Contacts of the helix formed by residues 49 - 76 (chain D) in PDB entry 1HQ3
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 LEU 49 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C MET* 6.5 0.9 - - + -
121C PRO* 3.6 24.1 - - + +
47D SER* 3.0 13.3 - - - +
48D GLY* 1.3 77.4 - - - +
50D ILE* 1.3 64.5 + - - +
51D TYR 3.2 2.2 + - - -
52D GLU* 3.7 6.7 + - - +
53D GLU* 3.6 18.0 + - - +
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Residues in contact with ILE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C PHE* 3.5 27.1 - - + -
119C ILE* 3.2 39.3 - - + +
120C MET* 3.8 15.3 - - - +
121C PRO* 4.1 1.3 - - + -
124C ILE* 4.2 10.5 - - + -
34D ILE* 4.1 10.5 - - + -
46D ILE* 3.2 27.1 - - + -
47D SER* 3.1 11.4 + - - +
49D LEU* 1.3 77.2 - - - +
51D TYR* 1.3 53.8 - - + +
53D GLU* 3.5 7.7 - - - +
54D THR* 2.7 66.1 + - - +
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Residues in contact with TYR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LYS* 3.5 59.4 - - + +
34D ILE* 3.6 32.1 - - + +
35D ARG* 4.2 14.2 - - - +
46D ILE* 3.5 34.1 + - + +
47D SER 3.9 13.9 - - - -
48D GLY* 3.2 28.0 - - - +
49D LEU 3.2 1.8 + - - -
50D ILE* 1.3 78.4 - - - +
52D GLU* 1.3 59.0 + - - +
54D THR* 3.4 3.3 + - - -
55D ARG* 3.0 46.0 + - - +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ILE* 5.7 1.4 - - - +
27D GLN* 3.3 23.2 + - - +
48D GLY 4.9 1.0 + - - +
49D LEU* 3.7 6.9 + - - +
50D ILE 3.4 0.2 - - - -
51D TYR* 1.3 75.4 - - - +
53D GLU* 1.3 67.7 - - - +
55D ARG* 3.0 30.4 + - - +
56D GLY* 3.0 19.1 + - - -
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PRO* 3.7 31.9 - - + +
124C ILE* 4.1 22.0 - - + -
125C GLN* 3.7 18.4 - - + +
49D LEU 3.6 11.5 + - - +
50D ILE* 3.5 13.2 - - - +
52D GLU* 1.3 77.4 - - - +
54D THR* 1.3 62.6 + - - +
56D GLY* 3.0 12.2 + - - -
57D VAL* 3.1 21.0 + - + +
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 4.2 24.2 - - + -
104C PHE* 3.5 15.8 - - + -
124C ILE* 4.0 7.1 - - - +
34D ILE* 4.0 26.5 - - + -
37D LEU* 6.3 0.2 - - + -
50D ILE* 2.7 45.7 + - - +
51D TYR 3.5 5.2 - - - -
53D GLU* 1.3 74.0 - - - +
55D ARG* 1.3 63.8 + - - +
57D VAL* 3.4 8.1 + - + +
58D LEU* 3.0 23.5 + - + +
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ILE* 3.6 34.6 - - + +
27D GLN* 3.5 32.1 + - - +
29D ILE* 2.7 32.0 + - + +
30D THR* 3.8 1.6 - - - +
31D LYS* 3.6 25.5 - - - +
34D ILE* 4.0 14.8 - - + +
51D TYR* 3.0 30.7 + - - +
52D GLU* 3.0 36.2 + - - +
54D THR* 1.3 75.7 - - - +
56D GLY* 1.3 63.1 + - - +
58D LEU* 4.5 3.1 - - - -
59D LYS* 3.0 26.0 + - - +
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Residues in contact with GLY 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLU* 3.0 13.7 + - - -
53D GLU* 3.0 5.1 + - - -
55D ARG* 1.3 77.1 - - - +
57D VAL* 1.3 61.8 + - - +
59D LYS* 3.2 8.4 + - - +
60D VAL* 3.1 27.5 + - - +
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Residues in contact with VAL 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C TYR* 4.4 7.3 + - + +
100C LEU* 4.0 13.7 - - + -
103C LEU* 3.9 22.4 - - + -
124C ILE* 4.3 13.5 - - + -
128C ARG* 3.8 41.1 + - - +
53D GLU* 3.1 17.9 + - + +
54D THR* 3.7 11.0 - - + +
56D GLY* 1.3 75.1 - - - +
58D LEU* 1.3 66.3 + - - +
60D VAL* 3.3 9.0 + - - +
61D PHE* 3.0 23.6 + - - +
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Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 4.8 5.8 - - + -
67C PHE* 5.0 1.6 - - + -
70C LEU* 4.3 6.3 - - + -
