Contacts of the helix formed by residues 48 - 82 (chain A) in PDB entry 3NRX
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 ASN 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 1.3 58.6 + - - +
50A LEU 3.4 1.6 - - - -
51A LYS* 3.6 40.2 - - - +
52A GLU* 2.8 50.4 + - + +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 5.6 13.7 - - + +
42A PHE* 6.5 0.9 - - + -
48A ASN* 1.3 77.9 - - - +
50A LEU* 1.3 68.2 + - + +
52A GLU* 3.8 6.3 - - + +
53A GLU* 2.9 51.7 + - + +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 1.3 85.9 - - + +
51A LYS* 1.3 60.8 + - - +
53A GLU* 4.2 5.6 - - + +
54A LYS* 2.9 63.5 + - + +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 3.4 33.2 + - - +
49A LEU 3.3 0.4 - - - -
50A LEU* 1.3 77.5 - - + +
52A GLU* 1.3 56.8 + - - +
54A LYS* 3.7 5.2 - - - +
55A GLN* 2.7 60.5 + - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 4.0 18.9 - - + +
35A LYS* 3.1 54.3 + - + +
36A ALA* 5.1 0.3 + - - -
41A ARG* 5.9 1.7 - - - +
48A ASN* 2.8 36.4 + - + +
49A LEU* 4.0 6.4 - - + +
51A LYS* 1.3 74.8 - - - +
53A GLU* 1.3 61.8 + - + +
55A GLN* 3.8 7.7 - - - +
56A ARG* 2.9 31.9 + - - +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 4.7 10.9 - - - +
41A ARG* 5.7 2.4 + - - -
49A LEU* 2.9 37.0 + - + +
50A LEU* 4.2 6.3 - - + +
52A GLU* 1.3 76.8 - - + +
54A LYS* 1.3 60.3 + - + +
56A ARG* 2.8 38.5 + - - +
57A ALA* 2.8 32.2 + - - +
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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
----------------------------------------------------------
50A LEU* 2.9 52.5 + - + +
51A LYS* 3.8 4.7 - - - +
53A GLU* 1.3 76.9 - - + +
55A GLN* 1.3 63.1 + - + +
57A ALA* 3.4 6.3 + - - +
58A LYS* 3.1 38.8 + - - +
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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
----------------------------------------------------------
32A PHE* 3.5 38.8 - - + -
51A LYS* 2.7 52.8 + - + +
52A GLU* 3.9 3.5 - - - +
54A LYS* 1.3 73.6 - - + +
56A ARG* 1.3 60.8 + - - +
58A LYS* 3.6 12.5 + - + +
59A LEU* 3.3 30.0 + - + +
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.8 5.0 - - + -
32A PHE* 3.1 43.0 - - + -
33A GLU* 3.2 29.3 + - + +
36A ALA* 3.7 17.6 - - - +
52A GLU 2.9 18.7 + - - +
53A GLU* 2.8 32.5 + - - +
55A GLN* 1.3 74.5 - - - +
57A ALA* 1.3 61.3 + - - +
59A LEU* 3.3 6.2 + - - +
60A GLN* 3.0 53.3 + - + +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU 2.8 17.9 + - - +
54A LYS* 3.7 6.7 - - - +
55A GLN 3.4 0.2 - - - -
56A ARG* 1.3 75.2 - - - +
58A LYS* 1.3 64.2 + - - +
60A GLN* 3.4 19.1 - - - +
61A LYS* 3.2 22.5 + - - +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 3.1 30.4 + - - +
55A GLN* 3.9 13.0 - - + +
56A ARG 3.3 0.2 - - - -
57A ALA* 1.3 75.1 - - + +
59A LEU* 1.3 59.8 + - + +
61A LYS* 3.3 7.6 + - - +
62A MET* 3.0 35.6 + - + +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 3.6 26.6 - - + +
28A LEU* 3.8 37.0 - - + -
29A PHE* 3.8 15.7 - - + +
32A PHE* 3.5 31.0 - - + -
55A GLN* 3.3 17.9 + - + +
56A ARG* 3.3 8.4 + - - +
57A ALA 3.3 0.4 - - - -
58A LYS* 1.3 75.2 - - + +
60A GLN* 1.3 62.3 - - - +
62A MET* 3.9 13.4 - - + +
63A LEU* 3.1 34.0 + - - +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.0 21.2 - - + -
33A GLU* 4.5 3.6 + - - -
56A ARG* 3.0 48.1 + - - +
57A ALA* 3.4 22.1 - - - +
59A LEU* 1.3 76.6 - - - +
61A LYS* 1.3 56.7 + - - +
63A LEU* 4.7 2.0 - - - +
64A PRO* 3.0 24.9 - - - +
100A TRP* 6.3 1.1 - - - -
