Contacts of the helix formed by residues 43 - 72 (chain A) in PDB entry 4NE1
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 43 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 1.3 77.4 - - - +
44A LYS* 1.3 65.1 + - - +
45A GLN* 3.4 14.4 + - - -
46A THR* 2.4 43.8 + - - -
47A ILE* 3.2 13.8 + - - +
64B ARG* 3.2 17.7 - - - +
65B VAL 4.1 2.6 + - - -
66B ASP* 3.1 25.1 + - - -
67B VAL* 4.4 0.2 - - - +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 5.2 0.5 - - - -
42A PHE 4.0 0.4 + - - -
43A SER* 1.3 70.5 - - - +
45A GLN* 1.3 67.7 + - + +
47A ILE* 3.3 18.6 + - + +
48A ALA* 3.1 26.5 + - - +
60H GLU 4.7 5.8 - - - +
61H ASP* 2.8 58.8 + - + +
63H LEU* 3.4 36.7 - - - +
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Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 3.4 18.6 + - - -
44A LYS* 1.3 87.6 + - + +
46A THR* 1.3 53.7 + - - +
48A ALA* 3.5 8.1 - - - +
49A ALA* 2.7 37.7 + - - +
66B ASP* 4.2 7.9 + - - -
67B VAL* 4.3 15.2 - - + +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 4.1 25.8 - - + -
43A SER* 2.4 36.2 + - - -
45A GLN* 1.3 74.0 - - - +
47A ILE* 1.3 64.9 + - - +
49A ALA* 3.1 5.6 + - - +
50A ILE* 3.0 37.9 + - + +
65B VAL* 4.0 11.4 + - + +
66B ASP 5.7 0.9 - - - -
67B VAL* 3.9 19.7 + - + +
70B LEU* 5.3 13.7 - - + -
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 3.7 25.8 - - + +
27A VAL* 5.0 2.3 - - + +
28A GLY* 4.8 12.6 - - - +
31A CYS* 3.9 32.1 - - + -
42A PHE* 4.1 20.9 - - + +
43A SER 3.2 12.8 + - - +
44A LYS* 3.4 24.7 - - + +
46A THR* 1.3 73.9 - - - +
48A ALA* 1.3 64.5 + - - +
50A ILE* 3.5 6.9 + - - +
51A SER* 3.0 25.7 + - - +
63H LEU* 5.6 4.7 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 3.1 23.2 - - + +
44A LYS 3.1 10.2 + - - +
45A GLN* 3.5 12.3 - - - +
47A ILE* 1.3 80.0 - - - +
49A ALA* 1.3 54.9 + - - +
51A SER* 3.1 4.7 + - - -
52A GLU* 3.0 46.5 + - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN 2.7 22.3 + - - +
46A THR* 3.1 9.6 + - - +
48A ALA* 1.3 72.4 - - - +
50A ILE* 1.3 57.6 + - - +
52A GLU* 3.8 12.8 - - - +
53A LEU* 3.0 33.9 + - + +
56A ARG* 4.3 2.2 + - - +
67B VAL* 5.0 13.7 - - + -
70B LEU* 5.0 11.4 - - + -
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.8 19.1 - - + -
31A CYS* 3.9 26.7 - - - -
42A PHE* 5.2 4.5 - - + -
46A THR* 3.0 29.6 + - + +
47A ILE 4.0 3.4 - - - +
49A ALA* 1.3 77.5 - - - +
51A SER* 1.3 56.8 + - - +
53A LEU* 3.5 10.2 - - + +
54A THR* 3.0 43.9 + - - +
45B PHE* 5.3 3.1 - - + -
46B VAL* 4.2 16.8 - - + -
49B ALA* 5.2 14.4 - - + -
50B ALA* 5.5 8.5 - - + +
70B LEU* 5.2 15.5 - - + -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 4.7 7.2 - - - +
23A VAL* 3.7 17.5 - - - +
24A HIS* 2.7 57.5 + - - -
27A VAL* 4.3 9.6 - - - +
47A ILE* 3.0 9.5 + - - +
48A ALA 3.1 5.9 + - - -
50A ILE* 1.3 73.3 - - - +
52A GLU* 1.3 65.2 + - - +
54A THR* 3.6 1.0 + - - -
55A PHE* 3.2 22.5 + - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 4.7 19.0 - - + +
48A ALA* 3.0 32.9 + - - +
49A ALA* 3.8 9.5 - - - +
51A SER* 1.3 76.5 - - - +
53A LEU* 1.3 61.0 + - - +
55A PHE* 3.2 8.6 + - - +
56A ARG* 3.0 56.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.0 21.6 + - + +
50A ILE* 3.3 13.6 + - + +
52A GLU* 1.3 76.5 - - - +
54A THR* 1.3 56.4 + - - +
56A ARG* 3.4 31.3 + - - +
57A GLN* 2.8 28.2 + - - +
45B PHE* 4.2 15.3 - - + -
