Contacts of the helix formed by residues 60 - 86 (chain A) in PDB entry 2HKU
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 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.3 10.8 + - - +
55A THR* 4.5 5.5 - - - +
58A TYR* 2.9 8.8 + - - +
59A GLY* 1.3 81.4 - - - +
61A LYS* 1.3 63.4 + - - +
62A GLU* 3.5 16.7 + - - +
63A ARG* 3.1 24.8 + - - +
64A LEU* 3.1 18.7 + - - +
124A GLU* 5.0 3.5 + - - -
125A LEU* 5.8 0.3 - - - +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 4.4 13.8 - - + -
36A GLU* 3.1 31.0 + - - +
37A GLY* 3.9 6.5 + - - -
38A VAL 2.7 32.1 + - - -
39A PRO* 4.1 4.8 - - - +
40A ILE* 4.1 32.3 - - + +
54A VAL* 4.7 7.4 - - - +
60A SER* 1.3 74.3 - - - +
62A GLU* 1.3 73.2 + - - +
64A LEU* 3.2 8.0 + - - +
65A PHE* 2.9 27.6 + - + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 4.3 11.7 - - - +
60A SER* 3.3 17.9 + - - +
61A LYS* 1.3 89.3 + - - +
63A ARG* 1.3 60.3 + - - +
65A PHE* 3.3 4.0 + - - +
66A VAL* 2.9 34.3 + - - +
118A MSE 4.0 24.9 - - + -
122A ARG* 5.6 6.7 - - - +
125A LEU* 4.2 15.7 - - + -
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.0 32.3 - - + +
59A GLY* 5.2 0.2 - - - -
60A SER* 3.1 14.1 + - - +
62A GLU* 1.3 75.3 - - - +
64A LEU* 1.3 66.2 + - - +
66A VAL* 3.5 1.0 + - - +
67A GLU* 2.7 59.2 + - + +
124A GLU* 3.8 36.5 + - - +
125A LEU* 3.8 18.4 - - + +
128A LEU* 4.1 26.3 - - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.7 3.4 - - + +
24A PHE* 4.3 5.8 - - + -
27A ALA* 3.9 24.2 - - + -
31A PHE* 4.3 3.1 - - + -
40A ILE* 4.0 25.8 - - + -
43A ILE* 4.4 9.6 - - + -
54A VAL* 4.4 12.1 - - + -
58A TYR* 3.7 48.5 - - + +
60A SER 3.1 13.2 + - - +
61A LYS* 3.5 9.0 - - - +
63A ARG* 1.3 77.0 - - - +
65A PHE* 1.4 55.6 + - - +
67A GLU* 3.8 0.9 - - - +
68A VAL* 2.9 49.1 + - + +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.6 31.2 - + + -
36A GLU* 3.4 50.7 - - + +
61A LYS* 2.9 17.2 + - + +
62A GLU* 3.3 11.2 + - - +
64A LEU* 1.4 71.9 - - - +
66A VAL* 1.4 63.6 + - - +
68A VAL* 3.4 2.3 + - - +
69A ALA* 2.9 28.1 + - + +
111A LEU* 3.4 39.0 - - + -
114A SER* 4.4 8.5 - - - -
115A ALA* 3.9 26.9 - - + -
118A MSE 4.0 20.0 - - + -
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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 GLU 2.9 23.3 + - - +
63A ARG 4.2 1.8 - - - +
65A PHE* 1.4 72.9 - - - +
67A GLU* 1.3 63.6 + - - +
69A ALA* 3.2 5.7 + - - +
70A CYS* 2.9 24.3 + - - -
115A ALA* 4.4 3.8 - - + -
118A MSE 3.6 29.2 - - - -
119A THR* 3.6 12.8 - - + -
125A LEU* 4.0 17.3 - - + +
128A LEU* 3.7 32.3 - - + -
129A ILE* 4.0 22.2 - - + -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.2 32.2 + - - -
24A PHE* 3.8 12.3 - - + -
57A TYR 5.4 0.3 - - - +
58A TYR* 3.5 16.0 - - + -
63A ARG* 2.7 50.3 + - - +
64A LEU* 3.8 3.8 - - - +
66A VAL* 1.3 76.6 - - - +
68A VAL* 1.3 62.2 + - - +
70A CYS* 3.4 4.5 + - - +
