Contacts of the helix formed by residues 53 - 81 (chain A) in PDB entry 2QWT
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 THR 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A MET* 3.5 14.0 - - - +
48A TYR* 4.7 2.9 - - - -
51A PHE 3.9 2.4 - - - +
52A PRO* 1.3 90.8 - - + +
54A LYS* 1.3 62.9 + - - +
55A GLN* 3.8 14.0 + - - +
56A ALA* 3.4 20.3 + - - +
57A LEU 3.3 14.9 + - - -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 4.4 19.5 - - + -
28A GLY 5.0 0.4 + - - -
29A LEU* 2.7 38.0 + - + +
31A VAL 2.7 26.1 + - - +
32A PRO* 4.7 1.5 - - - +
33A MET* 3.8 37.5 - - + +
36A ILE* 5.0 2.0 - - + +
48A TYR* 5.4 0.6 - - - -
53A THR* 1.3 71.5 - - - +
55A GLN* 1.3 66.9 + - - +
57A LEU* 3.1 4.1 + - + +
58A VAL* 2.9 23.1 + - + +
110A TYR* 3.1 29.2 - - + +
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A THR* 3.8 12.3 + - - +
54A LYS* 1.3 78.3 - - - +
56A ALA* 1.3 59.0 + - + +
58A VAL* 3.3 5.3 + - + +
59A VAL* 2.8 35.8 + - + +
110A TYR* 3.2 56.6 + - + +
112A LEU* 4.0 19.6 - - + +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 4.2 5.4 - - + -
52A PRO* 4.2 23.3 - - + -
53A THR* 3.4 22.5 + - - +
54A LYS 3.1 0.6 - - - -
55A GLN* 1.3 75.6 - - + +
57A LEU* 1.3 60.5 + - - +
59A VAL* 3.9 11.1 - - + +
60A ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.0 11.2 - - + -
17A LEU* 4.2 9.4 - - + -
20A ALA* 3.9 22.2 - - + -
24A PHE* 4.1 6.3 - - + -
33A MET* 3.5 28.3 - - + -
36A ILE* 3.6 28.9 - - + -
47A VAL* 5.0 0.9 - - + -
51A PHE* 3.8 37.5 - - + +
53A THR 3.3 9.3 + - - +
54A LYS* 3.1 9.8 + - + +
56A ALA* 1.3 75.7 - - - +
58A VAL* 1.3 55.8 + - - +
60A ALA* 3.1 2.3 + - - +
61A VAL* 2.8 38.2 + - - +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.7 26.2 - - + -
29A LEU* 3.9 21.8 - - + -
54A LYS* 2.9 19.3 + - + +
55A GLN* 3.5 9.0 - - - +
57A LEU* 1.3 75.2 - - - +
59A VAL* 1.3 62.7 + - + +
61A VAL* 3.5 2.1 + - - +
62A ALA* 3.0 21.1 + - - +
103A LEU* 4.5 5.5 - - + +
106A ALA* 4.0 7.2 - - + +
107A LEU* 3.7 41.1 - - + +
110A TYR* 4.1 12.3 - - + -
112A LEU* 6.4 0.9 - - + -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 2.8 37.7 + - + +
56A ALA* 3.9 9.4 - - + +
57A LEU 3.2 0.2 - - - -
58A VAL* 1.3 74.4 - - + +
60A ALA* 1.3 62.5 + - + +
62A ALA* 3.1 8.5 + - - +
63A GLU* 3.0 31.1 + - + +
107A LEU* 4.8 0.9 - - + -
112A LEU* 4.1 26.2 - - + -
117A ALA* 3.8 29.3 - - + +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.0 12.7 + - - +
17A LEU* 3.8 10.9 - - + +
51A PHE* 3.6 28.3 - - + -
56A ALA 2.9 18.5 + - - +
57A LEU 3.7 2.5 - - - +
59A VAL* 1.3 76.6 - - + +
61A VAL* 1.3 62.8 + - - +
63A GLU* 4.1 5.9 - - - +
64A ASP* 3.2 24.9 + - - +
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.7 21.8 - - + +
20A ALA* 3.6 30.3 - - + -
21A TYR* 3.9 33.2 - - + -
24A PHE* 3.7 9.9 - - + -
57A LEU* 2.8 24.3 + - + +
58A VAL 3.7 3.8 - - - +
