Contacts of the helix formed by residues 51 - 80 (chain A) in PDB entry 1M1J
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 ARG 51 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 3.8 23.5 + - - +
49A GLY 3.5 0.6 - - - -
50A CYS* 1.3 78.3 - - - +
52A MET* 1.3 71.0 + - + +
54A GLY* 3.9 0.2 - - - -
55A ILE* 3.4 30.7 + - + +
64B TYR* 3.8 29.5 - - - +
65B PRO* 4.4 2.7 - - - -
66B ASP* 2.6 50.6 + - - +
75E ASP 3.9 4.2 + - - -
76E GLU 2.5 41.9 + - - +
77E LEU 4.0 9.0 - - - +
78E GLY* 3.6 17.3 - - - +
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Residues in contact with MET 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.9 20.0 - - + -
48A SER 3.8 13.8 + - - +
49A GLY 4.0 3.7 + - - +
50A CYS 3.1 0.4 - - - -
51A ARG* 1.3 91.2 - - + +
53A GLN* 1.3 57.5 + - - +
54A GLY 2.8 9.2 + - - -
55A ILE* 3.1 13.8 + - + +
56A ILE* 2.9 33.4 + - + +
87B LEU* 3.3 30.3 - - + -
22C THR* 4.2 14.8 - - - +
25C ILE* 4.3 7.2 - - + -
26C ALA* 3.7 35.2 - - + -
29C PHE* 5.6 7.2 - - + -
77E LEU* 4.8 8.3 - - + -
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 3.7 2.3 + - - +
50A CYS 3.5 1.0 + - - -
52A MET* 1.3 78.3 - - - +
54A GLY* 1.3 54.4 + - - +
55A ILE 3.5 0.2 - - - -
56A ILE* 4.5 4.0 - - - +
57A ASP* 2.7 42.5 - - - +
67B ALA* 3.0 26.6 - - - +
68B GLY* 4.4 4.1 - - - -
82B PRO* 3.6 28.2 - - + +
86B GLU* 4.1 17.4 + - - +
87B LEU* 3.0 26.5 - - + +
90B THR* 3.7 28.0 + - - +
45D LYS* 6.1 0.4 - - - +
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS 2.9 15.9 + - - -
51A ARG 3.9 0.9 - - - -
52A MET 2.8 1.6 - - - -
53A GLN* 1.3 80.4 - - - +
55A ILE* 1.3 59.2 + - - +
57A ASP* 4.0 4.5 - - - +
58A ASP* 3.4 14.9 + - - +
65B PRO* 2.8 25.0 - - - +
66B ASP 3.5 15.5 - - - -
67B ALA* 3.8 8.5 - - - -
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.4 26.6 + - + +
52A MET* 3.1 13.9 + - + +
54A GLY* 1.3 76.3 - - - +
56A ILE* 1.3 54.2 + - + +
57A ASP 2.6 16.8 + - - -
58A ASP* 3.1 4.9 + - + +
59A THR* 3.0 29.2 + - - +
64B TYR* 5.0 1.3 - - + -
65B PRO* 3.5 21.1 - - + -
29C PHE* 3.5 29.6 - - + -
33C ARG* 4.1 7.9 - - - +
76E GLU* 3.5 39.9 - - + +
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A MET* 2.9 21.9 + - + +
53A GLN* 4.7 5.2 - - - +
55A ILE* 1.3 74.6 - - + +
57A ASP* 1.3 60.0 + - - +
59A THR* 4.6 0.2 - - - -
60A ASP* 3.5 11.4 + - - +
87B LEU* 4.3 14.1 - - + +
90B THR* 3.5 13.2 - - + -
91B LEU* 3.3 46.4 - - + -
94B GLN* 3.2 29.6 + - - +
25C ILE* 4.1 18.2 - - + -
29C PHE* 3.8 32.9 - - + -
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 2.7 39.7 + - - +
54A GLY 4.0 6.1 - - - +
55A ILE 2.6 1.8 + - - +
56A ILE* 1.3 81.5 - - - +
58A ASP* 1.3 70.7 + - - +
59A THR 3.1 0.9 - - - -
60A ASP* 2.9 7.1 + - - +
61A GLN* 2.8 24.7 + - - +
67B ALA* 4.6 9.2 - - - +
90B THR* 5.7 1.4 - - - +
94B GLN* 4.8 3.8 - - - +
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY 3.4 14.8 - - - +
55A ILE* 3.1 11.0 + - + +
57A ASP* 1.3 78.9 - - - +
59A THR* 1.3 54.1 + - - +
61A GLN* 3.0 17.7 + - - +
62A ASN* 2.7 36.5 + - - +
65B PRO* 4.0 15.8 - - - +
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.0 17.4 + - - +
56A ILE 4.6 1.6 - - - -
58A ASP* 1.3 78.1 - - - +
60A ASP* 1.3 65.9 + - - +
62A ASN* 3.1 8.4 + - - +
63A TYR* 2.9 59.9 + - + +
94B GLN* 6.2 0.4 - - - +
