Contacts of the helix formed by residues 59 - 82 (chain C) in PDB entry 3KAV
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 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU 4.5 0.2 + - - -
58C SER* 1.3 75.4 - - - +
60C ARG* 1.3 65.5 + - - +
61C GLU* 3.0 20.5 + - - +
62C GLN* 3.0 36.6 + - - +
63C ARG* 3.0 11.8 + - - +
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Residues in contact with ARG 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C SER* 1.3 72.6 - - - +
61C GLU* 1.3 74.9 + - + +
63C ARG* 3.2 34.1 - - - +
64C GLN* 3.0 28.7 + - - +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C SER* 2.9 10.9 + - - +
60C ARG* 1.3 97.4 + - + +
62C GLN* 1.3 62.7 + - + +
63C ARG 3.1 0.2 - - - -
64C GLN* 3.3 7.9 + - - +
65C HIS* 2.7 60.3 + - + -
104C ARG* 6.5 0.7 - - + -
85D PRO* 4.6 11.8 - - - +
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Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TYR* 3.3 21.1 + - - +
57C GLU 4.4 3.1 - - - +
58C SER* 3.5 7.6 - - - -
59C SER* 3.0 34.5 + - - +
61C GLU* 1.3 78.4 - - + +
63C ARG* 1.3 58.1 + - - +
65C HIS* 3.5 4.3 + - - -
66C ALA* 3.0 25.5 + - - +
104C ARG* 2.7 35.1 + - + +
105C CYS* 3.4 26.3 + - - +
106C ASP 5.1 2.6 + - - -
112C GLU* 6.4 0.2 - - - +
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Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TYR* 4.8 2.0 - - + -
52C LEU* 3.3 47.4 - - + +
55C CYS 5.3 1.0 + - - -
56C THR 5.0 4.6 + - - -
58C SER* 2.6 53.3 + - - +
59C SER* 3.0 6.3 + - - +
60C ARG* 3.2 39.9 - - - +
62C GLN* 1.3 75.3 - - - +
64C GLN* 1.3 59.9 + - - +
66C ALA* 4.5 1.3 - - - +
67C GLY* 2.8 25.3 + - - -
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Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ARG* 3.0 20.7 + - - +
61C GLU* 3.3 13.2 + - - +
63C ARG* 1.3 76.0 - - - +
65C HIS* 1.3 56.8 + - - +
67C GLY* 3.2 1.1 + - - -
68C ASP* 2.7 71.3 + - - +
82D ARG* 3.4 36.7 + - - +
83D ARG 4.6 1.7 - - - +
84D SER* 3.6 5.1 - - - +
85D PRO* 3.8 21.7 - - + +
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Residues in contact with HIS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU* 2.7 50.8 + - + -
62C GLN* 3.5 12.1 - - - +
64C GLN* 1.3 81.6 - - - +
66C ALA* 1.3 57.9 + - - +
68C ASP* 3.3 0.8 + - - -
69C CYS* 2.8 32.2 + - - +
100C ALA 4.1 8.5 - - - -
101C CYS* 4.1 12.3 - - + -
104C ARG* 2.7 50.5 + - + -
105C CYS* 4.6 2.0 - - - -
85D PRO* 5.2 5.6 - - + +
86D TRP* 3.4 37.3 - + + -
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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
----------------------------------------------------------
48C CYS* 3.4 28.0 - - + +
51C TYR* 3.6 28.3 - - + -
52C LEU* 4.2 4.9 - - + -
62C GLN 3.0 16.8 + - - +
63C ARG 3.9 3.1 - - - +
65C HIS* 1.3 76.6 - - - +
67C GLY* 1.3 62.1 + - - +
69C CYS* 3.7 0.6 - - - +
70C ALA* 3.1 19.8 + - - +
101C CYS* 3.8 17.5 - - - -
115C CYS* 4.7 0.2 - - - -
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 3.4 20.1 - - - +
