Contacts of the helix formed by residues 55 - 80 (chain A) in PDB entry 4ASQ
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 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR* 3.8 3.2 - - - -
53A ASN* 3.2 20.0 + - - +
54A ILE* 1.3 82.8 - - - +
56A ASP* 1.3 60.9 + - - +
57A GLU 4.0 1.1 - - - -
58A ASN* 3.1 21.2 + - - +
59A GLU* 3.0 30.0 + - - +
129A LYS* 6.1 1.3 - - - +
1623A NAG 2.7 37.3 + - - +
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Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 1.3 74.5 - - - +
57A GLU* 1.3 61.4 + - - +
59A GLU* 3.5 17.5 + - - +
60A LYS* 3.1 24.4 + - - +
129A LYS* 5.5 4.9 + - - -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.2 1.4 + - - -
56A ASP* 1.3 78.5 - - - +
58A ASN* 1.3 58.7 + - - +
60A LYS* 3.4 9.1 + - + +
61A LYS* 3.1 62.5 + - - +
1623A NAG 3.4 31.3 - - - +
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Residues in contact with ASN 58 (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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46A ALA 4.6 1.7 - - - +
49A ALA* 3.5 20.6 + - + +
50A TYR* 3.8 16.0 - - + +
53A ASN* 2.9 47.2 + - - +
55A THR* 3.1 17.4 + - - +
57A GLU* 1.3 74.6 - - - +
59A GLU* 1.3 61.1 + - - +
61A LYS* 3.5 19.8 + - - +
62A LYS* 3.0 30.3 + - - +
1623A NAG 3.5 10.8 + - - +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.5 22.6 + - + -
55A THR 3.0 16.6 + - - +
56A ASP* 3.6 19.9 - - - +
58A ASN* 1.3 75.9 - - - +
60A LYS* 1.3 57.5 + - - +
62A LYS* 3.4 3.9 + - + +
63A ASN* 3.0 44.5 + - - +
118A ASP* 4.3 9.7 - - - +
121A SER* 2.7 40.8 + - - +
122A ALA* 4.5 3.6 + - - +
125A SER* 5.4 2.9 + - - -
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Residues in contact with LYS 60 (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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56A ASP 3.1 15.0 + - - +
57A GLU* 3.5 9.2 - - + +
58A ASN 3.3 0.2 - - - -
59A GLU* 1.3 79.8 - - - +
61A LYS* 1.3 57.2 + - + +
63A ASN* 3.9 3.8 - - - +
64A GLU* 2.9 73.9 + - + +
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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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46A ALA* 4.5 4.7 - - + +
57A GLU* 3.1 51.4 + - + +
58A ASN* 3.8 16.5 + - - +
59A GLU 3.3 0.2 - - - -
60A LYS* 1.3 73.9 - - + +
62A LYS* 1.3 64.9 + - - +
64A GLU* 3.4 6.4 + - - +
65A ILE* 3.1 40.4 + - + +
1623A NAG 6.1 0.2 - - - -
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Residues in contact with LYS 62 (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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43A GLU* 5.1 2.4 - - + +
46A ALA* 3.8 23.3 - - - +
47A ALA* 4.2 26.2 + - + +
50A TYR* 3.6 38.3 - - + -
58A ASN 3.0 17.1 + - - +
59A GLU* 3.7 3.6 - - - +
61A LYS* 1.3 76.2 - - - +
63A ASN* 1.3 73.9 + - - +
65A ILE* 4.1 2.3 - - - +
66A SER* 3.1 33.7 + - - +
117A LEU* 6.0 3.2 - - - +
121A SER* 5.0 7.9 - - - +
124A GLU* 5.3 6.3 + - - -
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Residues in contact with ASN 63 (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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59A GLU* 3.0 27.0 + - - +
60A LYS* 4.2 3.6 - - - +
62A LYS* 1.3 94.8 - - - +
64A GLU* 1.3 61.3 + - + +
66A SER* 3.9 0.6 + - - -
67A ALA* 3.1 24.9 + - - +
117A LEU* 3.3 46.0 + - + +
118A ASP* 3.6 17.8 + - - +
121A SER* 3.3 23.6 + - - -
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Residues in contact with GLU 64 (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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60A LYS* 2.9 56.1 + - + +