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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
----------------------------------------------------------
57A ALA 3.2 9.6 + - - +
58A LYS* 3.6 10.8 - - - +
59A LEU 3.2 0.2 - - - -
60A GLN* 1.3 78.8 - - - +
62A MET* 1.3 63.1 + - - +
64A PRO* 3.3 16.3 - - - +
65A LYS* 3.5 37.0 - - + +
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Residues in contact with MET 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 5.9 2.7 - - - -
25A THR* 4.1 28.5 - - + -
58A LYS* 3.0 22.5 + - + +
59A LEU* 3.3 13.4 + - + +
61A LYS* 1.3 75.8 - - - +
63A LEU* 1.3 65.6 + - - +
65A LYS* 3.0 19.8 + - + +
66A LEU* 2.9 39.5 + - + +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TRP* 3.5 30.5 - - + +
25A THR* 3.9 21.3 - - + +
26A TRP* 4.0 17.0 - - + +
29A PHE* 3.6 37.2 - - + -
59A LEU 3.1 20.1 + - - +
60A GLN* 4.7 1.3 - - - +
62A MET* 1.3 75.4 - - - +
64A PRO* 1.3 70.2 - - + +
66A LEU* 3.4 5.7 + - + +
67A GLU* 2.9 32.7 + - - +
100A TRP* 3.7 28.5 - - + -
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Residues in contact with PRO 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN 3.0 26.2 - - - +
61A LYS* 3.3 13.2 - - - +
63A LEU* 1.3 89.1 - - + +
65A LYS* 1.3 58.3 + - + +
67A GLU* 3.3 8.1 + - + +
68A GLU* 3.0 30.7 + - - +
100A TRP* 5.7 3.6 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 3.5 45.5 - - + +
62A MET* 3.0 19.4 + - + +
64A PRO* 1.3 76.8 - - + +
66A LEU* 1.3 66.0 + - - +
68A GLU* 4.1 3.9 - - - +
69A GLU* 3.2 24.1 + - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY* 5.9 2.0 - - - +
21A LYS* 4.1 24.9 - - + +
22A TRP* 4.1 22.0 - - + -
25A THR* 3.6 33.7 - - + +
62A MET* 2.9 33.3 + - + +
63A LEU* 3.7 8.5 - - + +
65A LYS* 1.3 75.9 - - - +
67A GLU* 1.3 58.8 + - - +
69A GLU* 3.5 17.5 + - - +
70A LEU* 2.9 36.7 + - + +
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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
----------------------------------------------------------
22A TRP* 3.0 28.3 + - + +
63A LEU* 2.9 23.4 + - - +
64A PRO* 3.7 6.8 - - + +
66A LEU* 1.3 74.1 - - - +
68A GLU* 1.3 60.8 + - - +
70A LEU* 3.3 5.0 + - + -
71A LYS* 2.9 30.7 + - - +
93A MET* 3.6 17.9 - - + +
96A VAL* 3.4 21.1 - - + +
100A TRP* 2.7 34.0 + - - -
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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
----------------------------------------------------------
64A PRO 3.0 16.9 + - - +
65A LYS* 4.2 4.7 - - - +
67A GLU* 1.3 75.9 - - - +
69A GLU* 1.3 63.4 + - - +
71A LYS* 3.5 20.3 + - - +
72A ALA* 3.1 27.9 + - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS 3.2 18.4 + - - +
66A LEU* 3.6 19.3 - - - +
68A GLU* 1.3 77.6 - - - +
70A LEU* 1.3 64.9 + - + +
72A ALA* 3.3 8.6 + - - +
73A ARG* 3.1 67.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.8 32.3 - - + +
18A GLY* 3.5 32.8 - - - +
19A VAL* 4.0 4.9 - - + +
22A TRP* 4.0 12.6 - - + -
66A LEU* 2.9 23.4 + - + +
67A GLU* 3.3 5.1 + - + +
69A GLU* 1.3 79.4 - - + +
71A LYS* 1.3 57.2 - - - +
73A ARG* 3.2 10.0 + - + +
74A ILE* 2.9 44.7 + - + +
92A PHE* 3.9 22.0 - - + -
93A MET* 4.3 9.0 - - - -
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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
----------------------------------------------------------
67A GLU 2.9 17.3 + - - +
68A GLU* 3.9 20.5 + - - +
70A LEU* 1.3 74.1 - - - +
72A ALA* 1.3 57.6 + - - +
74A ILE* 3.2 3.6 + - + +
75A GLU* 2.9 67.0 + - + +
93A MET* 4.1 30.4 - - + -
