Contacts of the helix formed by residues 56 - 85 (chain D) in PDB entry 3WKJ
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 56 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 3.4 16.9 - - - +
78C ILE 2.8 13.9 + - - -
79C ILE* 3.8 14.9 - - - -
80C PRO* 3.8 5.5 - - - +
55D ILE* 1.3 77.0 - - - +
57D SER* 1.3 59.4 + - - +
58D LYS* 3.6 5.0 + - - +
59D ALA* 3.2 22.9 + - - +
60D MET* 3.0 21.7 + - - +
19I A 3.4 14.1 - - - -
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ILE 3.8 0.6 + - - -
56D SER* 1.3 68.8 - - - +
58D LYS* 1.3 63.0 + - - +
60D MET* 3.2 9.3 + - - +
61D SER* 2.8 30.0 + - - -
19I A 2.8 34.3 + - - -
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PRO* 3.7 23.1 - - + -
104C GLN* 4.4 21.1 - - + -
56D SER* 3.3 5.6 + - - +
57D SER* 1.3 79.4 + - - +
59D ALA* 1.3 58.7 + - - +
61D SER* 2.7 23.7 + - - -
62D ILE* 2.8 22.5 + - + +
99F GLY* 5.0 4.7 - - - +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 3.5 9.9 - - + +
79C ILE 3.9 14.6 - - - -
80C PRO* 4.0 3.0 - - - +
83C LEU* 3.6 15.3 - - + +
55D ILE* 3.4 19.7 - - + -
56D SER* 3.2 21.9 + - - +
58D LYS* 1.3 79.6 - - - +
60D MET* 1.3 57.1 + - - +
62D ILE* 3.2 6.5 - - - +
63D MET* 2.8 30.7 + - - +
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Residues in contact with MET 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D SER* 3.5 51.6 - - - +
42D ILE* 3.7 33.4 - - + -
43D TYR* 4.0 15.3 - - + +
46D LEU* 6.1 0.4 - - + -
55D ILE* 3.7 27.5 - - + +
56D SER 3.0 14.4 + - - +
57D SER* 3.5 12.1 - - - +
58D LYS 3.2 0.4 - - - -
59D ALA* 1.3 72.9 - - - +
61D SER* 1.3 61.7 + - - +
63D MET* 3.0 6.2 + - - +
64D ASN* 2.7 26.6 + - - +
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D SER 2.8 15.1 + - - -
58D LYS* 2.7 23.7 + - - -
60D MET* 1.3 70.1 - - - +
62D ILE* 1.3 66.0 + - - +
64D ASN* 2.8 20.0 + - - +
65D SER* 2.8 18.9 + - - -
99F GLY* 4.1 20.4 + - - -
102F GLY* 3.9 30.5 - - - +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PRO* 4.8 4.9 - - + -
83C LEU* 3.5 21.1 - - + -
102C ILE* 4.1 17.3 - - + -
103C ALA* 4.1 16.2 - - + +
58D LYS* 2.8 29.9 + - + +
59D ALA* 3.2 10.5 - - - +
61D SER* 1.3 80.2 + - - +
63D MET* 1.3 66.7 + - - +
65D SER* 2.9 12.3 + - - -
66D PHE* 3.0 11.4 + - + +
98F TYR* 3.4 33.9 - - + +
99F GLY* 3.4 30.7 - - - +
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Residues in contact with MET 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 4.0 29.2 - - + +
62C ILE* 3.3 42.6 - - + -
63C LEU* 4.2 11.7 - - + -
83C LEU* 3.8 11.4 - - + -
42D ILE* 3.9 19.7 - - + -
55D ILE* 4.1 18.2 - - + -
59D ALA 2.8 20.5 + - - +
60D MET* 3.2 9.4 - - - +
62D ILE* 1.3 73.5 - - - +
64D ASN* 1.3 62.0 + - - +