29C PHE* 3.6 28.7 - - + -
32C TYR* 5.0 4.0 - - + -
33C ARG* 3.9 15.1 + - + +
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE 3.5 9.8 + - - +
57A ASP* 2.9 8.4 + - - +
59A THR* 1.3 77.4 - - - +
61A GLN* 1.3 63.6 + - - +
63A TYR* 3.5 7.4 + - - +
64A SER* 3.2 25.7 + - - -
94B GLN* 3.3 51.5 + - - +
98B VAL* 4.3 10.7 - - - +
32C TYR* 4.2 6.5 + - - -
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP 2.8 11.7 + - - +
58A ASP* 3.2 22.0 - - - +
60A ASP* 1.3 75.0 - - - +
62A ASN* 1.3 66.3 + - - +
64A SER* 3.1 10.1 + - - +
65A GLN* 3.1 39.5 + - - +
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Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASP 2.7 16.5 + - - +
59A THR* 3.5 11.9 - - - +
61A GLN* 1.3 72.7 - - - +
63A TYR* 1.3 59.7 + - + +
65A GLN* 2.8 21.9 + - - +
66A ARG* 2.7 60.7 + - - +
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 2.9 42.2 + - + +
60A ASP* 3.6 10.1 - - - +
62A ASN* 1.3 86.6 - - - +
64A SER* 1.3 52.9 + - - +
66A ARG* 2.9 5.4 + - - +
67A ILE* 2.7 46.8 + - + +
98B VAL* 5.0 9.2 - - + -
32C TYR* 4.1 21.1 - + - -
33C ARG* 3.1 24.3 + - - +
36C THR* 3.2 29.8 - - + -
37C ASP* 2.8 30.0 + - - -
40C LEU* 3.7 27.1 - - + -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP* 3.2 12.5 + - - -
61A GLN* 3.1 16.3 + - - +
63A TYR* 1.3 78.3 - - - +
65A GLN* 1.3 51.9 + - - +
67A ILE* 3.9 13.8 - - - +
68A ASP* 2.5 37.9 + - - +
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 3.1 30.3 + - + +
62A ASN* 2.8 29.1 + - - +
64A SER* 1.3 79.3 - - - +
66A ARG* 1.3 59.7 + - + +
67A ILE 3.3 0.2 - - - -
68A ASP* 3.6 6.8 + - - +
69A ASN* 3.0 35.2 + - - +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 2.7 44.4 + - - +
63A TYR* 3.7 7.6 - - - +
65A GLN* 1.3 72.3 - - + +
67A ILE* 1.3 65.2 + - - +
68A ASP 3.2 0.2 - - - -
69A ASN* 3.5 10.5 + - - +
70A ILE* 3.2 26.2 + - - +
37C ASP* 4.3 8.6 + - - +
40C LEU* 2.8 47.7 - - + +
41C LEU* 3.2 22.4 - - - +
44C GLU* 2.8 43.0 + - - +
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 2.7 26.1 + - + +
64A SER* 4.0 11.2 - - - +
66A ARG* 1.3 76.4 - - - +
68A ASP* 1.3 63.5 + - - +
70A ILE* 3.2 17.9 + - - +
71A ARG* 3.2 46.2 + - - +
98B VAL* 4.6 13.5 - - + -
101B VAL* 3.6 22.9 - - + -
102B LEU* 4.0 13.9 - - + -
105B LEU* 4.0 12.3 - - + -
40C LEU* 4.0 19.7 - - + -
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 2.5 26.1 + - - +
65A GLN* 3.7 9.8 - - - +
66A ARG 3.2 0.4 - - - -
67A ILE* 1.3 73.3 - - - +
69A ASN* 1.3 58.6 + - - +
70A ILE 2.9 5.2 + - - -
71A ARG* 2.9 33.3 + - - +
72A GLN* 2.7 36.9 + - + +
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 3.0 22.4 + - - +
66A ARG* 3.7 12.1 - - - +
67A ILE 3.4 0.4 - - - -
68A ASP* 1.3 79.8 - - - +
70A ILE* 1.3 61.4 + - - +
72A GLN* 3.8 12.7 - - - +
73A GLN* 3.1 24.6 + - - +
44C GLU* 6.0 0.4 - - - +
47C LEU* 4.8 0.3 - - - +
----------------------------------------------------------
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 3.2 15.8 + - + +
67A ILE* 3.2 8.7 + - - +
68A ASP 2.9 0.8 - - - -
69A ASN* 1.3 75.5 - - + +
71A ARG* 1.3 56.5 + - - +
73A GLN* 3.0 3.1 + - - -
74A LEU* 2.7 36.3 + - + +
105B LEU* 3.4 37.7 - - + -
109B VAL* 4.1 17.0 - - + -
40C LEU* 4.4 14.1 - - + -
43C ILE* 3.4 26.2 - - + -
44C GLU* 4.2 23.1 - - + +
