Contacts of the helix formed by residues 56 - 87 (chain A) in PDB entry 4WB7
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 ASP 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP 3.9 15.0 + - - +
53A VAL 3.2 4.1 + - - +
54A LEU 3.2 0.8 - - - -
55A SER* 1.3 81.4 + - - +
57A PRO* 1.3 67.7 - - - +
58A ARG* 3.3 16.5 + - - +
59A LYS* 3.0 44.7 + - + +
60A ARG* 2.8 29.5 + - - +
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 5.4 10.3 - - - +
55A SER 3.7 7.8 - - - +
56A ASP* 1.3 89.6 - - - +
58A ARG* 1.3 62.6 + - - +
60A ARG* 3.8 8.7 - - + +
61A GLU* 3.0 26.0 + - - +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 3.3 13.9 + - - +
57A PRO* 1.3 78.4 - - - +
59A LYS* 1.3 64.9 + - + +
61A GLU* 3.3 11.5 + - - +
62A ILE* 3.1 30.7 + - + +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.3 27.6 + - - +
53A VAL* 3.7 29.5 - - + +
56A ASP* 3.0 28.5 + - - +
58A ARG* 1.3 77.1 - - + +
60A ARG* 1.3 58.9 + - - +
62A ILE* 3.3 16.0 + - + +
63A PHE* 2.9 27.5 + - - +
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 2.9 27.2 + - - +
12A ARG 2.9 25.5 + - - -
13A GLY* 3.8 2.4 - - - -
14A ALA 2.8 33.7 + - - +
16A ASP* 4.1 12.1 + - - -
19A ILE* 3.5 19.0 - - - +
53A VAL* 3.4 13.6 + - - +
54A LEU* 3.6 21.1 + - + +
56A ASP 2.8 17.5 + - - +
57A PRO* 3.8 8.1 - - - +
59A LYS* 1.3 76.6 - - - +
61A GLU* 1.3 58.8 + - - +
63A PHE* 3.2 6.8 + - - +
64A ASP* 2.8 36.6 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 3.0 18.9 + - - +
58A ARG* 3.5 10.5 - - - +
60A ARG* 1.3 78.9 - - - +
62A ILE* 1.3 62.6 + - + +
64A ASP* 3.4 8.3 + - - +
65A ARG* 2.6 67.9 + - + +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.1 19.8 + - + +
59A LYS* 3.5 15.0 - - + +
61A GLU* 1.3 77.5 - - + +
63A PHE* 1.3 58.0 + - - +
65A ARG* 3.4 8.2 + - - +
66A TYR* 2.9 30.3 + - + +
69A GLU* 5.2 0.3 - - - +
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Residues in contact with PHE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 3.3 28.7 - - + -
3A ASP* 4.7 2.0 - - - -
4A TYR* 3.5 43.7 - + + -
5A TYR* 3.8 28.9 - + - -
53A VAL* 3.9 11.0 - - + -
54A LEU* 4.1 7.9 - - + -
59A LYS 2.9 16.1 + - - +
60A ARG 3.6 3.4 - - - +
62A ILE* 1.3 76.4 - - - +
64A ASP* 1.3 75.6 + - - +
66A TYR* 3.3 21.6 + + - +
67A GLY* 3.0 20.7 + - - -
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 2.7 38.4 + - - -
12A ARG* 3.6 33.6 + - - +
60A ARG* 2.8 33.0 + - - +
61A GLU* 3.8 7.6 - - + +
63A PHE* 1.3 76.1 - - - +
65A ARG* 1.3 64.2 + - + +
67A GLY* 3.1 12.2 + - - -
68A GLU* 3.2 15.8 + - - +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 2.6 55.1 + - + +
62A ILE* 3.8 7.0 - - - +
64A ASP* 1.3 75.0 - - + +
66A TYR* 1.3 58.3 + - - +
68A GLU* 3.0 13.3 + - - +
69A GLU* 2.8 40.6 + - + +
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY* 4.3 23.7 + - - -
62A ILE* 2.9 20.7 + - + +
63A PHE* 3.3 22.9 + + + +
65A ARG* 1.3 75.0 - - - +
67A GLY* 1.3 66.0 + - - +
69A GLU* 3.2 26.5 + - + +
70A VAL* 3.0 47.9 + - + +
358A ILE* 4.3 24.7 - - + +
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 3.0 15.5 + - - -