66D PHE* 3.3 19.0 + - + +
67D VAL* 3.1 26.9 + - - +
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLU 5.4 0.6 + - - -
37D SER* 3.1 24.0 + - - +
38D TYR* 3.4 34.8 + - - +
39D SER* 3.5 12.1 + - - -
42D ILE* 4.0 7.3 - - - +
60D MET* 2.7 15.4 + - - +
61D SER* 2.8 17.1 + - - +
63D MET* 1.3 69.8 - - - +
65D SER* 1.3 63.7 + - - +
67D VAL* 3.2 4.0 + - - +
68D THR* 3.0 35.5 + - - +
102F GLY* 4.8 10.8 + - - +
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Residues in contact with SER 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D SER 2.8 16.6 + - - -
62D ILE 3.3 8.1 - - - -
64D ASN* 1.3 73.4 - - - +
66D PHE* 1.3 57.5 + - - +
68D THR* 3.6 8.4 + - - -
69D ASP* 3.0 31.4 + - - +
97F LEU 4.8 2.0 + - - -
98F TYR* 3.4 29.4 - - - -
99F GLY 3.9 10.7 + - - -
101F GLY* 4.1 18.7 + - - -
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Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C LEU* 4.0 31.9 - - + -
59C THR* 4.2 10.5 - - + -
62C ILE* 4.1 22.4 - - + -
93C LEU* 5.2 0.7 - - + -
96C LEU* 4.5 8.7 - - + -
97C LEU* 3.8 28.5 - - + -
62D ILE* 3.0 10.1 + - + +
63D MET* 3.4 29.6 - - + +
65D SER* 1.3 74.5 - - - +
67D VAL* 1.3 74.1 + - + +
69D ASP* 3.3 0.9 + - - +
70D ILE* 3.1 61.3 + - + +
98F TYR* 3.3 27.0 - + + -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 3.9 18.4 - - + -
55C LEU* 3.9 20.4 - - + +
59C THR* 3.7 29.4 - - + -
38D TYR* 3.7 33.2 - - + -
42D ILE* 4.0 15.7 - - + -
63D MET 3.1 15.3 + - - +
64D ASN 3.2 4.9 + - - +
66D PHE* 1.3 82.2 - - + +
68D THR* 1.3 64.1 + - - +
69D ASP 3.2 0.2 + - - -
70D ILE 3.4 0.3 + - - -
71D PHE* 3.0 21.7 + - - +
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR* 4.0 22.9 - - + -
64D ASN* 3.0 26.1 + - - +
65D SER* 3.6 8.5 + - - -
67D VAL* 1.3 75.6 - - - +
69D ASP* 1.3 59.6 + - - +
71D PHE* 3.6 9.6 - - - +
72D GLU* 3.0 27.2 + - - +
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C VAL* 4.4 0.3 - - - +
65D SER 3.0 20.3 + - - +
66D PHE 3.4 1.3 - - - +
67D VAL 3.1 0.2 - - - -
68D THR* 1.3 75.3 + - - +
70D ILE* 1.3 61.9 + - - +
72D GLU* 2.9 24.7 + - - +
73D ARG* 2.9 50.4 + - - +
91F LYS* 4.2 21.1 + - - +
96F THR* 4.4 6.4 + - - +
98F TYR* 2.7 31.9 + - + +
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 5.0 0.7 - - + -
55C LEU* 3.7 19.7 - - + -
58C LEU* 4.0 22.4 - - + -
96C LEU* 4.9 12.8 - - + -
97C LEU* 4.6 6.1 - - + -
66D PHE* 3.1 51.2 + - + +
67D VAL* 5.3 0.2 - - - -
69D ASP* 1.3 84.3 - - + +
71D PHE* 1.3 61.0 + - - +
73D ARG* 3.8 15.9 - - + +
74D ILE* 2.8 56.4 + - + +
102D LEU* 6.4 0.4 - - + -
103D LEU* 5.2 2.9 - - + -
98F TYR* 4.2 2.2 - - - +
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Residues in contact with PHE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.7 16.4 - - + -
