Contacts of the helix formed by residues 59 - 82 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 5.4 0.2 - - - +
57D GLU 3.7 1.9 + - - -
58D SER* 1.3 75.6 - - - +
60D ARG* 1.3 87.0 + - - +
61D GLU* 3.4 8.5 + - - +
62D GLN* 2.8 37.7 + - - +
63D ARG* 3.0 29.0 + - - +
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Residues in contact with ARG 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 5.6 2.2 - - - +
42A GLN* 5.2 11.7 + - - +
46A ARG* 5.1 11.5 - - - +
58D SER 5.0 0.2 + - - -
59D SER* 1.3 102.0 - - - +
61D GLU* 1.3 66.7 + - + +
63D ARG* 3.3 25.4 + - - +
64D GLN* 2.9 28.4 + - - +
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PRO* 5.3 7.2 - - - +
59D SER* 3.3 8.2 + - - +
60D ARG* 1.3 89.9 - - + +
62D GLN* 1.3 56.7 + - + +
64D GLN* 3.2 10.4 + - - +
65D HIS* 2.9 56.7 + - + +
104D ARG* 4.0 22.1 + - - +
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D TYR* 3.3 25.3 + - - +
57D GLU 4.0 4.0 - - - +
58D SER* 3.5 6.1 - - - -
59D SER* 2.8 40.3 + - - +
61D GLU* 1.3 75.7 - - + +
63D ARG* 1.3 61.3 + - - +
65D HIS* 3.3 4.4 + - - -
66D ALA* 2.9 32.6 + - - +
104D ARG* 2.6 33.3 + - + +
105D CYS* 3.7 19.7 + - - +
106D ASP 5.5 0.8 + - - -
112D GLU* 6.0 0.4 + - - -
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 4.2 5.6 + - - -
38A ARG* 4.0 4.2 - - - +
39A LEU* 3.6 43.8 - - - +
42A GLN* 4.2 6.3 - - - +
82C ARG* 4.2 2.0 + - - -
51D TYR* 4.7 2.9 - - - -
52D LEU* 3.3 39.9 - - + +
58D SER* 3.0 36.5 + - - +
59D SER* 3.0 24.7 + - - +
60D ARG* 3.4 23.8 - - - +
61D GLU 3.2 0.2 - - - -
62D GLN* 1.3 78.3 - - - +
64D GLN* 1.3 57.3 + - - +
66D ALA* 4.7 0.4 - - - -
67D GLY* 2.9 25.3 + - - -
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 3.3 42.4 + - - +
83C ARG 4.1 4.5 - - - +
84C SER* 3.5 5.3 - - - +
85C PRO* 3.8 22.6 - - + +
60D ARG 2.9 13.2 + - - +
61D GLU* 3.4 17.2 - - - +
63D ARG* 1.3 76.8 - - - +
65D HIS* 1.3 55.6 + - - +
67D GLY 3.1 1.0 + - - -
68D ASP* 2.7 73.0 + - - +
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Residues in contact with HIS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C PRO* 4.8 8.5 - - + +
86C TRP* 3.7 44.9 + + + -
61D GLU* 2.9 44.9 + - + +
62D GLN* 3.7 6.3 - - - +
64D GLN* 1.3 79.8 - - + +
66D ALA* 1.3 53.1 + - - +
68D ASP* 4.6 0.2 - - - -
69D CYS* 2.7 37.9 + - - +
100D ALA* 4.3 7.5 - - + +
101D CYS* 4.0 12.3 - - - -
104D ARG* 3.5 50.5 + - + -
105D CYS* 4.6 1.8 - - - -
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D CYS* 3.4 22.4 - - + +
51D TYR* 3.6 27.8 - - + -
52D LEU* 4.2 10.2 - - + +
62D GLN 2.9 20.4 + - - +
63D ARG 4.0 2.9 - - - +
65D HIS* 1.3 73.7 - - - +
67D GLY* 1.3 62.4 + - - +
70D ALA* 3.1 18.7 + - - +
101D CYS* 3.7 19.0 - - - -
105D CYS* 4.5 0.7 - - - -
115D CYS* 4.7 0.7 - - - -
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Residues in contact with GLY 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 3.2 22.8 - - - -
52D LEU* 3.8 17.2 - - - +
63D ARG 2.9 13.8 + - - -