47C LEU* 3.8 19.1 - - + +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.4 37.3 - - - +
68A ASP* 2.9 27.1 + - - +
70A ILE* 1.3 77.0 - - - +
72A GLN* 1.3 57.8 + - - +
74A LEU* 3.7 11.8 - - + +
75A ALA* 3.0 32.2 + - - +
101B VAL* 4.4 18.2 - - - +
105B LEU* 4.1 17.0 - - + +
108B ARG* 5.3 8.7 - - - +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 2.7 20.4 + - + +
69A ASN* 3.9 14.4 - - - +
71A ARG* 1.3 75.2 - - - +
73A GLN* 1.3 64.5 + - - +
75A ALA* 4.2 2.7 - - - +
76A ASP* 3.3 25.8 + - - +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN 3.1 16.6 + - - +
70A ILE 3.0 2.9 + - - +
72A GLN* 1.3 80.3 - - - +
74A LEU* 1.3 66.9 + - - +
75A ALA 3.2 0.9 - - - -
76A ASP* 3.7 10.3 - - + +
77A SER* 3.1 24.9 + - - +
47C LEU* 2.8 39.3 - - + +
48C GLN* 5.3 8.7 + - - +
51C THR* 3.0 29.3 + - + +
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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
----------------------------------------------------------
70A ILE 2.7 22.8 + - - +
71A ARG* 3.7 7.4 - - + +
73A GLN* 1.3 74.6 - - - +
75A ALA* 1.3 52.6 + - + +
77A SER* 4.0 1.7 - - - -
78A GLN* 2.7 62.2 + - - +
105B LEU* 4.7 7.9 - - + -
108B ARG* 3.3 39.0 - - + +
109B VAL* 4.3 17.7 - - + -
112B PHE* 4.0 25.4 - - + -
47C LEU* 3.8 21.7 - - + +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG 3.0 18.2 + - - +
72A GLN* 4.2 4.3 - - - +
74A LEU* 1.3 75.7 - - + +
76A ASP* 1.3 68.6 + - - +
78A GLN* 3.0 12.5 + - - +
79A ASN* 3.0 35.0 + - - +
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Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN* 3.3 23.8 + - - +
73A GLN* 3.7 14.0 - - + +
75A ALA* 1.3 82.1 - - - +
77A SER* 1.3 64.8 + - - +
79A ASN* 3.3 4.9 + - - +
80A LYS* 3.1 41.8 + - - +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 3.1 15.3 + - - +
74A LEU 4.1 1.3 - - - -
76A ASP* 1.3 81.9 + - - +
78A GLN* 1.3 61.7 + - - +
79A ASN 3.1 1.8 + - - -
80A LYS* 3.1 19.2 + - - +
81A TYR* 3.3 14.9 + - - +
112B PHE* 3.7 15.3 - - - -
51C THR* 2.8 39.4 - - - +
54C THR* 3.8 11.7 + - - +
----------------------------------------------------------
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 2.7 54.0 + - - +
75A ALA* 3.0 10.5 + - - +
77A SER* 1.3 72.2 - - - +
79A ASN* 1.3 62.2 + - - +
81A TYR* 3.8 13.5 - - + +
82A LYS* 4.1 9.7 - - - +
108B ARG* 4.9 9.1 - - - +
112B PHE* 3.5 34.2 - - + +
----------------------------------------------------------
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Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.0 24.8 + - - +
76A ASP* 3.8 4.6 - - - +
78A GLN* 1.3 78.3 - - - +
80A LYS* 1.3 55.7 + - - +
81A TYR 2.8 15.1 + - - -
82A LYS* 2.9 44.5 + - + +
83A THR* 3.4 8.7 + - - -
----------------------------------------------------------
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP* 3.1 35.2 + - - +
77A SER* 3.1 12.4 + - - +
79A ASN* 1.3 73.6 - - - +
81A TYR* 1.3 53.1 + - - +
82A LYS 3.4 2.5 - - - +
83A THR* 4.3 11.7 - - + -
84A SER* 4.1 4.7 - - - -
54C THR* 3.8 22.1 + - + +
55C GLY* 5.7 0.9 - - - -
58C GLU* 3.0 44.6 - - - +
----------------------------------------------------------
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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