33C LEU* 3.5 32.1 - - + -
34C LEU* 3.7 21.3 - - + -
39C TYR* 3.8 27.4 - + - -
51C LEU* 3.4 26.7 - - + +
55C LEU* 3.7 21.9 - - + +
38D TYR* 4.0 14.1 - - - +
67D VAL 3.0 19.3 + - - +
68D THR* 3.6 10.3 - - - +
70D ILE* 1.3 75.7 - - - +
72D GLU* 1.3 61.8 - - - +
74D ILE* 3.9 4.1 - - - +
75D ALA* 2.9 28.2 + - + +
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 4.4 16.5 - - - +
68D THR 3.0 13.9 + - - +
69D ASP* 2.9 13.5 + - - +
71D PHE* 1.3 82.7 - - + +
73D ARG* 1.3 71.4 + - - +
75D ALA* 4.0 0.6 - - - +
76D SER* 2.8 51.0 + - - -
91F LYS* 5.8 4.8 + - - +
80H ARG* 5.5 4.7 + - - -
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Residues in contact with ARG 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 3.0 38.9 + - - +
97C LEU* 4.2 4.0 - - - +
100C VAL* 3.8 17.8 - - - +
69D ASP* 2.9 52.0 + - - +
70D ILE* 3.8 18.8 - - + +
72D GLU* 1.3 85.9 - - - +
74D ILE* 1.3 62.8 + - + +
76D SER* 3.9 3.2 - - - -
77D GLU* 3.2 23.6 + - - +
80D ARG* 5.4 0.5 + - - -
102D LEU* 4.0 28.0 - - + +
96F THR* 5.6 1.8 + - - -
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.4 31.6 - - + -
54C VAL* 4.7 4.9 - - + -
70D ILE* 2.8 49.1 + - + +
71D PHE 3.9 0.4 - - - +
73D ARG* 1.3 70.8 - - + +
75D ALA* 1.3 54.6 - - - +
77D GLU* 3.2 4.0 + - - +
78D ALA* 2.8 35.0 + - - +
95D ILE* 3.9 24.5 - - + +
98D ALA* 3.7 11.4 - - + +
99D VAL* 3.7 29.8 - - + -
102D LEU* 4.3 19.3 - - + -
103D LEU* 5.3 4.5 - - + -
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.2 15.5 - - + -
39C TYR* 3.4 42.4 - - + +
51C LEU* 5.2 1.9 - - + +
71D PHE* 2.9 23.8 + - + +
72D GLU 4.0 0.7 - - - +
74D ILE* 1.3 73.1 - - - +
76D SER* 1.3 51.8 + - - +
78D ALA* 2.9 10.3 + - - +
79D SER* 2.6 35.5 + - - -
90D ILE* 5.9 0.2 - - - -
95D ILE* 5.2 2.5 - - - -
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Residues in contact with SER 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 4.0 9.4 - - - -
72D GLU* 2.8 40.6 + - - -
73D ARG* 3.9 3.8 - - - -
75D ALA* 1.3 77.8 - - - +
77D GLU* 1.3 62.6 + - - +
79D SER* 3.0 10.3 + - - -
80D ARG* 3.0 46.2 + - - +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 2.5 33.9 + - - -
92B ARG* 3.8 16.3 + - - +
73D ARG 3.2 16.0 + - - +
74D ILE 3.7 2.9 - - - +
76D SER* 1.3 78.6 - - - +
78D ALA* 1.3 57.2 + - - +
80D ARG* 2.4 31.4 + - - +
81D LEU* 2.8 34.9 + - + +
84D TYR* 4.7 4.0 - - - -
98D ALA* 3.9 13.2 - - + -
101D LEU* 3.2 24.2 - - + +
102D LEU* 3.9 17.8 - - + +
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ILE 2.8 15.8 + - - +
75D ALA* 3.0 16.4 - - - +
77D GLU* 1.3 76.6 - - - +
79D SER* 1.3 60.7 + - - +
81D LEU* 3.3 7.6 + - - +