63C ARG 2.8 13.8 + - - -
64C GLN* 3.6 1.6 - - - -
66C ALA* 1.3 78.3 - - - +
68C ASP* 1.3 60.1 + - - +
70C ALA* 3.5 5.2 + - - +
71C ASP* 2.9 27.4 + - - +
82D ARG* 3.3 16.9 + - - -
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLN* 2.7 47.8 + - - +
65C HIS* 4.4 0.2 - - - -
67C GLY* 1.3 69.6 - - - +
69C CYS* 1.3 60.2 + - - +
71C ASP* 3.3 6.4 + - - +
72C LEU* 2.9 35.9 + - - +
79D LEU* 3.2 13.9 - - + +
82D ARG* 3.1 29.6 - - - -
84D SER* 2.9 21.2 + - - -
85D PRO* 4.1 2.3 - - - +
86D TRP* 3.4 25.1 - - + -
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Residues in contact with CYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C CYS* 3.8 16.6 - - - -
48C CYS* 3.8 17.9 - - - -
65C HIS 2.8 18.6 + - - +
66C ALA 3.7 4.7 - - - +
68C ASP* 1.3 77.4 - - - +
70C ALA* 1.3 58.3 + - - +
72C LEU* 3.1 13.2 + - - +
73C CYS* 2.8 34.9 + - - -
94C ALA 5.2 0.7 - - - -
97C TYR 4.5 3.4 - - - +
98C ALA* 3.6 30.5 - - - -
101C CYS* 4.1 13.2 - - + -
119C CYS* 3.9 4.5 - - - -
86D TRP* 4.0 1.7 - - - -
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.9 30.7 - - + +
48C CYS* 4.2 10.7 - - + +
49C GLU* 4.5 12.6 - - + +
66C ALA 3.1 14.9 + - - +
67C GLY* 3.7 6.7 - - - +
68C ASP 3.3 0.2 - - - -
69C CYS* 1.3 79.5 - - - +
71C ASP* 1.3 60.2 + - - +
73C CYS* 3.1 6.0 + - - +
74C ARG* 2.9 35.0 + - - +
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Residues in contact with ASP 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY 2.9 6.4 + - - +
68C ASP* 3.3 8.7 + - - +
69C CYS 3.2 0.4 - - - -
70C ALA* 1.3 78.1 - - - +
72C LEU* 1.3 63.5 + - - +
74C ARG* 2.9 33.8 + - - +
75C LEU* 3.1 9.7 + - - +
75D LEU* 3.8 20.7 - - + +
78D LEU* 3.6 25.7 - - + +
79D LEU* 4.7 3.8 - - + +
82D ARG* 2.9 37.8 + - - -
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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
----------------------------------------------------------
68C ASP* 2.9 23.1 + - + +
69C CYS* 3.5 6.1 - - - +
71C ASP* 1.3 74.1 - - - +
73C CYS* 1.3 61.4 + - - +
75C LEU* 3.4 6.0 + - + +
76C ALA 3.2 16.3 + - - -
90C ALA 5.4 0.2 - - - +
93C LEU* 3.5 24.9 - - + -
94C ALA* 3.7 23.1 - - + +
97C TYR* 3.5 39.9 - - + -
75D LEU* 3.5 32.3 - - + +
79D LEU* 4.2 13.0 - - + -
86D TRP* 3.8 13.2 - - + -
90D ALA* 5.0 0.2 - - + -
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Residues in contact with CYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA* 4.1 7.6 - - + +
44C CYS* 3.6 32.5 - - - -
45C ILE* 3.4 18.6 - - + -
69C CYS* 2.8 19.9 + - - -
70C ALA 3.1 9.4 + - - +
72C LEU* 1.3 76.3 - - - +
74C ARG* 1.3 58.7 + - - +
76C ALA* 3.3 7.3 + - - +
77C ALA* 2.9 32.2 + - - +
94C ALA* 4.5 2.7 - - - -
98C ALA* 4.9 0.2 - - - -
122C PHE* 3.7 28.9 - - - -
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Residues in contact with ARG 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.4 22.6 - - + +
49C GLU* 2.6 39.6 + - - -
70C ALA* 2.9 18.6 + - - +
71C ASP* 2.9 28.6 + - - +
73C CYS* 1.3 75.8 - - - +
