Contacts of the helix formed by residues 59 - 82 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU 5.2 0.4 - - - -
58B SER* 1.3 75.9 - - - +
60B ARG* 1.3 92.9 + - - +
61B GLU* 3.1 11.5 + - - +
62B GLN* 2.9 30.1 + - - +
63B ARG* 2.9 24.8 + - - +
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B SER 4.7 1.6 + - - -
59B SER* 1.3 98.0 + - - +
61B GLU* 1.3 72.8 + - + +
63B ARG* 3.4 30.1 + - - +
64B GLN* 3.1 22.3 + - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 3.3 8.7 + - - +
60B ARG* 1.3 83.6 - - + +
62B GLN* 1.3 67.4 + - + +
64B GLN* 3.0 13.3 + - - +
65B HIS* 2.9 40.7 + - - +
104B ARG* 2.7 39.9 + - + +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 3.1 20.3 + - - +
57B GLU 4.0 4.7 - - - +
58B SER* 3.7 7.1 - - - -
59B SER* 2.9 39.4 + - - +
61B GLU* 1.3 79.6 - - + +
63B ARG* 1.3 60.8 + - - +
65B HIS* 3.1 5.0 + - - -
66B ALA* 3.0 19.8 + - - +
104B ARG* 2.7 36.4 + - + +
105B CYS* 3.2 24.5 - - - +
106B ASP 5.5 1.0 + - - -
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 4.5 1.1 - - + -
52B LEU* 3.1 40.7 - - + +
58B SER* 3.2 33.6 + - - +
59B SER 2.9 12.6 + - - +
60B ARG* 3.4 39.1 + - - +
62B GLN* 1.3 75.1 - - - +
64B GLN* 1.3 57.6 + - - +
66B ALA* 3.2 1.0 + - - -
67B GLY* 2.9 26.2 + - - -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PRO* 4.5 19.1 - - - +
60B ARG 3.1 14.2 + - - +
61B GLU* 3.0 17.2 + - - +
63B ARG* 1.3 78.3 - - - +
65B HIS* 1.3 59.2 + - + +
67B GLY* 3.5 2.4 + - - -
68B ASP* 2.9 52.7 + - - +
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Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 2.9 34.5 + - - +
62B GLN* 3.1 9.2 + - - +
64B GLN* 1.3 76.9 - - + +
66B ALA* 1.3 65.5 + - - +
68B ASP* 3.4 8.6 + - - +
69B CYS* 3.2 23.4 + - - +
97B TYR* 4.7 10.7 - + - +
100B ALA* 3.5 37.0 - - + +
101B CYS* 3.9 15.5 - - - +
104B ARG* 2.8 52.4 + - + -
105B CYS* 4.3 5.2 - - - -
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B CYS* 3.5 16.0 - - + +
51B TYR* 3.5 24.5 - - + -
52B LEU* 3.5 27.1 - - + -
62B GLN 3.0 8.5 + - - +
63B ARG 3.2 1.1 + - - +
65B HIS* 1.3 77.8 - - - +
67B GLY* 1.3 58.1 + - - +
69B CYS 3.3 1.2 + - - -
70B ALA* 2.9 28.9 + - - +
101B CYS* 3.7 17.0 - - - -
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.0 16.3 - - - +
63B ARG 2.9 15.8 + - - -
64B GLN* 3.9 4.0 - - - -
66B ALA* 1.3 74.3 - - - +
68B ASP* 1.3 59.6 + - - +
70B ALA* 3.7 3.9 - - - +
71B ASP* 2.9 41.3 + - - +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 3.5 15.0 - - - +
86A TRP* 3.2 28.4 + - - +
64B GLN* 2.9 48.3 + - - +
65B HIS* 3.8 8.6 + - - +
66B ALA 3.3 0.4 - - - -
67B GLY* 1.3 76.1 - - - +
69B CYS* 1.3 58.3 + - - +
71B ASP* 3.8 1.3 - - - +