82D ALA* 3.0 24.6 + - - +
90D ILE* 3.9 26.9 - - + +
94D GLU* 4.0 14.7 - - + +
95D ILE* 4.1 11.9 - - + -
98D ALA* 4.0 5.1 - - + +
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Residues in contact with SER 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN 5.0 1.0 + - - -
39C TYR* 2.8 41.5 + - - +
75D ALA 2.6 15.7 + - - -
76D SER* 3.2 14.1 - - - -
78D ALA* 1.3 74.1 - - - +
80D ARG* 1.3 63.1 + - - +
82D ALA* 3.3 4.7 + - - +
83D HIS* 3.2 19.9 + - - +
90D ILE* 4.0 5.8 - - - +
38G ASN* 5.1 4.3 + - - +
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 5.3 0.2 + - - -
91B LYS* 6.6 0.2 - - - +
92B ARG* 5.7 0.6 - - - +
73D ARG 5.4 0.4 + - - -
76D SER* 3.0 36.2 + - - +
77D GLU* 2.4 51.1 + - - +
79D SER* 1.3 75.8 - - - +
81D LEU* 1.3 67.6 + - - +
83D HIS* 3.0 9.5 + - - +
84D TYR* 3.0 57.9 + - + +
72H GLU* 6.2 2.5 - - - -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.6 33.4 - - + -
75B HIS* 3.8 28.2 + - + +
77D GLU* 2.8 20.9 + - + +
78D ALA* 3.5 7.0 - - - +
80D ARG* 1.3 77.8 - - - +
82D ALA* 1.3 58.9 + - - +
84D TYR* 3.7 9.2 + - + +
85D SER* 2.9 25.7 + - - -
94D GLU* 4.2 5.6 - - + +
97D THR* 3.1 41.3 - - + +
98D ALA* 4.1 9.6 - - - +
101D LEU* 4.2 13.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER* 5.1 4.5 - - - -
78D ALA 3.0 12.6 + - - +
79D SER 3.4 10.3 - - - +
80D ARG 3.1 0.2 - - - -
81D LEU* 1.3 76.0 - - - +
83D HIS* 1.3 63.6 + - - +
85D SER* 3.4 8.9 + - - -
87D ARG* 2.9 43.1 + - - +
89D THR 4.6 8.5 - - - +
90D ILE* 4.2 17.9 - - + -
94D GLU* 4.2 11.6 - - + +
----------------------------------------------------------
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D SER 3.2 9.4 + - - +
80D ARG* 3.0 12.0 + - - +
82D ALA* 1.3 76.8 - - - +
84D TYR* 1.3 74.0 + - + +
86D LYS* 2.9 18.6 + - - +
87D ARG 4.6 3.8 - - - +
36G LYS* 3.6 24.4 + - - +
37G GLY* 4.7 8.0 - - - -
38G ASN* 5.0 8.5 - - - -
----------------------------------------------------------
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Residues in contact with TYR 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.8 25.5 + + - -
88B TYR* 3.2 64.6 - + + +
77D GLU* 4.7 0.6 + - - -
80D ARG* 3.0 57.8 + - + -
81D LEU* 3.7 19.5 - - + +
83D HIS* 1.3 80.8 - - + +
85D SER* 1.3 57.6 + - - +
86D LYS* 3.4 13.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.6 21.0 - - - -
76B ALA* 5.1 15.0 - - - -
81D LEU 2.9 17.2 + - - -
82D ALA* 3.7 4.7 + - - -
83D HIS 3.1 0.8 - - - -
84D TYR* 1.3 78.9 - - - +
86D LYS* 1.3 70.3 + - - +
87D ARG* 2.8 26.2 + - - +
----------------------------------------------------------
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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