49B ALA* 5.7 0.7 - - + -
70B LEU* 5.6 4.9 - - + -
74B LEU* 4.0 30.5 - - + -
77B LEU* 3.7 29.6 - - + -
78B LEU* 5.1 16.6 - - + -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 5.0 9.9 - - + -
27A VAL* 4.8 4.3 - - + +
50A ILE* 3.0 23.7 + - - +
51A SER 4.2 3.8 - - - -
53A LEU* 1.3 73.8 - - - +
55A PHE* 1.3 55.7 - - - +
57A GLN* 2.9 12.0 + - + +
58A CYS* 2.6 42.0 + - - +
61A PHE* 4.6 0.9 - - + -
10B PHE* 5.6 5.2 - - + -
18B LEU* 6.2 1.6 - - + -
42B LEU* 4.0 28.9 - - + -
45B PHE* 4.1 20.0 - - + -
46B VAL* 4.4 8.1 - - + +
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 4.3 29.2 - - + -
19A LEU 6.2 0.2 - - - -
20A LYS* 3.5 52.3 - - + -
23A VAL* 5.3 6.1 - - + +
51A SER 3.2 12.9 + - - +
52A GLU 3.2 11.2 + - - +
54A THR* 1.3 77.9 - - - +
56A ARG* 1.3 67.2 + - + +
58A CYS* 3.3 20.9 + - - +
59A GLU* 3.6 8.4 + - - +
18B LEU* 4.5 20.2 - - + -
21B LEU* 6.0 2.0 - - + -
22B HIS* 4.8 23.5 + + - -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 4.3 2.8 + - - +
52A GLU* 3.0 46.8 + - - +
53A LEU* 3.4 43.9 - - - +
55A PHE* 1.3 82.0 - - + +
57A GLN* 1.3 62.4 + - - +
59A GLU* 3.2 25.8 - - - +
60A ASN* 3.6 11.0 + - - +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 2.8 17.0 + - - +
54A THR* 2.9 16.8 + - - +
56A ARG* 1.3 77.3 - - - +
58A CYS* 1.3 57.8 + - - +
60A ASN* 3.1 29.0 + - - +
61A PHE* 2.9 46.6 + - + -
45B PHE* 3.5 23.0 - - + -
78B LEU* 2.8 29.5 - - - +
81B PHE* 3.4 35.8 - - - +
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Residues in contact with CYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 2.6 25.8 + - - -
55A PHE* 3.4 13.0 - - - +
56A ARG 3.2 0.4 - - - -
57A GLN* 1.3 72.1 - - - +
59A GLU* 1.3 58.6 + - - +
61A PHE* 3.6 23.0 - - - +
62A ALA* 3.0 31.9 + - - +
18B LEU* 4.3 36.8 - - + -
19B LEU* 4.2 10.2 - - + +
22B HIS* 4.2 16.5 - - + +
42B LEU* 5.2 6.3 - - - -
----------------------------------------------------------
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.6 7.2 + - - +
56A ARG* 3.2 19.3 + - - +
58A CYS* 1.3 77.4 - - - +
60A ASN* 1.3 67.1 + - - +
62A ALA* 4.0 1.9 - - - +
63A LYS* 3.3 52.1 + - - +
22B HIS* 4.5 23.0 - - + +
----------------------------------------------------------
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG 3.6 14.6 + - - +
57A GLN* 3.1 38.3 + - - +
59A GLU* 1.3 80.6 - - - +
61A PHE* 1.3 62.6 + - + +
63A LYS* 5.2 3.3 + - - -
64A ASP* 3.1 34.4 + - - +
85A LEU* 5.5 0.2 - - - +
78B LEU* 5.0 3.0 - - - +
81B PHE 5.7 2.7 - - - +
----------------------------------------------------------
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.6 1.6 - - + -
57A GLN* 2.9 52.9 + - + -
58A CYS* 3.6 22.4 - - - +
60A ASN* 1.3 77.2 - - + +
62A ALA* 1.3 63.9 + - - +
64A ASP* 3.9 1.2 - - - +
65A LEU* 3.1 36.1 + - + +
85A LEU* 3.9 23.5 - - + +
19B LEU* 3.6 18.4 - - + -
38B MET* 4.8 11.0 - - + -
41B LEU* 5.6 8.7 - - + -
42B LEU* 3.4 33.4 - - + -
45B PHE* 4.2 14.6 - + + -
81B PHE* 4.9 9.0 - + + -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A CYS 3.0 16.6 + - - +
59A GLU 3.4 1.5 + - - +
61A PHE* 1.3 76.4 - - - +
63A LYS* 1.3 66.6 + - - +
65A LEU* 3.5 2.7 + - - +
66A GLU* 3.2 23.4 + - - +
19B LEU* 4.1 19.7 - - + +
22B HIS* 3.5 38.4 - - + -
23B PHE* 3.8 12.5 - - + +
----------------------------------------------------------