64A ASP* 3.1 5.8 + - - -
66A TYR* 1.3 81.1 - - - +
68A GLU* 1.3 64.0 + - - +
70A VAL* 3.5 6.7 + - - +
71A LYS* 3.2 27.1 + - - +
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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
----------------------------------------------------------
12A ARG* 3.8 22.5 + - - +
64A ASP 3.2 11.6 + - - +
65A ARG* 3.0 13.6 + - - +
67A GLY* 1.3 75.6 - - - +
69A GLU* 1.3 64.9 + - + +
71A LYS* 3.3 31.8 + - - +
72A GLU* 3.0 24.1 + - - +
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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
----------------------------------------------------------
62A ILE 5.2 0.3 - - - +
65A ARG* 2.8 27.3 + - + +
66A TYR* 3.5 35.1 + - + +
68A GLU* 1.3 72.2 - - - +
70A VAL* 1.3 58.3 + - + +
72A GLU* 3.2 6.7 + - - +
73A PHE* 2.9 30.2 + - - +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.0 54.9 + - + +
67A GLY* 3.8 7.2 - - - +
68A GLU 3.2 0.2 - - - -
69A GLU* 1.3 76.1 - - + +
71A LYS* 1.3 60.9 + - + +
73A PHE* 3.3 7.2 + - + +
74A LEU* 2.9 29.6 + - + +
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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 GLY 3.2 15.7 + - - +
68A GLU* 3.6 32.8 + - - +
69A GLU 3.3 0.2 - - - -
70A VAL* 1.3 80.2 - - + +
72A GLU* 1.3 58.3 + - - +
74A LEU* 3.4 12.0 + - + +
75A ALA* 3.0 27.4 + - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLU 3.0 16.8 + - - +
69A GLU* 3.7 7.2 - - - +
71A LYS* 1.3 74.8 - - - +
73A PHE* 1.3 64.5 + - - +
75A ALA* 3.2 12.5 + - - +
76A LYS* 3.0 58.1 + - - +
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU 2.9 16.9 + - - +
70A VAL* 3.6 7.9 - - - +
72A GLU* 1.3 77.6 - - - +
74A LEU* 1.3 57.6 + - - +
76A LYS* 3.3 14.0 + - + +
77A ALA* 3.0 31.5 + - + +
155A PHE* 6.0 4.0 - + - -
361A TYR* 3.5 32.1 - + - -
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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 VAL* 2.9 19.1 + - + +
71A LYS* 3.7 11.2 - - + +
73A PHE* 1.3 75.5 - - - +
75A ALA* 1.3 61.9 + - - +
77A ALA* 3.1 9.0 + - + +
78A LYS* 2.8 58.9 + - + +
214A SER* 3.5 36.6 - - - +
215A LEU* 5.2 0.9 - - + -
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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
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71A LYS 3.0 15.1 + - - +
72A GLU* 3.2 21.3 + - - +
74A LEU* 1.3 77.8 - - - +
76A LYS* 1.3 57.8 + - - +
78A LYS* 3.5 8.2 + - - +
79A GLU* 3.0 28.2 + - - +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 3.0 45.5 + - + +
73A PHE* 3.7 16.4 - - + +
74A LEU 3.3 0.2 - - - -
75A ALA* 1.3 75.3 - - - +
77A ALA* 1.3 56.9 + - - +
79A GLU* 3.3 7.8 + - - +
80A ASP* 3.0 30.3 + - - +
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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
----------------------------------------------------------
73A PHE* 3.0 22.7 + - + +
74A LEU* 3.1 13.0 + - + +
76A LYS* 1.3 77.5 - - - +
78A LYS* 1.3 61.5 + - - +
80A ASP* 3.4 5.4 + - - +
81A PHE* 3.0 24.1 + - - +
211A TYR* 4.3 26.0 + - + +