61A LYS* 4.0 6.2 - - - +
63A ASN* 1.3 75.6 - - + +
65A ILE* 1.3 66.0 + - + +
67A ALA* 3.5 7.6 + - - +
68A GLU* 3.2 22.5 + - - +
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Residues in contact with ILE 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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39A ARG 5.3 1.3 - - - +
42A VAL* 3.8 26.7 - - + -
43A GLU* 3.7 27.6 - - + +
46A ALA* 3.7 22.0 - - + -
61A LYS* 3.1 25.1 + - + +
62A LYS 4.1 2.7 - - - +
64A GLU* 1.3 75.4 - - + +
66A SER* 1.3 61.1 + - - +
68A GLU* 3.2 17.9 + - + +
69A LEU* 3.0 27.1 + - + +
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Residues in contact with SER 66 (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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43A GLU* 2.9 34.1 + - - +
62A LYS* 3.1 25.7 + - - +
63A ASN* 3.7 6.7 - - - -
65A ILE* 1.3 76.1 - - - +
67A ALA* 1.3 56.2 + - - +
69A LEU* 3.3 2.9 + - - +
70A ALA* 2.9 30.0 + - - +
113A TYR* 3.6 12.4 + - - -
117A LEU* 3.8 20.4 - - - +
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Residues in contact with ALA 67 (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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63A ASN 3.1 19.0 + - - +
64A GLU* 3.6 8.5 - - - +
66A SER* 1.3 75.8 - - - +
68A GLU* 1.3 61.5 + - - +
70A ALA* 3.5 2.6 + - - +
71A LYS* 3.1 23.2 + - - +
110A GLU* 6.0 5.4 - - + +
113A TYR* 3.7 20.0 - - + -
114A ALA* 5.7 7.6 - - + -
117A LEU* 4.6 1.8 - - + -
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Residues in contact with GLU 68 (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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39A ARG* 5.1 13.2 + - - +
64A GLU 3.2 13.7 + - - +
65A ILE* 3.2 21.0 + - + +
67A ALA* 1.3 74.7 - - - +
69A LEU* 1.3 63.1 + - - +
71A LYS* 3.4 11.4 + - + +
72A PHE* 3.2 19.6 + - - +
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Residues in contact with LEU 69 (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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36A LEU* 4.8 2.9 - - + -
39A ARG* 3.8 38.4 - - + +
40A THR* 4.2 19.3 - - + +
43A GLU* 3.3 39.9 - - + +
65A ILE* 3.0 16.0 + - + +
66A SER* 3.8 5.6 - - - +
68A GLU* 1.3 73.4 - - - +
70A ALA* 1.3 60.5 + - - +
72A PHE* 3.1 8.7 + - + +
73A MET* 2.9 53.2 + - + +
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Residues in contact with ALA 70 (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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66A SER 2.9 17.2 + - - +
67A ALA 3.7 4.3 - - - +
69A LEU* 1.3 75.0 - - - +
71A LYS* 1.3 62.2 - - - +
73A MET* 3.2 5.6 + - - +
74A LYS* 3.0 30.8 + - - +
106A ALA* 3.8 25.7 - - + +
113A TYR* 3.5 32.5 - - + +
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Residues in contact with LYS 71 (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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67A ALA 3.1 14.3 + - - +
68A GLU* 3.4 14.1 - - + +
69A LEU 3.2 0.2 - - - -
70A ALA* 1.3 76.5 - - - +
72A PHE* 1.3 62.6 + - - +
74A LYS* 3.4 15.9 - - + +
75A GLU* 3.4 36.2 + - - +
110A GLU* 4.5 20.4 - - + +
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Residues in contact with PHE 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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32A LEU* 3.9 12.6 - - + -
35A GLU* 3.5 37.9 - - + -
36A LEU* 3.7 22.7 - - + -
39A ARG* 3.5 44.9 - - - +
68A GLU 3.2 6.9 + - - +
69A LEU* 3.1 11.7 + - + +
71A LYS* 1.3 76.9 - - - +
73A MET* 1.3 68.1 + - - +
75A GLU* 3.1 23.7 + - + +
76A VAL* 3.0 40.8 + - + +