64D GLN 3.1 0.2 + - - -
66D ALA* 1.3 77.8 - - - +
68D ASP* 1.3 60.6 + - - +
70D ALA* 3.4 5.9 + - - +
71D ASP* 3.2 25.6 + - - +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LEU* 3.6 11.0 - - + +
82C ARG* 2.9 26.5 + - - -
84C SER* 2.7 30.3 + - - +
85C PRO* 4.0 1.7 - - - +
86C TRP* 3.6 23.0 - - + -
64D GLN* 2.7 45.1 + - - +
65D HIS* 4.4 0.5 + - - -
67D GLY* 1.3 69.2 - - - +
69D CYS* 1.3 67.0 + - - +
71D ASP* 3.1 8.5 + - - +
72D LEU* 2.9 28.1 + - + +
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Residues in contact with CYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TRP* 4.0 8.2 - - + -
44D CYS* 3.8 15.5 - - - -
48D CYS* 3.9 3.4 - - - -
65D HIS 2.7 23.5 + - - +
66D ALA 3.7 4.9 - - - +
68D ASP* 1.3 72.8 - - - +
70D ALA* 1.3 63.1 + - - +
72D LEU* 3.1 9.4 + - - +
73D CYS* 2.9 28.0 + - - -
94D ALA 5.3 0.9 - - - -
97D TYR* 5.7 0.4 - - - -
98D ALA* 3.8 16.8 - - - -
101D CYS* 3.8 27.4 - - + -
119D CYS* 3.8 18.8 - - - -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ILE* 3.9 21.8 - - - +
48D CYS* 4.1 13.2 - - + -
49D GLU* 4.8 5.4 - - + +
52D LEU* 5.7 2.0 - - + -
66D ALA 3.1 14.2 + - - +
67D GLY* 3.6 7.0 - - - +
68D ASP 3.2 0.2 - - - -
69D CYS* 1.3 79.6 - - - +
71D ASP* 1.3 61.2 + - - +
73D CYS* 3.3 2.9 + - - +
74D ARG* 2.9 48.6 + - - +
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Residues in contact with ASP 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LEU* 3.7 22.3 - - + +
78C LEU* 3.2 41.8 - - + +
79C LEU* 4.1 5.8 - - + +
82C ARG* 3.6 13.3 + - - -
67D GLY 3.2 15.1 + - - +
68D ASP* 3.1 9.4 + - - +
70D ALA* 1.3 77.0 - - - +
72D LEU* 1.3 62.5 + - - +
74D ARG* 3.2 26.5 + - - +
75D LEU* 3.1 17.3 + - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LEU* 3.5 31.9 - - + -
79C LEU* 4.5 12.6 - - + -
86C TRP* 4.0 11.9 - - + -
68D ASP 2.9 20.7 + - - +
69D CYS* 3.6 7.2 - - - +
71D ASP* 1.3 76.4 - - - +
73D CYS* 1.3 63.9 + - - +
75D LEU* 3.0 7.2 + - + +
76D ALA* 2.9 22.7 + - - +
90D ALA 5.7 0.4 - - - +
93D LEU* 3.3 31.9 - - + +
94D ALA* 4.0 17.7 - - + +
97D TYR* 3.9 35.4 - - + -
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Residues in contact with CYS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA* 3.8 10.8 - - + +
44D CYS* 3.5 33.0 - - - -
45D ILE* 3.3 25.1 - - + -
69D CYS* 2.9 26.7 + - - +
72D LEU* 1.3 73.7 - - - +
74D ARG* 1.3 53.1 + - - +
76D ALA* 3.6 7.9 - - - +
77D ALA* 2.8 35.9 + - - +
94D ALA* 4.5 3.6 - - - -
98D ALA* 5.1 0.7 - - - -
122D PHE* 3.9 26.7 - - - -
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Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LEU* 6.2 1.1 - - - -
45D ILE* 4.1 19.4 - - + +
49D GLU* 2.5 32.4 + - - +
70D ALA* 2.9 41.4 + - - +
71D ASP* 3.3 25.0 + - - +
72D LEU 3.1 0.2 - - - -
73D CYS* 1.3 74.4 - - - +
75D LEU* 1.3 59.8 + - - +
77D ALA* 3.3 6.2 + - - +
78D LEU* 2.9 30.9 + - - +
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Residues in contact with LEU 75 (chain D).