71A ALA* 3.0 25.5 + - - +
128A LEU* 3.8 22.4 - - + -
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Residues in contact with VAL 68 (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 19.4 - - + +
27A ALA* 3.7 26.5 - - + -
28A THR* 3.6 35.7 + - + +
31A PHE* 3.9 15.0 - - + -
64A LEU* 2.9 33.2 + - + +
65A PHE 3.6 3.4 - - - +
67A GLU* 1.3 79.4 - - - +
69A ALA* 1.4 56.8 + - - +
71A ALA* 3.9 1.0 - - - +
72A ALA* 2.9 30.1 + - - +
111A LEU* 4.0 15.5 - - + -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 2.9 18.2 + - + +
66A VAL 3.2 2.0 + - - +
68A VAL* 1.4 73.3 - - - +
70A CYS* 1.3 65.6 + - - +
72A ALA* 3.5 2.1 + - - +
73A VAL* 3.1 24.8 + - - +
108A SER 4.5 0.5 - - - +
111A LEU* 3.7 31.9 - - + +
112A PHE* 3.9 9.3 - - + +
115A ALA* 3.5 30.1 - - + -
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Residues in contact with CYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 2.9 36.2 + - - +
67A GLU* 3.6 5.2 - - - +
69A ALA* 1.3 78.1 - - - +
71A ALA* 1.3 62.4 + - - +
73A VAL* 3.4 1.9 - - - +
74A LEU* 3.1 31.9 + - + +
112A PHE* 3.8 19.1 - - - -
128A LEU* 3.7 17.7 - - + -
129A ILE* 4.1 2.7 - - - -
132A THR* 3.1 31.9 - - - +
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.6 20.2 - - + -
67A GLU 3.0 19.0 + - - +
68A VAL 3.9 0.4 - - - +
70A CYS* 1.3 72.1 - - - +
72A ALA* 1.3 57.8 + - - +
74A LEU* 3.4 8.3 + - - +
75A ARG* 2.8 62.2 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A THR* 5.2 7.2 - - + +
32A LEU* 4.4 14.8 - - + -
68A VAL 2.9 23.0 + - - +
69A ALA* 3.7 6.7 - - - +
71A ALA* 1.3 73.3 - - - +
73A VAL* 1.3 57.9 + - - +
75A ARG* 3.8 4.0 - - - +
76A ALA* 2.8 29.6 + - - +
108A SER* 3.4 28.3 + - - +
111A LEU* 4.4 4.3 - - + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA 3.1 8.4 + - - +
70A CYS 3.4 11.0 - - - +
72A ALA* 1.3 77.2 - - - +
74A LEU* 1.3 61.4 + - - +
76A ALA* 4.2 4.5 - - + -
77A GLY* 2.8 25.5 + - - -
108A SER* 4.1 4.8 + - - +
109A VAL* 4.1 28.7 - - + -
112A PHE* 3.6 35.2 - - + -
132A THR* 3.4 22.4 - - + -
136A LEU* 3.9 24.9 - - + +
167A TRP* 4.5 6.7 - - + -
171A PHE* 4.9 0.7 - - + -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A CYS* 3.1 23.4 + - + +
71A ALA* 3.6 7.6 - - - +
73A VAL* 1.3 72.8 - - - +
75A ARG* 1.3 63.9 + - + +
77A GLY* 3.4 1.0 + - - -
78A LYS* 2.9 29.1 + - - +
132A THR* 3.9 25.4 - - + +
135A THR* 3.9 31.4 - - + +
136A LEU* 4.0 18.8 - - + +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.3 12.3 - - - -
71A ALA* 2.8 50.7 + - - +
72A ALA* 3.9 4.5 - - - +
74A LEU* 1.3 79.9 - - + +
76A ALA* 1.3 56.5 + - - +
78A LYS* 3.2 7.3 + - - +
79A ARG* 2.8 32.8 + - - +
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA 2.8 18.6 + - - +
73A VAL* 3.7 5.6 - - - +
75A ARG* 1.3 75.4 - - - +
77A GLY* 1.3 61.4 + - - +
79A ARG* 3.5 6.4 + - - +
80A ALA* 3.1 18.7 + - - +
