Contacts of the helix formed by residues 52 - 81 (chain D) in PDB entry 6LTJ
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 52 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 4.2 7.5 - - - +
78C ILE 3.0 28.2 + - - +
79C ILE* 3.7 14.7 - - - -
80C PRO* 4.0 3.5 - - - +
51D ILE* 1.3 73.5 - - - +
53D SER* 1.3 53.2 + - - +
54D LYS* 3.9 4.3 + - - +
55D ALA* 2.8 15.8 + - - +
56D MET* 2.7 29.9 + - - -
22Y A 3.1 17.9 - - - -
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Residues in contact with SER 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE 3.7 3.3 + - - -
52D SER* 1.3 68.5 - - - +
54D LYS* 1.3 58.6 + - - +
56D MET* 3.6 14.7 - - - +
57D SER* 3.0 26.3 + - - -
22Y A 2.5 38.9 + - - +
23Y C 5.2 2.1 + - - -
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PRO* 3.8 20.4 - - + -
103C ALA* 4.8 10.5 - - - -
104C GLN* 4.1 27.1 - - + +
52D SER* 4.1 7.4 - - - +
53D SER* 1.3 77.1 - - - +
55D ALA* 1.3 56.2 + - - +
57D SER* 3.1 9.1 + - - -
58D ILE* 3.0 28.7 + - + +
99F GLY* 4.4 14.2 + - - +
100F PHE* 3.8 28.5 - - - -
22Y A 4.0 2.2 + - - +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE 3.4 14.1 - - - +
79C ILE 3.9 3.1 - - - +
80C PRO* 3.9 21.3 - - + +
83C LEU* 4.3 11.6 - - + +
51D ILE* 4.1 7.4 - - + -
52D SER* 2.8 22.5 + - - +
54D LYS* 1.3 74.0 - - - +
56D MET* 1.3 61.2 + - - +
57D SER 3.2 0.2 - - - -
58D ILE* 3.2 10.0 + - - +
59D MET* 2.9 31.9 + - - +
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Residues in contact with MET 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR 4.5 1.1 - - - +
35D ALA* 3.5 40.8 - - + +
38D VAL* 3.8 23.1 - - + -
39D TYR* 4.0 17.7 - - + +
51D ILE* 3.8 31.6 - - + +
52D SER 2.7 15.8 + - - +
53D SER* 3.6 18.8 - - - +
54D LYS 3.2 0.2 - - - -
55D ALA* 1.3 74.0 - - - +
57D SER* 1.3 56.0 + - - +
59D MET* 3.3 3.4 + - - +
60D ASN* 2.9 27.7 + - + +
23Y C 5.3 4.5 - - - +
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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
----------------------------------------------------------
53D SER 3.0 13.9 + - - -
54D LYS* 3.1 11.2 + - - -
56D MET* 1.3 74.3 - - - +
58D ILE* 1.3 61.3 + - - +
60D ASN* 3.6 8.3 - - - +
61D SER* 3.0 28.6 + - - -
99F GLY* 3.4 23.0 + - - -
100F PHE 5.1 0.2 - - - -
101F GLY* 4.6 7.8 + - - -
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PRO* 3.6 23.8 - - + -
83C LEU* 3.7 20.0 - - + -
102C ILE* 3.6 17.3 - - + -
103C ALA* 3.4 32.1 - - + +
54D LYS* 3.0 14.0 + - + +
55D ALA* 3.2 8.7 + - - +
57D SER* 1.3 77.4 - - - +
59D MET* 1.3 56.3 + - - +
61D SER* 3.3 3.6 + - - -
62D PHE* 2.9 27.3 + - + +
98F TYR* 3.8 19.1 - - + -
99F GLY* 3.5 23.1 - - - +
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Residues in contact with MET 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 3.7 28.9 - - + +
62C ILE* 3.7 29.6 - - + -
63C LEU* 4.2 11.9 - - + -
83C LEU* 3.7 24.9 - - + -
38D VAL* 3.8 24.2 - - + -