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.3 46.3 + - - +
60A ASN* 4.2 2.3 + - - +
62A ALA* 1.3 78.5 - - - +
64A ASP* 1.3 73.1 - - - +
66A GLU* 3.3 10.8 + - - +
67A MET* 3.1 39.8 + - + +
22B HIS 5.1 4.9 + - - +
----------------------------------------------------------
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASN* 3.1 25.2 - - - +
61A PHE 3.5 2.6 + - - +
62A ALA 3.3 0.4 - - - -
63A LYS* 1.3 83.8 - - - +
65A LEU* 1.3 64.2 - - - +
67A MET* 3.4 15.7 + - - +
68A PHE* 3.2 37.4 + - + -
85A LEU* 4.0 14.4 - - + +
87A ARG* 4.4 13.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 3.1 32.8 + - + +
62A ALA* 3.8 4.7 - - - +
64A ASP* 1.3 76.9 - - - +
66A GLU* 1.3 62.6 + - - +
68A PHE* 3.2 9.1 + - + +
69A ALA* 3.1 23.1 + - - +
77A ILE* 4.8 13.2 - - + +
81A ASP* 4.0 32.4 - - + +
82A VAL* 4.3 10.5 - - + +
85A LEU* 3.5 28.0 - - + -
19B LEU* 4.1 25.4 - - + -
23B PHE* 4.5 13.5 - - + -
38B MET* 5.3 6.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 3.2 12.5 + - - +
63A LYS* 3.3 14.0 + - - +
65A LEU* 1.3 76.0 - - - +
67A MET* 1.3 65.0 + - - +
69A ALA* 3.4 6.8 + - + +
70A ARG* 3.0 33.2 + - + +
77A ILE* 5.3 2.2 - - - -
23B PHE* 4.5 13.5 - - + -
24B LYS* 3.9 29.0 + - - +
25B ASP* 4.5 18.3 + - + +
28B THR* 5.0 10.1 - - - +
----------------------------------------------------------
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Residues in contact with MET 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.1 46.8 + - + +
64A ASP* 3.8 17.5 - - - +
65A LEU 3.3 0.4 - - - -
66A GLU* 1.3 85.3 - - - +
68A PHE* 1.3 61.1 + - + +
70A ARG* 4.1 8.9 - - - +
71A HIS* 3.3 22.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 3.2 22.4 + - + -
65A LEU* 3.2 10.5 + - - +
67A MET* 1.3 79.3 - - + +
69A ALA* 1.3 63.4 + - - +
70A ARG 3.4 0.4 - - - -
71A HIS* 3.4 28.5 + + + +
72A ALA* 3.5 6.9 + - - +
81A ASP* 3.6 41.6 - - + +
84A LEU* 4.6 30.5 - - + -
85A LEU* 3.6 27.1 - - + -
87A ARG* 5.0 10.8 - - - -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU 3.1 15.6 + - - +
66A GLU* 3.9 5.6 - - + +
68A PHE* 1.3 74.9 - - - +
70A ARG* 1.3 58.2 + - - +
72A ALA* 3.4 6.2 + - - +
74A ARG* 2.8 52.3 + - - +
75A THR* 4.9 3.8 - - - +
77A ILE* 3.9 26.5 - - + -
81A ASP* 3.8 10.5 + - - +
28B THR* 5.9 1.6 - - - +
----------------------------------------------------------
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 3.0 22.9 + - + +
67A MET* 4.2 7.6 - - - +
69A ALA* 1.3 72.8 - - - +
71A HIS* 1.3 62.5 + - - +
72A ALA 3.2 2.3 + - - -
73A LYS* 3.7 21.5 + - - +
74A ARG 3.8 16.3 + - - +
75A THR* 4.4 15.0 - - - +
25B ASP* 5.4 2.4 + - - -
----------------------------------------------------------
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET 3.3 17.2 + - - +
68A PHE* 3.4 19.9 + + + +
70A ARG* 1.3 75.2 - - - +
72A ALA* 1.3 67.1 + - + +
73A LYS* 3.5 8.4 + - - +
81A ASP* 5.9 0.7 - - - -
----------------------------------------------------------
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE 3.5 6.7 + - - +
69A ALA 3.4 2.0 + - - +
70A ARG 3.2 1.0 - - - -
71A HIS* 1.3 85.8 - - + +
73A LYS* 1.3 82.0 + - - +
74A ARG* 3.3 42.2 + - - +
81A ASP* 5.4 0.4 - - - +
----------------------------------------------------------
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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