100A SER* 4.8 1.6 + - - -
101A LEU* 3.5 14.8 - - + +
105A GLY* 4.1 21.2 - - - +
108A SER* 3.7 20.0 - - - +
109A VAL* 5.1 2.7 - - + -
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL 2.8 20.6 + - - -
74A LEU 3.8 1.6 - - - -
75A ARG 3.4 0.2 - - - -
76A ALA* 1.3 72.5 - - - +
78A LYS* 1.3 62.2 + - - +
80A ALA* 3.4 3.0 + - - +
81A GLU* 3.1 34.1 + - - +
101A LEU* 3.8 14.9 - - - +
136A LEU* 5.0 3.1 - - - -
139A SER* 6.0 0.9 - - - -
167A TRP* 4.5 13.7 - - - -
302A EDO 5.0 1.1 - - - -
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU 2.9 17.9 + - - +
75A ARG* 3.2 6.2 + - - +
77A GLY* 1.3 74.7 - - - +
79A ARG* 1.3 53.0 + - - +
81A GLU* 3.2 14.4 + - + +
82A ASP* 2.8 70.2 + - - +
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG 2.8 20.6 + - - +
76A ALA* 3.9 7.4 - - - +
78A LYS* 1.3 70.7 - - - +
80A ALA* 1.4 57.1 + - - +
82A ASP* 3.2 21.6 + - - +
83A ASP* 2.8 72.2 + - - +
100A SER* 4.1 11.9 - - - +
104A PRO* 6.4 1.1 - - + -
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA 3.1 13.1 + - - +
77A GLY 3.7 4.3 - - - +
79A ARG* 1.4 78.0 - - - +
81A GLU* 1.3 57.1 + - - +
83A ASP* 3.8 1.2 - - - +
84A ALA* 2.9 30.0 + - - +
97A LEU* 3.5 36.1 - - + +
100A SER* 3.6 19.9 + - - -
101A LEU* 3.6 20.4 - - + -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 3.1 19.3 + - - +
78A LYS* 3.6 12.5 + - + +
80A ALA* 1.3 71.5 - - - +
82A ASP* 1.3 63.2 + - - +
84A ALA* 3.4 6.4 + - - +
85A ALA* 2.9 29.1 + - - +
93A TYR* 4.8 3.9 + - - +
97A LEU* 4.2 6.3 - - + -
139A SER* 3.4 23.3 + - - +
143A ALA* 3.6 18.6 - - + +
302A EDO 2.6 46.3 + - - +
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 2.8 55.8 + - - +
79A ARG* 3.5 26.4 + - - +
81A GLU* 1.3 78.4 - - - +
83A ASP* 1.3 63.0 + - - +
85A ALA* 3.2 18.9 + - - +
86A THR* 3.3 16.4 - - - +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 2.8 59.0 + - - +
80A ALA* 4.1 4.3 - - - +
82A ASP* 1.3 75.8 - - - +
84A ALA* 1.3 57.3 + - - +
86A THR* 3.1 25.8 + - - +
96A LYS* 3.6 20.4 + - + +
100A SER* 4.8 9.1 + - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA 2.9 19.0 + - - +
81A GLU 3.6 6.1 - - - +
83A ASP* 1.3 73.4 - - - +
85A ALA* 1.3 59.1 + - - +
86A THR 3.1 6.9 + - - -
87A ALA 3.6 12.5 + - - +
93A TYR* 2.9 56.7 - - + +
96A LYS* 3.9 11.1 - - - +
97A LEU* 3.7 12.8 - - + +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU 2.9 14.1 + - - +
82A ASP* 3.2 13.6 + - - +
84A ALA* 1.3 75.6 - - - +
86A THR* 1.3 58.7 + - + +
87A ALA* 3.3 10.4 + - - -
88A GLU 4.8 0.3 + - - -
93A TYR* 4.0 11.2 - - + -
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP 3.3 19.1 - - - +
83A ASP* 3.1 17.8 + - - +
84A ALA 3.1 1.4 - - - -
85A ALA* 1.3 79.0 - - + +
87A ALA* 1.3 60.1 + - - +
96A LYS* 4.3 12.3 + - - -
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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