51D ILE* 4.3 10.3 - - + -
55D ALA 2.9 19.8 + - - +
56D MET 3.3 4.9 + - - +
58D ILE* 1.3 75.5 - - - +
60D ASN* 1.3 58.2 + - - +
62D PHE* 3.3 22.1 + - + +
63D VAL* 3.0 34.4 + - - +
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Residues in contact with ASN 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D SER* 2.5 37.5 + - - +
34D TYR* 3.2 38.7 + - - +
35D ALA* 5.5 0.2 - - - +
38D VAL* 5.2 0.8 - - - +
56D MET* 2.9 18.1 + - + +
57D SER* 3.6 10.0 - - - +
59D MET* 1.3 77.2 - - - +
61D SER* 1.3 62.0 + - - +
63D VAL* 3.3 6.6 - - - +
64D ASN* 3.1 29.0 + - - +
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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 3.0 14.0 + - - -
58D ILE 3.3 6.6 + - - -
60D ASN* 1.3 76.0 - - - +
62D PHE* 1.3 59.8 + - - +
64D ASN* 3.6 10.5 - - - +
65D ASP* 3.0 28.9 + - - +
97F LEU 5.3 1.1 - - - -
98F TYR* 3.2 32.5 - - - +
99F GLY 3.6 5.6 + - - -
101F GLY 3.9 25.5 - - - -
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Residues in contact with PHE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 6.5 0.4 - - + -
58C LEU* 4.4 22.0 - - + -
59C THR* 4.5 4.5 - - - -
62C ILE* 3.9 26.2 - - + -
93C LEU* 5.7 0.2 - - + -
96C LEU* 5.0 5.4 - - + -
97C LEU* 3.6 25.4 - - + -
58D ILE* 2.9 19.5 + - + +
59D MET* 3.5 23.6 - - + +
60D ASN 3.2 0.2 - - - -
61D SER* 1.3 75.8 + - - +
63D VAL* 1.3 79.1 + - + +
65D ASP* 3.2 1.7 + - - +
66D VAL* 2.9 49.2 + - + +
98F TYR* 3.7 34.5 - + + -
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 4.2 14.4 - - + -
55C LEU* 4.1 12.5 - - + +
59C THR* 3.4 28.7 - - + +
34D TYR* 3.6 39.3 - - + -
38D VAL* 5.0 2.2 - - + -
59D MET* 3.0 16.4 + - + +
60D ASN 3.3 11.9 - - - +
62D PHE* 1.3 87.8 - - + +
64D ASN* 1.3 61.4 + - - +
66D VAL* 4.5 4.0 - - - +
67D PHE* 2.9 31.7 + - - +
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 5.4 2.6 - - - +
34D TYR* 3.2 28.2 + - - -
60D ASN* 3.1 29.5 + - - +
61D SER* 3.6 9.7 - - - +
62D PHE 3.2 0.2 - - - -
63D VAL* 1.3 77.8 - - - +
65D ASP* 1.3 56.2 + - - +
67D PHE* 3.6 6.7 - - - +
68D GLU* 2.9 33.9 + - + +
101F GLY 4.4 12.1 + - - -
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Residues in contact with ASP 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 4.4 0.3 - - - +
61D SER 3.0 14.8 + - - +
62D PHE 3.2 0.8 + - - +
64D ASN* 1.3 78.5 - - - +
66D VAL* 1.3 60.5 + - - +
68D GLU* 3.4 4.6 + - - +
69D ARG* 2.6 60.2 + - - +
91F LYS* 6.0 2.8 - - - +
96F THR* 4.9 11.3 - - - +
98F TYR* 2.5 38.6 + - + +
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 3.7 20.9 - - + -
58C LEU* 3.8 22.4 - - + -
96C LEU* 4.7 11.9 - - + -
97C LEU* 4.8 0.9 - - + -
62D PHE* 2.9 44.1 + - + +
63D VAL* 4.4 0.9 - - - +
65D ASP* 1.3 82.2 - - - +
67D PHE* 1.3 66.1 + - - +
69D ARG* 3.8 16.3 - - - +
70D ILE* 2.9 36.1 + - + +
99D LEU* 5.7 1.6 - - + -
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Residues in contact with PHE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.6 17.9 - - + -