60A ALA* 1.3 71.6 - - - +
62A ALA* 1.3 58.9 + - - +
64A ASP* 3.3 5.3 + - - +
65A ARG* 2.9 28.8 + - + +
103A LEU* 3.6 20.9 - - + -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL 3.0 14.7 + - - +
59A VAL* 3.4 9.0 - - - +
61A VAL* 1.3 76.6 - - - +
63A GLU* 1.3 61.6 + - - +
65A ARG* 3.9 1.6 - - - +
66A VAL* 3.2 28.4 + - - +
103A LEU* 4.3 13.1 - - + +
107A LEU* 3.9 25.6 - - + -
114A LEU* 3.9 17.6 - - + +
117A ALA* 4.3 6.3 - - + -
118A ALA* 4.2 2.9 - - + -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.0 16.4 + - + +
60A ALA* 4.1 7.0 - - - +
62A ALA* 1.3 71.5 - - - +
64A ASP* 1.3 61.7 + - - +
66A VAL* 3.2 5.1 + - - +
67A ARG* 2.4 76.1 + - - +
117A ALA 3.3 16.7 - - - +
118A ALA* 3.4 13.6 - - - +
119A PRO* 3.0 35.6 - - - +
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 6.4 0.2 - - - -
17A LEU* 3.7 33.3 - - + +
18A GLU* 5.4 1.6 + - - +
60A ALA 3.2 18.2 + - - +
61A VAL* 3.7 4.9 - - - +
63A GLU* 1.3 80.1 - - - +
65A ARG* 1.3 51.8 + - - +
67A ARG* 3.2 14.2 + - - +
68A ARG* 2.8 70.5 + - - +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.5 25.7 + - + -
61A VAL 2.9 17.5 + - - +
62A ALA 3.9 3.8 - - - +
64A ASP* 1.3 73.6 + - - +
66A VAL* 1.3 62.8 + - + +
68A ARG* 3.2 15.8 + - - +
69A ILE* 2.8 62.6 + - + +
93A MET* 4.7 3.4 - - - +
96A SER* 2.7 34.7 + - - -
100A ASP* 2.7 33.4 + - - +
103A LEU* 3.9 17.7 - - + -
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 3.2 15.0 + - - +
63A GLU* 3.4 9.9 - - - +
65A ARG* 1.3 76.2 - - + +
67A ARG* 1.3 65.9 + - + +
69A ILE* 3.3 11.7 + - + +
70A VAL* 3.1 26.6 + - + +
114A LEU* 3.9 27.6 - - + -
118A ALA* 4.0 10.8 - - + -
121A ALA* 4.1 28.5 - - + +
124A ALA* 5.0 10.8 - - + -
125A PHE 6.2 0.2 - - - +
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 2.4 52.4 + - - +
64A ASP* 3.5 13.4 - - - +
66A VAL* 1.3 78.5 - - + +
68A ARG* 1.3 59.4 + - + +
70A VAL* 3.3 8.3 + - - +
71A ASP* 2.9 39.1 + - - +
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 5.1 13.1 - - - +
64A ASP* 2.8 49.4 + - - +
65A ARG* 3.2 18.6 + - - +
67A ARG* 1.3 75.5 - - - +
69A ILE* 1.3 59.5 + - - +
71A ASP* 3.4 10.4 + - + +
72A HIS* 2.9 28.9 + - - +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 2.8 68.0 + - + +
66A VAL* 3.3 10.7 + - + +
68A ARG* 1.3 72.0 - - - +
70A VAL* 1.3 63.9 + - + +
72A HIS* 3.4 7.0 + - - +
73A ALA* 3.2 18.9 + - - +
89A PHE* 3.8 32.1 - - + -
93A MET* 4.0 20.0 - - + -
100A ASP* 4.7 2.7 - - - +
125A PHE* 3.9 21.8 - - + -
128A THR* 5.4 0.9 - - + -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 3.1 16.7 + - + +
67A ARG* 3.3 9.2 + - - +
69A ILE* 1.3 77.4 - - + +
71A ASP* 1.3 65.1 + - - +
73A ALA* 3.7 4.0 + - - +
74A ARG* 3.5 33.5 + - + +
124A ALA* 4.0 25.1 - - + +
125A PHE* 4.8 2.7 - - + +
128A THR* 3.4 30.2 - - + +
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 2.9 27.3 + - - +
68A ARG* 4.0 11.5 + - + +