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Residues in contact with MET 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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36A LEU* 3.4 39.3 - - + -
69A LEU* 2.9 36.7 + - + +
70A ALA* 3.4 10.1 - - - +
72A PHE* 1.3 75.9 - - - +
74A LYS* 1.3 55.7 + - - +
76A VAL* 3.1 14.0 + - + +
77A ALA* 2.9 25.8 + - - +
100A LEU* 5.1 12.1 - - + +
102A LYS 5.5 5.6 - - - +
103A LEU* 3.3 23.3 - - + +
106A ALA* 4.1 9.4 - - + -
383A PHE* 6.0 2.9 - - + -
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Residues in contact with LYS 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 ALA* 3.0 17.4 + - - +
71A LYS* 3.4 16.4 - - + +
72A PHE 3.3 0.2 - - - -
73A MET* 1.3 76.3 - - - +
75A GLU* 1.3 56.6 - - + +
77A ALA* 3.5 2.6 + - - +
78A SER* 3.1 28.6 + - - -
103A LEU* 3.8 14.9 - - + +
106A ALA* 2.8 28.9 + - - +
107A ALA 4.0 9.2 - - - -
108A LEU 2.7 30.2 + - - -
109A PRO* 4.7 4.5 - - - -
110A GLU* 4.6 8.1 - - - +
113A TYR* 5.4 2.2 - - - +
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Residues in contact with GLU 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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71A LYS* 3.4 29.2 + - + +
72A PHE* 3.1 25.0 + - + +
74A LYS* 1.3 74.3 - - + +
76A VAL* 1.3 61.5 + - - +
78A SER* 3.4 7.1 + - - -
79A ASP* 2.9 40.1 + - - +
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Residues in contact with VAL 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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28A TYR* 4.3 2.6 + - - +
32A LEU* 3.7 35.4 - - + -
36A LEU* 4.6 4.3 - - + -
72A PHE* 3.0 47.2 + - + +
73A MET* 3.1 15.0 + - + +
75A GLU* 1.3 73.4 - - + +
77A ALA* 1.3 64.9 + - - +
79A ASP* 3.0 19.3 + - - +
80A THR* 3.1 14.3 + - + +
100A LEU* 3.9 30.1 - - + +
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Residues in contact with ALA 77 (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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73A MET 2.9 15.8 + - - +
74A LYS 3.8 5.2 - - - +
76A VAL* 1.3 76.3 - - - +
78A SER* 1.3 60.0 - - - +
80A THR* 2.7 24.9 + - - -
81A THR* 4.1 6.8 + - - +
100A LEU 3.9 15.7 + - - +
101A THR* 4.4 8.8 - - - +
103A LEU* 3.8 29.2 - - + -
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Residues in contact with SER 78 (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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74A LYS 3.1 17.5 + - - -
75A GLU* 3.5 8.7 - - - -
76A VAL 3.2 0.2 - - - -
77A ALA* 1.3 77.2 - - - +
79A ASP* 1.3 60.2 + - - +
81A THR* 2.6 32.9 + - - -
82A LYS* 4.3 5.1 + - - +
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Residues in contact with ASP 79 (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 TYR* 3.4 29.6 + - + +
75A GLU* 2.9 25.4 + - - +
76A VAL* 3.0 4.1 + - - +
78A SER* 1.3 78.6 + - - +
80A THR* 1.3 63.1 + - - +
81A THR 3.1 0.2 - - - -
82A LYS* 3.1 47.4 + - + +
83A PHE* 3.6 9.9 - - + -
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 5.2 2.7 - - - +
76A VAL* 3.1 15.9 + - + +
77A ALA* 2.7 22.0 + - - +
79A ASP* 1.3 75.8 - - - +
81A THR* 1.3 58.4 + - - +
82A LYS 3.1 0.9 - - - -
83A PHE* 3.0 26.3 + - - +
85A TRP* 3.5 13.3 + - - -
97A PHE* 3.9 29.8 - - + +
100A LEU* 3.9 30.1 - - + -
101A THR* 3.6 20.5 - - + +
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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
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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) + - + + + + + -
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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