75C LEU* 1.3 57.7 + - - +
77C ALA* 3.6 6.0 - - - +
78C LEU* 2.9 33.8 + - + +
78D LEU* 6.3 0.2 - - - -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ASP 3.1 10.1 + - - +
72C LEU* 3.6 9.6 - - + +
74C ARG* 1.3 74.4 - - - +
76C ALA* 1.3 55.9 + - - +
78C LEU* 3.2 7.6 + - + +
79C LEU* 2.8 52.5 + - + +
90C ALA* 4.5 12.1 - - + -
71D ASP* 3.7 43.3 - - + +
72D LEU* 3.5 24.7 - - + +
75D LEU* 3.3 36.1 - - + -
93D LEU* 5.3 2.9 - - + -
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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
----------------------------------------------------------
72C LEU 3.2 11.4 + - - +
73C CYS 3.3 7.4 + - - +
75C LEU* 1.3 79.3 - - - +
77C ALA* 1.3 52.1 + - - +
79C LEU* 3.0 3.0 + - - +
80C MSE 2.7 43.0 + - - +
87C ALA 5.4 0.2 - - - -
90C ALA* 4.2 12.8 - - - +
91C CYS* 4.2 26.7 - - - +
94C ALA* 4.2 15.3 - - + -
122C PHE* 4.4 9.4 - - + -
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 4.1 15.2 - - + +
41C ALA* 4.2 17.4 - - + +
42C GLN* 4.9 9.4 - - + +
45C ILE* 6.1 0.9 - - + -
73C CYS 2.9 19.6 + - - +
74C ARG* 3.6 7.0 - - - +
76C ALA* 1.3 75.3 - - - +
78C LEU* 1.3 58.3 + - - +
80C MSE 3.3 5.4 + - - +
81C GLU* 3.0 43.3 + - - +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ARG* 2.9 19.8 + - + +
75C LEU* 3.4 8.5 - - + +
77C ALA* 1.3 77.8 - - - +
79C LEU* 1.3 62.4 + - + +
81C GLU* 3.3 13.5 + - - +
82C ARG* 3.1 54.3 + - + +
71D ASP* 3.2 32.8 - - + +
74D ARG* 6.2 0.9 - - - -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 2.8 34.9 + - + +
76C ALA* 3.6 4.5 - - - +
78C LEU* 1.3 74.5 - - + +
80C MSE 1.3 61.2 + - - +
82C ARG* 3.7 1.5 + - - +
83C ARG 3.4 1.6 + - - -
84C SER* 2.9 34.4 + - - +
86C TRP* 3.9 13.0 - - + +
87C ALA* 3.8 15.5 - - - +
90C ALA* 3.4 28.9 - - + -
68D ASP* 3.6 37.2 - - + +
71D ASP* 4.1 20.4 - - + +
72D LEU* 4.5 13.7 - - + -
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Residues in contact with MSE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 3.2 50.0 - - + +
37C CYS* 3.4 41.1 - - + -
38C ARG* 3.7 32.8 + - + +
41C ALA* 5.8 0.7 - - - -
76C ALA* 2.7 28.8 + - - +
77C ALA* 3.8 5.2 - - - +
79C LEU* 1.3 72.5 - - - +
81C GLU* 1.3 66.2 + - - +
83C ARG* 3.1 9.7 + - - +
87C ALA* 4.1 13.7 - - + -
91C CYS* 3.5 17.5 - - - -
122C PHE* 5.6 0.7 - - - -
129C LEU* 3.4 19.3 - - + -
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.3 36.3 + - - +
42C GLN* 3.8 13.9 - - - +
77C ALA* 3.0 25.4 + - - +
78C LEU* 3.6 11.3 - - + +
79C LEU 3.3 0.2 - - - -
80C MSE 1.3 73.7 - - - +
82C ARG* 1.3 59.7 + - + +
83C ARG* 2.8 13.0 + - - +
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 3.1 39.5 + - + +
79C LEU* 4.3 4.0 - - - +
81C GLU* 1.3 77.7 - - + +
83C ARG* 1.3 70.6 + - - +
84C SER* 2.9 1.7 + - - -
52D LEU* 5.7 1.6 - - - +
63D ARG 4.2 1.4 + - - -
64D GLN* 3.3 36.8 + - - +
67D GLY* 3.2 30.9 - - - -
68D ASP* 2.9 29.3 + - - +
71D ASP* 3.6 6.1 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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