214A SER* 5.9 0.7 - - - +
215A LEU* 3.9 8.0 - - + +
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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* 2.8 41.8 + - + +
75A ALA* 3.9 7.4 - - - +
77A ALA* 1.3 75.7 - - - +
79A GLU* 1.3 57.4 + - - +
81A PHE* 3.4 1.2 + - - +
82A LEU* 2.9 45.3 + - + +
214A SER 3.7 18.8 - - - +
215A LEU* 3.7 23.1 - - + -
216A ASP* 5.9 1.8 - - - -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 3.0 17.6 + - - +
76A LYS* 3.6 8.3 - - - +
77A ALA 3.3 0.2 - - - -
78A LYS* 1.3 77.8 - - - +
80A ASP* 1.3 64.5 + - - +
82A LEU* 4.0 4.4 - - - +
83A LYS* 2.5 67.8 + - - +
504A ZN 2.1 36.9 - - - -
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS 3.0 17.4 + - - +
77A ALA* 3.9 5.8 - - - +
78A LYS 3.3 0.2 - - - -
79A GLU* 1.3 86.0 + - - +
81A PHE* 1.3 63.1 + - - +
83A LYS* 3.6 1.4 + - - +
84A LYS* 2.9 64.4 + - - +
152A ALA 4.4 2.3 - - - +
154A ASN* 4.2 17.3 + - - +
504A ZN 3.6 15.1 - - - -
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 3.0 17.8 + - - +
78A LYS 3.8 2.5 - - - +
80A ASP* 1.3 77.6 + - - +
82A LEU* 1.3 69.3 + - + +
84A LYS* 3.2 3.5 + - - +
85A TRP* 2.8 63.6 + + + +
149A ILE* 4.5 4.3 - - + -
152A ALA* 3.5 40.6 - - + +
153A VAL* 4.0 11.4 - - + -
211A TYR* 5.1 0.9 - - - +
215A LEU* 4.0 31.0 - - + -
217A LEU* 3.9 30.3 - - + -
245A ARG* 3.8 23.8 - - - -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 2.9 33.0 + - + +
79A GLU* 4.0 4.3 - - - +
81A PHE* 1.3 86.0 - - + +
83A LYS* 1.3 62.4 + - + +
85A TRP* 4.2 8.3 - - + -
86A GLU* 2.8 57.4 + - - +
245A ARG* 3.8 27.4 - - - +
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 2.5 65.2 + - + +
80A ASP* 4.0 4.9 - - - +
82A LEU* 1.3 77.0 - - + +
84A LYS* 1.3 63.8 + - + +
86A GLU* 4.1 6.4 - - - +
87A SER* 3.2 25.3 + - - +
504A ZN 4.7 0.9 - - - -
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 2.9 42.1 + - - +
81A PHE 3.2 1.4 + - - -
83A LYS* 1.3 78.9 - - + +
85A TRP* 1.3 61.8 + - - +
87A SER 4.6 3.1 - - - -
88A PRO* 3.4 25.8 - - - +
89A ALA 4.8 0.7 + - - -
148A ARG 5.1 1.4 - - - +
151A GLN* 3.7 19.4 + - + +
152A ALA* 3.6 33.6 + - + +
153A VAL 4.9 2.4 + - - -
154A ASN* 4.4 14.6 - - - +
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Residues in contact with TRP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 2.8 46.3 + + + +
82A LEU* 3.9 10.3 - - + +
84A LYS* 1.3 78.0 - - - +
86A GLU* 1.3 75.9 + - + +
88A PRO* 3.5 5.7 - - - +
145A ASN* 4.9 10.3 - - - -
148A ARG* 2.9 90.7 + - + +
149A ILE* 3.5 30.7 - - + -
152A ALA* 3.9 4.9 - - + +
245A ARG* 3.7 42.9 - - + +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 2.8 43.6 + - - +
83A LYS* 4.3 6.0 + - - +
85A TRP* 1.3 92.6 - - + +
87A SER* 1.3 62.6 + - - +
88A PRO* 3.7 4.6 - - - +
148A ARG* 4.3 6.6 + - - +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS 3.2 15.2 + - - +
84A LYS* 3.6 6.9 - - - +
86A GLU* 1.3 84.0 + - - +
88A PRO* 1.3 67.3 - - - +
89A ALA 3.5 1.2 + - - -
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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