70A VAL* 1.3 79.6 - - - +
72A HIS* 1.3 67.4 + - - +
74A ARG* 3.2 8.0 + - - +
75A THR* 3.0 28.2 + - - +
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Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG 2.9 18.8 + - - +
69A ILE* 3.5 9.2 - - - +
71A ASP* 1.3 75.1 - - - +
73A ALA* 1.3 51.8 + - - +
75A THR* 3.1 13.3 + - + +
76A LEU* 2.8 69.4 + - + +
89A PHE* 4.5 8.3 - + - -
92A ASP* 2.5 39.9 + - + +
93A MET* 6.4 1.3 - - - -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE 3.2 3.2 + - - +
70A VAL 3.8 5.6 - - - +
72A HIS* 1.3 77.5 - - - +
74A ARG* 1.3 57.5 + - + +
76A LEU* 3.3 7.0 + - - +
77A LEU* 3.0 26.8 + - + +
89A PHE* 3.8 22.4 - - + -
128A THR* 3.3 34.8 - - + -
132A LEU* 3.7 20.5 - - + +
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 3.5 22.4 + - + +
71A ASP* 3.2 11.2 + - - +
73A ALA* 1.3 75.2 - - + +
75A THR* 1.3 63.4 + - - +
77A LEU* 3.5 16.1 + - + +
78A ALA* 3.2 22.9 + - - +
131A GLU* 4.1 27.1 + - - +
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP* 3.0 16.7 + - - +
72A HIS* 3.4 16.8 - - + +
74A ARG* 1.3 75.2 - - - +
76A LEU* 1.3 57.6 + - + +
78A ALA* 3.2 8.2 + - - +
79A ALA* 2.8 40.6 + - + +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A HIS* 2.8 51.7 + - + +
73A ALA* 3.4 9.4 - - - +
75A THR* 1.3 78.1 - - + +
77A LEU* 1.3 58.2 + - - +
79A ALA* 4.3 4.3 - - + +
80A GLU* 2.7 51.5 + - + +
81A GLY 3.6 0.2 + - - -
85A ALA* 3.7 12.7 - - + +
88A VAL* 3.9 20.4 - - + -
89A PHE* 3.7 36.6 - - + +
92A ASP* 3.7 3.1 - - - +
132A LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 3.0 12.2 + - + +
74A ARG* 3.7 19.7 - - + +
75A THR 3.3 0.2 - - - -
76A LEU* 1.3 74.1 - - - +
78A ALA* 1.3 58.6 + - - +
81A GLY* 2.9 28.6 + - - -
82A PRO* 4.0 15.7 - - + +
85A ALA* 3.7 15.3 - - + -
131A GLU* 4.9 13.7 - - + +
132A LEU* 3.7 34.8 - - + +
135A ALA* 3.8 28.3 - - + -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG 3.2 10.5 + - - +
75A THR* 3.3 11.0 - - - +
77A LEU* 1.3 81.5 - - - +
79A ALA* 1.3 61.6 + - + +
81A GLY* 3.9 3.3 + - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 2.8 29.2 + - + +
76A LEU* 4.1 4.9 - - + +
78A ALA* 1.3 75.0 - - + +
80A GLU* 1.3 72.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 2.7 38.1 + - + +
79A ALA* 1.3 84.0 - - + +
81A GLY* 1.3 67.4 + - - +
84A GLU* 4.2 18.6 + - + +
85A ALA* 4.1 11.2 - - - +
88A VAL* 3.9 27.7 - - + +
----------------------------------------------------------
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 2.9 20.3 + - - -
78A ALA 3.9 2.6 + - - -
79A ALA 3.6 1.6 - - - -
80A GLU* 1.3 79.9 - - - +
82A PRO* 1.3 77.6 - - - +
83A GLY 3.2 2.5 - - - -
84A GLU 3.3 1.2 + - - -
85A ALA* 3.1 25.2 + - - +
----------------------------------------------------------
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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