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* 3.8 41.7 - - + +
72C LEU* 3.5 29.2 - - + +
75C LEU* 3.3 34.5 - - + -
93C LEU* 5.5 1.1 - - + -
71D ASP 3.1 8.2 + - - +
72D LEU* 3.0 9.7 + - + +
74D ARG* 1.3 80.4 - - - +
76D ALA* 1.3 63.2 + - - +
78D LEU* 3.0 9.4 + - + +
79D LEU* 3.0 31.9 + - + +
90D ALA* 4.1 14.6 - - + +
93D LEU* 6.4 1.3 - - + -
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU 2.9 12.5 + - - +
73D CYS* 3.6 9.0 - - - +
75D LEU* 1.3 79.4 - - - +
77D ALA* 1.3 57.6 + - - +
79D LEU* 3.3 2.4 + - - +
80D MSE 3.0 35.1 + - - +
87D ALA* 5.0 0.2 - - - +
90D ALA* 4.1 13.7 - - - -
91D CYS* 4.2 23.9 - - - +
94D ALA* 4.2 17.3 - - + -
122D PHE* 4.4 8.5 - - + -
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ARG* 4.2 14.8 - - + +
41D ALA* 4.3 16.1 - - + +
42D GLN* 4.8 8.5 - - + -
45D ILE* 6.0 0.9 - - + -
73D CYS 2.8 22.5 + - - +
74D ARG* 3.6 7.0 - - - +
75D LEU 3.2 0.2 - - - -
76D ALA* 1.3 74.0 - - - +
78D LEU* 1.3 57.6 + - - +
80D MSE 3.4 4.9 + - - +
81D GLU* 3.0 44.1 + - - +
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Residues in contact with LEU 78 (chain D).
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* 3.6 33.7 - - + +
74C ARG* 6.3 0.4 - - - -
74D ARG 2.9 17.0 + - - +
75D LEU* 3.0 8.7 + - + +
77D ALA* 1.3 74.4 - - - +
79D LEU* 1.3 64.0 + - + +
81D GLU* 3.3 17.5 + - + +
82D ARG* 2.9 55.5 + - + +
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ASP* 3.2 44.4 - - + +
71C ASP* 4.7 5.6 - - + +
72C LEU* 4.2 18.6 - - + -
93C LEU* 6.1 0.2 - - + -
75D LEU* 3.0 23.7 + - + +
76D ALA 3.8 4.0 - - - +
78D LEU* 1.3 77.4 - - + +
80D MSE 1.3 61.1 + - - +
82D ARG* 3.5 6.4 + - - -
83D ARG 3.2 2.1 + - - -
84D SER* 2.7 36.7 + - - +
86D TRP* 3.9 19.5 - - + +
87D ALA* 3.9 10.4 - - - +
90D ALA* 3.5 28.0 - - + -
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Residues in contact with MSE 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLU* 3.4 39.5 - - + +
37D CYS* 3.2 38.1 - - + -
38D ARG* 3.7 24.0 - - + -
41D ALA* 5.6 0.7 - - - -
76D ALA* 3.0 25.0 + - - +
77D ALA* 3.7 5.2 - - - +
78D LEU 3.2 0.2 - - - -
79D LEU* 1.3 75.2 - - - +
81D GLU* 1.3 58.1 + - - +
83D ARG* 2.8 34.3 + - - -
87D ALA* 4.0 14.1 - - + -
88D PRO* 6.0 0.4 - - + -
91D CYS* 3.4 17.7 - - - -
122D PHE* 5.6 0.9 - - - -
129D LEU* 3.2 23.1 - - + -
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ARG* 3.4 41.1 + - - +
42D GLN* 3.7 9.4 - - - +
77D ALA* 3.0 28.3 + - - +
78D LEU* 3.5 18.8 - - + +
80D MSE 1.3 78.1 - - - +
82D ARG* 1.3 58.4 + - - +
83D ARG* 3.2 11.1 + - - +
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Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 5.7 0.2 - - - +
64C GLN* 3.4 23.0 + - - +
67C GLY* 3.3 28.5 + - - -
68C ASP* 3.1 20.3 + - - +
71C ASP* 2.9 25.2 + - - -
78D LEU* 2.9 32.9 - - + +
79D LEU* 3.5 13.2 - - - +
81D GLU* 1.3 75.9 - - + +
83D ARG* 1.3 68.7 + - - +
84D SER 2.9 3.4 + - - -
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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
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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