
138C GLU* 3.0 42.0 + - + +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 6.0 3.4 - - + -
72C LEU 2.8 15.6 + - - +
73C ASP* 3.4 7.2 + - - +
75C THR* 1.3 76.7 - - - +
77C ASP* 1.3 64.4 + - - +
79C ASP 3.3 22.1 - - - +
80C PRO* 3.7 7.6 - - - +
83C GLY* 4.0 21.6 - - - +
86C LEU* 4.3 12.9 - - + +
87C ASP* 5.9 0.9 - - - +
90C LEU* 5.2 6.1 - - + -
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Residues in contact with ASP 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASP* 2.8 33.3 + - - +
74C ALA* 4.2 6.8 - - - +
76C ALA* 1.3 81.0 - - - +
78C THR* 1.3 64.5 + - - +
80C PRO* 4.3 7.7 - - - +
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Residues in contact with THR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA 2.7 23.3 + - - -
75C THR* 3.3 7.6 + - - -
77C ASP* 1.3 78.5 - - - +
79C ASP* 1.3 61.4 + - + +
80C PRO* 3.5 7.9 - - - +
138C GLU* 5.0 7.1 + - - +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER* 4.9 4.6 + - - +
75C THR* 3.0 12.4 + - + +
76C ALA 3.3 7.4 - - - +
78C THR* 1.3 79.9 - - + +
80C PRO* 1.3 58.8 - - - +
81C ALA* 3.0 23.7 + - - +
82C LEU* 3.1 35.7 + - + +
83C GLY 2.9 22.7 + - - -
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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) + - + + + + + -
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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