72B LEU* 3.0 37.4 + - - +
97B TYR* 3.7 25.8 - - + -
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Residues in contact with CYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B CYS* 3.6 28.5 - - - -
48B CYS* 4.1 6.5 - - - -
65B HIS 3.2 14.4 + - - +
66B ALA 3.7 3.1 - - - +
68B ASP* 1.3 80.0 - - - +
70B ALA* 1.3 57.5 + - - +
72B LEU* 3.9 2.9 - - - +
73B CYS* 2.8 39.0 + - - +
94B ALA 4.5 1.1 - - - -
97B TYR* 3.8 19.7 - - - +
98B ALA* 3.4 30.3 - - - -
101B CYS* 4.1 2.7 - - + -
119B CYS* 4.0 7.9 - - - -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 3.4 27.0 - - + +
48B CYS* 3.8 17.4 - - + -
49B GLU* 4.4 15.9 - - + +
52B LEU* 5.2 2.0 - - + -
66B ALA 2.9 17.2 + - - +
67B GLY* 3.7 8.3 - - - +
68B ASP 3.3 0.2 - - - -
69B CYS* 1.3 77.2 - - - +
71B ASP* 1.3 64.2 + - - +
74B ARG* 3.1 24.2 + - - +
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Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.6 30.4 - - + +
82A ARG* 4.4 16.1 + - - -
84A SER* 2.4 32.1 + - - +
85A PRO* 4.7 2.6 - - - +
86A TRP* 4.4 13.6 - - + -
67B GLY* 2.9 27.8 + - - +
68B ASP* 3.8 2.9 - - - +
70B ALA* 1.3 76.2 - - - +
72B LEU* 1.3 66.7 + - - +
74B ARG* 2.9 20.8 + - - +
75B LEU* 3.1 11.5 + - - +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TRP* 3.6 45.8 - - + -
89A ALA* 5.7 1.1 - - + -
68B ASP 3.0 20.0 + - - +
69B CYS* 4.0 2.0 - - - +
71B ASP* 1.3 76.6 - - - +
73B CYS* 1.3 57.0 + - - +
75B LEU* 3.1 18.6 + - + +
76B ALA* 3.0 28.9 + - - +
90B ALA* 4.9 1.7 - - - +
93B LEU* 3.6 28.5 - - + +
94B ALA* 3.8 17.6 - - + +
97B TYR* 3.5 39.5 - - + -
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Residues in contact with CYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA* 3.9 9.4 - - + +
44B CYS* 3.9 28.0 - - - -
45B ILE* 3.3 22.8 - - + +
69B CYS* 2.8 27.4 + - - +
72B LEU* 1.3 77.3 - - - +
74B ARG* 1.3 56.6 + - - +
76B ALA* 4.1 3.4 - - - +
77B ALA* 2.9 30.8 + - - +
94B ALA* 4.3 5.8 - - - -
122B PHE* 3.9 32.3 - - - -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.7 19.7 - - + +
78A LEU* 4.2 29.1 - - - +
79A LEU* 5.3 1.8 - - - -
82A ARG* 4.3 7.5 - - - +
45B ILE* 4.0 22.1 - - + +
46B ARG* 3.0 25.3 - - - +
49B GLU* 2.8 29.7 + - - -
70B ALA* 3.1 19.3 + - - +
71B ASP* 2.9 18.6 + - - +
73B CYS* 1.3 75.8 - - - +
75B LEU* 1.3 59.5 + - - +
77B ALA* 3.5 4.6 + - - +
78B LEU* 3.0 30.7 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 4.3 14.8 - - + -
75A LEU* 3.4 23.3 - - + +
79A LEU* 5.8 2.2 - - + -
86A TRP* 5.7 1.3 - - + +
89A ALA* 4.7 11.9 - - + +
90A ALA* 4.5 23.3 - - + +
93A LEU* 3.8 32.3 - - + -
71B ASP 3.1 9.5 + - - +
72B LEU* 3.4 21.3 - - + +
74B ARG* 1.3 75.1 - - - +
76B ALA* 1.3 65.3 + - - +