33C LEU* 3.6 43.1 - - + -
34C LEU* 4.2 11.0 - - + -
39C TYR* 3.8 18.6 - - - -
51C LEU* 3.6 31.7 - - + +
55C LEU* 3.9 25.0 - - + +
34D TYR* 4.6 11.2 - - - +
63D VAL 2.9 20.9 + - - +
64D ASN* 3.6 9.9 - - - +
66D VAL* 1.3 77.6 - - - +
68D GLU* 1.3 67.2 + - + +
70D ILE* 3.9 2.9 - - - +
71D ALA* 2.9 32.6 + - - +
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Residues in contact with GLU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLY* 5.4 2.4 - - - +
39C TYR* 2.7 36.0 + - - +
64D ASN* 2.9 19.6 + - + +
65D ASP* 3.9 4.7 - - - +
67D PHE* 1.3 84.4 - - + +
69D ARG* 1.3 58.1 + - - +
72D GLY* 2.9 27.2 + - - -
91F LYS* 6.3 1.1 - - - +
79H HIS* 6.0 1.9 - - - -
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 3.4 43.8 + - - +
97C LEU* 4.8 2.2 - - - +
100C VAL* 4.7 12.5 - - - +
65D ASP* 2.6 52.1 + - - +
66D VAL* 3.8 12.3 - - - +
67D PHE 3.3 0.2 - - - -
68D GLU* 1.3 75.3 - - - +
70D ILE* 1.3 65.4 + - - +
72D GLY* 3.4 1.3 + - - -
73D GLU* 3.1 18.5 + - - +
98D LEU* 3.6 37.0 - - + +
96F THR* 5.4 4.4 - - - +
98F TYR* 4.5 0.8 + - - -
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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
----------------------------------------------------------
51C LEU* 3.7 25.4 - - + -
54C VAL* 3.8 29.8 - - + -
55C LEU* 5.0 0.4 - - + -
66D VAL* 2.9 35.4 + - + +
67D PHE 4.0 2.2 - - - +
69D ARG* 1.3 75.5 - - + +
71D ALA* 1.3 59.8 + - - +
73D GLU 3.3 1.4 + - - -
74D ALA* 2.9 26.5 + - - +
91D ILE* 4.3 17.3 - - + +
94D ALA* 3.7 16.0 - - + +
95D GLY* 4.8 6.1 - - - +
98D LEU* 3.7 21.8 - - + -
99D LEU* 4.6 10.1 - - + -
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.8 17.5 - - + -
39C TYR* 3.7 37.6 - - + +
51C LEU* 4.7 6.1 - - + -
67D PHE* 2.9 20.5 + - + +
68D GLU 4.2 0.4 - - - +
70D ILE* 1.3 78.9 - - - +
72D GLY* 1.3 57.5 + - - +
74D ALA* 3.7 7.0 - - - +
75D SER* 2.9 29.3 + - - -
86D ILE* 4.8 0.5 - - - +
91D ILE* 5.3 1.3 - - - -
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Residues in contact with GLY 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 4.3 7.7 - - - -
68D GLU* 2.9 19.0 + - - -
69D ARG 3.9 0.9 - - - -
71D ALA* 1.3 78.3 - - - +
73D GLU* 1.3 62.2 + - - +
75D SER* 3.2 7.2 + - - -
76D ARG* 3.1 37.3 + - - +
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 2.7 30.3 + - - -
92B ARG* 3.8 14.5 - - - +
69D ARG 3.1 17.2 + - - +
70D ILE 3.7 2.2 - - - +
72D GLY* 1.3 74.4 - - - +
74D ALA* 1.3 56.8 + - - +
76D ARG* 3.4 23.5 + - - +
77D LEU* 2.9 30.0 + - + +
94D ALA* 4.1 14.8 - - + -
97D LEU* 3.4 27.2 - - + +
98D LEU* 3.7 18.7 - - + +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE 2.9 16.6 + - - +
71D ALA* 3.7 6.3 - - - +
73D GLU* 1.3 75.6 - - - +
75D SER* 1.3 59.5 + - - +
77D LEU* 3.3 8.0 + - - +
78D ALA* 3.0 27.9 + - - +
86D ILE* 4.2 13.0 - - + +
90D GLU* 4.1 17.1 - - + +
91D ILE* 3.8 27.4 - - + -
94D ALA* 4.0 4.9 - - + +