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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
----------------------------------------------------------
68A GLU* 3.1 22.7 + - - +
69A GLU* 3.3 12.3 - - - +
71A LYS* 1.3 77.1 - - - +
73A ARG* 1.3 63.5 + - + +
75A GLU* 4.1 5.7 - - - +
76A LEU* 3.3 34.4 + - + +
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 5.8 0.7 - - - +
14A GLU* 3.7 33.8 + - - +
15A LEU* 3.6 21.4 - - + +
18A GLY* 6.0 4.2 - - - -
69A GLU* 3.1 55.2 + - + +
70A LEU* 3.8 10.6 - - + +
72A ALA* 1.3 76.0 - - + +
74A ILE* 1.3 65.4 + - - +
76A LEU* 3.6 9.5 + - + +
77A TRP* 3.0 24.1 + - - +
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.2 11.9 - - + -
70A LEU* 2.9 27.1 + - + +
71A LYS* 3.7 3.8 - - + +
73A ARG* 1.3 74.9 - - - +
75A GLU* 1.3 62.3 + - + +
77A TRP* 3.0 4.8 + - - +
78A GLU* 2.8 43.3 + - - +
85A PHE* 3.5 54.1 - - + +
91A LYS* 6.0 0.4 - - - -
92A PHE* 4.2 10.5 - - + -
93A MET* 4.0 31.6 - - + -
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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
----------------------------------------------------------
71A LYS* 2.9 56.8 + - + +
72A ALA* 4.1 5.8 - - - +
74A ILE* 1.3 72.9 - - + +
76A LEU* 1.3 63.6 + - + +
78A GLU* 3.4 13.1 + - - +
79A GLN* 3.0 46.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 3.3 24.1 + - + +
73A ARG* 3.8 8.3 - - + +
74A ILE 3.3 0.6 - - - -
75A GLU* 1.3 78.0 - - + +
77A TRP* 1.3 62.4 + - - +
79A GLN* 3.3 19.3 + - - +
80A GLU* 3.0 24.0 + - - +
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Residues in contact with TRP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.5 30.2 - - + +
12A HIS* 3.4 57.5 - + + +
15A LEU* 3.6 17.5 - - + -
73A ARG 3.0 18.5 + - - +
74A ILE 3.4 2.9 - - - +
76A LEU* 1.3 75.9 - - - +
78A GLU* 1.3 62.9 + - - +
80A GLU* 3.2 4.4 + - - -
81A HIS* 2.9 71.4 + + + +
83A LYS* 4.1 22.7 - - + -
84A ALA 4.0 7.6 - - - -
85A PHE* 3.9 34.5 - - + -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 2.8 36.7 + - + +
75A GLU* 3.8 13.0 - - - +
77A TRP* 1.3 74.9 - - + +
79A GLN* 1.3 55.9 + - + +
82A SER* 2.7 35.0 + - - -
83A LYS 3.2 21.5 + - - +
84A ALA* 3.3 0.6 - - - -
85A PHE* 2.7 32.8 + - + +
91A LYS* 3.0 33.0 + - - -
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Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 3.0 46.4 + - - +
76A LEU* 3.5 25.6 - - - +
78A GLU* 1.3 79.5 - - + +
80A GLU* 1.3 61.9 + - - +
82A SER* 3.8 9.0 + - - -
----------------------------------------------------------
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 2.6 44.7 + - + +
76A LEU 3.0 17.4 + - - +
77A TRP* 3.6 5.6 - - - +
79A GLN* 1.3 78.4 - - - +
81A HIS* 1.3 69.4 - - + +
82A SER* 3.7 4.5 + - - -
----------------------------------------------------------
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Residues in contact with HIS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.5 47.0 + + - -
9A TYR* 4.7 12.3 - + - -
11A VAL* 5.2 1.4 - - - +
77A TRP* 2.9 64.9 + + + +
80A GLU* 1.3 84.5 - - + +
82A SER* 1.3 72.2 + - - +
83A LYS* 3.2 36.4 + - + +
----------------------------------------------------------
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU 2.7 19.0 + - - -
79A GLN* 3.8 6.6 + - - +
80A GLU 3.5 7.2 + - - -
81A HIS* 1.3 77.1 - - - +
83A LYS* 1.3 57.9 + - - +
----------------------------------------------------------
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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