96C SER* 4.0 19.5 - - - +
99C TYR* 5.3 0.4 - - + -
100C LEU* 3.9 33.0 - - + -
26D ILE* 4.0 8.5 - - + -
29D ILE* 3.9 37.9 - - + -
54D THR* 3.0 18.1 + - + +
55D ARG* 3.8 4.3 - - - +
57D VAL* 1.3 81.0 - - - +
59D LYS* 1.3 58.5 + - - +
61D PHE* 3.2 9.1 + - + +
62D LEU* 2.9 46.8 + - + +
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Residues in contact with LYS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 5.2 0.6 - - - +
73C GLU* 4.0 19.2 + - - -
74C ILE* 4.5 17.7 - - + +
23D ARG 5.8 0.6 + - - -
26D ILE* 4.1 32.3 - - + +
55D ARG 3.0 18.1 + - - +
56D GLY* 3.6 7.0 - - - +
58D LEU* 1.3 78.1 - - - +
60D VAL* 1.3 58.5 + - + +
62D LEU* 3.8 4.9 - - - +
63D GLU* 2.9 58.8 + - + +
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ARG* 4.3 18.4 - - - +
56D GLY 3.1 15.4 + - - +
57D VAL* 3.6 9.9 - - - +
58D LEU 3.2 0.2 - - - -
59D LYS* 1.3 73.2 - - + +
61D PHE* 1.3 66.8 + - - +
63D GLU* 3.2 13.8 + - - +
64D ASN* 3.0 41.8 + - - +
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Residues in contact with PHE 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 5.1 2.0 - - + -
95C ALA* 4.1 6.5 - - + -
96C SER* 3.7 37.2 - - - -
99C TYR* 3.7 49.4 - + + +
57D VAL 3.0 14.7 + - - +
58D LEU* 3.5 9.9 - - + +
60D VAL* 1.3 80.2 - - - +
62D LEU* 1.3 69.3 + - + +
64D ASN* 3.3 5.8 + - + +
65D VAL* 3.1 48.6 + - + +
90D LEU* 4.3 6.5 - - + -
93D GLN* 5.3 5.2 - - + -
95D ARG* 3.8 33.2 - - - -
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE* 3.9 19.5 - - + -
70C LEU* 3.5 36.1 - - + -
71C VAL* 4.5 3.4 - - + -
74C ILE* 3.8 15.9 - - + -
92C LEU* 4.1 15.7 - - + -
96C SER* 3.4 23.1 - - - +
58D LEU* 2.9 33.3 + - + +
59D LYS* 5.2 0.2 - - - -
61D PHE* 1.3 79.8 - - + +
63D GLU* 1.3 57.8 + - - +
65D VAL* 4.5 1.8 - - - +
66D ILE* 2.8 51.9 + - + +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 4.0 27.2 - - + +
78C PHE* 3.7 11.9 - - + -
59D LYS* 2.9 54.4 + - - +
60D VAL* 3.6 16.2 - - - +
62D LEU* 1.3 76.0 - - - +
64D ASN* 1.3 61.3 + - - +
67D ARG* 3.0 32.2 + - - +
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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
----------------------------------------------------------
95A LYS* 5.1 11.4 + - - +
60D VAL* 3.0 38.4 + - - +
61D PHE* 3.7 6.9 - - + +
63D GLU* 1.3 80.6 - - - +
65D VAL* 1.3 62.4 + - + +
67D ARG* 3.7 8.8 + - - +
68D ASP* 3.3 27.5 + - - +
93D GLN* 3.6 25.4 - - + +
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 3.9 23.1 - - + -
61D PHE* 3.1 34.1 + - + +
62D LEU* 4.1 2.7 - - - +
64D ASN* 1.3 76.6 - - - +
66D ILE* 1.3 60.6 + - - +
68D ASP 3.3 1.4 + - - -
69D ALA* 2.9 25.2 + - + +
86D VAL* 4.5 2.9 - - + +
89D ALA* 3.5 15.8 - - + +
90D LEU* 3.7 39.3 - - + +
93D GLN* 4.1 21.5 - - + +
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 4.2 22.9 - - + -
74C ILE* 3.9 23.3 - - + -
75C ALA* 3.9 26.0 - - + +
78C PHE* 4.2 4.7 - - + -
84C PHE* 4.1 6.5 - - + -
92C LEU* 4.0 22.2 - - + -
62D LEU* 2.8 45.2 + - + +
65D VAL* 1.3 70.7 - - - +
67D ARG* 1.3 67.0 + - - +
69D ALA* 3.7 5.6 - - + -
70D VAL* 2.9 45.3 + - + +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG 5.8 3.7 + - - -
102B LEU 5.9 1.5 + - - -
103B PRO* 5.9 0.4 - - - +
104B GLY* 4.5 28.9 + - - +
107B ALA* 5.9 3.2 - - - +
108B LYS* 5.6 7.7 - - - +
78C PHE* 3.5 36.5 - - + -
63D GLU 3.0 20.9 + - - +
64D ASN* 3.7 9.5 + - - +
66D ILE* 1.3 78.3 - - - +
68D ASP* 1.3 67.1 + - - +
70D VAL* 3.5 4.3 - - + +