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Residues in contact with SER 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 2.3 49.6 + - - +
71D ALA 2.9 18.9 + - - -
72D GLY* 3.2 6.0 + - - -
74D ALA* 1.3 76.6 - - - +
76D ARG* 1.3 58.4 + - - +
78D ALA* 3.2 6.0 + - - +
79D HIS* 3.0 27.0 + - - +
86D ILE* 4.1 6.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 4.8 0.9 - - - -
91B LYS* 5.4 12.7 + - - +
92B ARG* 5.7 7.0 - - - +
72D GLY* 3.1 25.4 + - - +
73D GLU* 3.4 35.3 + - - +
75D SER* 1.3 77.4 - - - +
77D LEU* 1.3 59.5 + - - +
79D HIS* 4.2 7.0 - - - +
80D TYR* 2.9 68.0 + - + +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.6 34.3 - - + -
75B HIS* 3.4 33.4 - - + +
73D GLU* 2.9 29.1 + - + +
74D ALA* 3.5 6.3 - - - +
75D SER 3.2 0.2 - - - -
76D ARG* 1.3 75.1 - - - +
78D ALA* 1.3 62.7 + - - +
80D TYR* 3.7 3.2 + - + +
81D ASN* 2.9 33.8 + - - +
90D GLU* 3.9 13.7 - - + +
93D THR* 3.3 28.0 - - - +
94D ALA* 4.0 11.7 - - - +
97D LEU* 4.7 5.4 - - + -
----------------------------------------------------------
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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
----------------------------------------------------------
75B HIS* 5.6 0.2 - - - -
40C ALA* 5.1 5.2 - - + -
74D ALA 3.0 13.8 + - - +
75D SER* 3.2 8.3 + - - +
77D LEU* 1.3 76.9 - - - +
79D HIS* 1.3 62.1 + - - +
81D ASN* 3.4 2.3 + - - -
82D LYS 3.3 3.6 + - - -
83D ARG* 3.0 45.0 + - - +
85D THR 3.8 19.1 - - - +
86D ILE* 4.4 9.9 - - + -
90D GLU* 4.4 10.0 - - + +
----------------------------------------------------------
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Residues in contact with HIS 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D SER* 3.0 15.3 + - - +
76D ARG* 4.0 7.6 - - - +
77D LEU 3.3 0.2 - - - -
78D ALA* 1.3 75.1 - - - +
80D TYR* 1.3 74.6 + + - +
82D LYS* 3.4 32.5 + - + +
83D ARG 4.6 3.1 - - - +
36G LYS* 4.0 39.0 + - + -
37G GLY* 4.1 17.6 + - - -
68H GLU* 4.9 12.5 + - - -
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Residues in contact with TYR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.7 31.4 - + + -
88B TYR* 3.4 73.8 + + + +
91B LYS* 4.3 15.1 + - - +
76D ARG* 2.9 53.8 + - + +
77D LEU* 4.1 3.6 - - - +
78D ALA 3.3 0.2 - - - -
79D HIS* 1.3 87.2 - + - +
81D ASN* 1.3 68.6 + - - +
82D LYS* 3.3 12.6 + - - +
----------------------------------------------------------
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Residues in contact with ASN 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 5.4 3.6 + - - +
75B HIS* 3.0 34.4 + - - +
76B ALA* 4.2 20.8 - - + +
78B ARG* 5.3 4.3 + - - -
77D LEU* 2.9 24.7 + - - +
78D ALA 3.4 2.5 + - - +
79D HIS 3.2 0.6 - - - -
80D TYR* 1.3 86.1 - - - +
82D LYS* 1.3 70.0 + - - +
83D ARG* 3.3 25.4 + - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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).
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