78B LEU* 3.2 3.3 + - - +
79B LEU* 3.0 32.3 + - + +
90B ALA* 4.5 9.4 - - + -
93B LEU* 6.2 3.1 - - + -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU 3.0 15.0 + - - +
73B CYS* 4.1 3.8 - - - +
75B LEU* 1.3 76.0 - - - +
77B ALA* 1.3 57.1 + - - +
79B LEU* 3.4 3.3 + - - +
80B MSE 2.9 36.1 + - - +
87B ALA* 4.9 0.6 - - - +
90B ALA* 3.9 15.4 - - - +
91B CYS* 3.9 37.3 - - - +
94B ALA* 4.3 6.7 - - + -
122B PHE* 5.0 5.8 - - + -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ARG* 4.3 10.9 - - + +
41B ALA* 4.5 14.8 - - + +
42B GLN* 4.8 11.2 - - + -
45B ILE* 6.2 1.3 - - + -
73B CYS 2.9 21.3 + - - +
74B ARG* 3.7 6.5 - - - +
76B ALA* 1.3 77.8 - - - +
78B LEU* 1.3 64.0 + - - +
80B MSE 3.0 9.7 + - - +
81B GLU* 3.0 35.8 + - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASP* 3.3 40.6 - - + +
72A LEU* 3.4 34.5 - - + +
75A LEU* 3.9 22.2 - - + -
74B ARG 3.0 18.4 + - - +
75B LEU 3.2 2.9 + - - +
77B ALA* 1.3 75.4 - - - +
79B LEU* 1.3 69.3 + - + +
81B GLU* 3.4 14.3 + - - +
82B ARG* 3.0 41.0 + - + +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.0 20.2 - - + -
93A LEU* 3.7 24.0 - - + -
97A TYR* 5.0 2.7 - - + -
75B LEU* 3.0 20.2 + - + +
76B ALA 3.8 2.5 - - - +
78B LEU* 1.3 87.6 - - + +
80B MSE 1.3 64.5 + - - +
82B ARG* 3.3 2.7 + - + -
83B ARG 3.1 3.3 + - - -
84B SER* 2.9 48.9 + - - +
86B TRP* 3.9 14.4 - - + +
87B ALA* 3.7 16.4 - - - +
90B ALA* 3.5 30.1 - - + -
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Residues in contact with MSE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLU* 3.0 67.8 - - + +
37B CYS* 3.3 32.3 - - + +
38B ARG* 3.7 27.4 - - + -
41B ALA* 5.5 2.2 - - - -
76B ALA* 2.9 26.3 + - - +
77B ALA* 3.0 6.0 + - - +
79B LEU* 1.3 77.5 - - - +
81B GLU* 1.3 62.1 + - - +
83B ARG* 3.4 20.1 + - - +
87B ALA* 4.1 13.0 - - + -
91B CYS* 3.9 20.2 - - - -
122B PHE* 5.9 0.2 - - - -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 5.2 0.2 - - - -
38B ARG* 3.7 30.7 + - - +
42B GLN* 5.0 6.8 - - - +
77B ALA* 3.0 28.9 + - - +
78B LEU* 3.6 12.3 + - - +
79B LEU 3.2 0.2 - - - -
80B MSE 1.3 77.2 - - - +
82B ARG* 1.3 67.6 + - - +
83B ARG* 2.8 30.5 + - - +
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 3.3 25.8 + - - +
67A GLY* 3.5 7.5 - - - -
68A ASP* 2.6 60.5 + - + +
71A ASP* 3.0 29.4 + - + +
72A LEU* 6.0 1.3 - - + -
97A TYR* 5.4 2.6 + - + -
78B LEU* 3.0 34.0 + - + +
79B LEU* 3.3 4.7 + - + +
81B GLU* 1.3 82.7 + - - +
83B ARG* 1.3 70.6 + - - +
84B SER* 3.0 8.3 + - - +
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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
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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