71D THR* 2.9 30.9 + - - +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG 5.3 0.3 - - - +
100B LEU* 3.5 34.8 - - + +
64D ASN 3.3 8.5 + - - +
65D VAL 3.3 3.8 + - - +
66D ILE 3.2 0.2 - - - -
67D ARG* 1.3 84.0 - - - +
69D ALA* 1.3 66.5 + - - +
71D THR* 3.1 4.4 + - - -
72D TYR* 3.1 27.1 + - + -
89D ALA* 3.8 20.0 - - + +
92D ARG* 4.0 18.3 + - + +
93D GLN* 3.3 22.7 + - - +
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C PHE* 5.6 0.9 - - + -
92C LEU* 6.0 0.2 - - + -
65D VAL* 2.9 17.8 + - + +
66D ILE* 3.2 9.2 + - + +
68D ASP* 1.3 75.9 - - - +
70D VAL* 1.3 63.0 + - + +
72D TYR* 3.1 7.0 + - - +
73D THR* 3.1 23.1 + - - -
81D VAL* 4.2 9.2 - - + -
85D ASP* 3.8 15.5 - - - +
86D VAL* 4.1 20.6 - - + -
89D ALA* 3.3 15.0 - - + +
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ALA* 4.7 5.8 - - + -
78C PHE* 4.2 24.7 - - + -
82C LEU* 4.1 27.1 - - + -
84C PHE* 4.8 0.9 - - + -
66D ILE* 2.9 29.6 + - + +
67D ARG* 3.5 11.2 - - + +
69D ALA* 1.3 74.0 - - + +
71D THR* 1.3 67.2 + - - +
73D THR* 3.6 8.2 - - - -
74D GLU* 2.8 46.4 + - + +
81D VAL* 4.4 11.4 - - + -
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Residues in contact with THR 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 3.6 26.7 - - + +
99B ARG* 4.6 19.7 - - + +
100B LEU* 3.8 20.7 - - + +
67D ARG* 2.9 21.3 + - - +
68D ASP* 3.4 10.8 + - - -
70D VAL* 1.3 80.9 - - - +
72D TYR* 1.3 61.9 + - - +
74D GLU* 3.6 10.1 + - - +
75D HIS* 3.0 22.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 2.9 28.5 + - - -
80B LEU* 3.7 24.9 - - + -
83B TYR* 4.3 16.4 - + + -
84B ASN* 5.5 0.5 - - - +
100B LEU* 3.6 19.5 - - + -
68D ASP 3.1 27.7 + - - -
69D ALA 3.4 6.3 - - - +
71D THR* 1.3 77.9 - - - +
73D THR* 1.3 63.2 + - - +
75D HIS* 3.5 6.5 + - - +
76D ALA* 3.2 22.9 + - - +
78D ARG* 4.2 1.7 + - - -
85D ASP* 3.9 27.4 - - - +
88D TYR* 3.8 35.3 + + + -
89D ALA* 3.8 12.3 - - - -
92D ARG* 3.3 22.2 - - + +
----------------------------------------------------------
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 4.3 6.1 - - + -
69D ALA 3.1 11.4 + - - -
70D VAL* 3.1 11.6 + - - -
72D TYR* 1.3 76.1 - - - +
74D GLU* 1.3 61.6 + - - +
76D ALA* 3.2 5.0 + - - +
77D LYS 3.2 3.5 + - - -
78D ARG* 3.0 52.5 + - + +
79D LYS 4.1 3.1 - - - +
80D THR 3.8 23.1 - - - +
81D VAL* 3.5 16.5 - - + +
85D ASP* 2.7 23.9 + - - -
----------------------------------------------------------
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Residues in contact with GLU 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 3.1 11.5 + - - -
99B ARG* 6.1 0.5 - - - -
78C PHE 5.0 1.7 - - - +
79C LYS* 3.5 41.9 - - + +
82C LEU* 5.5 3.4 - - + -
70D VAL* 2.8 32.4 + - + +
71D THR* 4.0 10.8 + - - +
73D THR* 1.3 70.1 - - + +
75D HIS* 1.3 59.4 + - - +
77D LYS* 2.7 24.5 + - - +
78D ARG 4.4 7.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.9 14.5 - - + +
81B ALA* 6.0 0.2 - - - -
84B ASN* 3.7 26.4 + - + -
86B ARG* 6.5 0.2 - - + -
92B ARG* 2.9 54.1 + - + +
93B GLU* 3.4 38.2 + - + +
96B THR* 2.7 42.0 - - + +
71D THR 3.0 19.0 + - - +
72D TYR* 3.6 6.5 + - - +
74D GLU* 1.3 76.3 - - - +
76D ALA* 1.3 58.7 + - - +
77D LYS* 3.2 2.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 5.9 0.2 - - + -
84B ASN* 3.1 31.8 + - - +
72D TYR 3.2 8.3 + - - +
73D THR 3.6 2.5 - - - +
74D GLU 3.1 0.4 - - - -
75D HIS* 1.3 77.2 + - - +
77D LYS* 1.3 71.5 + - - +
78D ARG* 3.3 40.4 + - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il