Contacts of the helix formed by residues 55 - 83 (chain A) in PDB entry 2ITB
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 HIS 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.2 31.8 + + + +
53A ASN 3.7 0.4 - - - -
54A THR* 1.3 84.9 + - - +
56A LEU* 1.3 64.4 + - - +
57A ASP 3.5 2.0 - - - -
58A LEU* 3.3 10.7 + - + -
59A ILE* 3.1 24.6 + - - +
111A LEU* 3.5 18.9 - - + +
165A TYR* 3.3 41.5 - + - +
505A EDO 2.7 33.8 + - - -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR 3.2 5.8 + - - +
55A HIS* 1.3 71.5 - - - +
57A ASP* 1.3 69.1 + - - +
59A ILE* 3.1 5.4 + - + +
60A ASN* 3.0 41.8 + - - +
165A TYR* 4.1 1.2 + - - -
77B LEU* 4.6 20.0 - - + +
81B LYS* 5.0 23.6 - - + -
87B LEU* 3.8 28.5 - - + -
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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
----------------------------------------------------------
56A LEU* 1.3 82.3 - - - +
58A LEU* 1.3 57.4 + - - +
60A ASN* 3.5 7.6 + - - +
61A MSE 3.0 31.1 + - + +
161A LEU* 3.9 13.7 - - + +
164A ASN* 3.4 24.6 + - - +
165A TYR* 3.5 12.0 + - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.8 27.8 - - + +
49A ILE* 4.2 0.9 - - - -
52A TYR* 3.9 20.9 - - + +
55A HIS* 3.6 15.5 - - + +
56A LEU 3.3 0.4 - - - -
57A ASP* 1.3 73.4 - - - +
59A ILE* 1.3 75.8 + - + +
61A MSE 3.3 0.5 + - - -
62A MSE 2.8 52.9 + - + +
111A LEU* 3.9 30.7 - - + -
115A LEU* 4.5 11.7 - - + -
161A LEU* 3.9 15.7 - - + +
165A TYR* 3.2 17.1 + - + +
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.8 19.6 - - + +
52A TYR 3.8 9.4 - - - +
53A ASN 3.6 31.4 - - - +
55A HIS 3.1 15.9 + - - +
56A LEU* 3.1 6.5 + - + +
58A LEU* 1.3 82.9 - - + +
60A ASN* 1.3 58.7 + - - +
62A MSE 3.3 0.2 + - - -
63A SER* 2.8 30.0 + - - -
73B HIS* 3.6 27.6 - - + -
77B LEU* 3.7 14.4 - - + -
87B LEU* 3.8 17.9 - - + -
513B EDO 3.8 16.4 - - - +
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.0 40.3 + - - +
57A ASP* 4.0 6.7 + - - +
59A ILE* 1.3 75.5 - - - +
61A MSE 1.3 62.7 + - - +
63A SER* 3.5 4.9 + - - -
64A ARG* 3.3 31.2 + - - +
74B GLU* 4.5 11.9 - - - +
77B LEU* 3.3 27.4 - - - +
78B ARG* 5.6 4.0 - - - +
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Residues in contact with MSE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP 3.0 17.4 + - - +
58A LEU 3.8 2.5 - - - +
60A ASN* 1.3 78.7 - - - +
62A MSE 1.3 61.7 + - + +
64A ARG* 3.4 9.1 + - + +
65A LEU* 2.9 35.8 + - + +
157A GLY* 3.3 44.9 - - - +
158A TYR* 4.3 1.8 - - - -
160A LYS* 5.0 10.3 - - + -
161A LEU* 3.6 27.8 - - + -
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Residues in contact with MSE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 5.5 0.4 - - + -
45A ALA* 3.0 45.6 - - + +
48A LEU* 3.2 28.7 - - + -
49A ILE* 3.6 21.7 - - + +
58A LEU* 2.8 44.2 + - + +
61A MSE 1.3 72.2 - - - +
63A SER* 1.3 66.0 + - - +
65A LEU* 4.2 8.1 - - - -
66A ALA* 2.9 26.3 + - - +
115A LEU* 5.5 0.4 - - - -
158A TYR* 4.1 29.6 - - - +
161A LEU* 4.8 8.3 - - + -
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.7 7.5 - - - +
59A ILE 2.8 18.6 + - - -
60A ASN* 3.8 2.7 - - - -
62A MSE 1.3 78.6 - - - +
64A ARG* 1.3 61.5 + - - +
66A ALA* 3.4 4.9 + - - +
67A ARG* 3.2 22.2 + - - +
70B LEU* 3.5 16.1 + - - +
73B HIS* 3.2 28.0 + - - -
74B GLU* 2.7 34.7 + - - +
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASN* 3.3 17.3 + - - +
61A MSE 3.7 9.2 - - + +
63A SER* 1.3 74.9 - - - +
65A LEU* 1.3 66.0 + - - +
67A ARG* 3.3 18.3 + - - +
68A GLU* 3.0 35.2 + - - +
74B GLU* 3.5 19.3 - - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA 4.3 2.5 - - - +
45A ALA* 3.9 18.8 - - + -
61A MSE 2.9 26.8 + - + +
62A MSE 3.9 9.2 - - - +
64A ARG* 1.3 75.7 - - - +
66A ALA* 1.3 54.6 + - - +
68A GLU* 3.0 10.1 + - - +
69A GLU* 2.7 62.4 + - + +
122A GLU* 4.1 1.1 - - - +
154A HIS* 3.7 35.0 - - + +
158A TYR* 3.8 37.7 - - + +
510A EDO 4.2 2.0 - - - +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 3.9 19.4 - - + +
45A ALA* 3.9 9.6 - - + -
46A LEU* 3.9 25.6 - - + -
62A MSE 2.9 18.4 + - - +
63A SER 3.6 4.3 - - - +
65A LEU* 1.3 78.8 - - - +
67A ARG* 1.3 60.8 + - - +
69A GLU* 3.3 2.3 + - - +
70A LEU* 3.0 30.8 + - + +
70B LEU* 3.9 6.7 - - + -
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 3.2 8.4 + - - +
64A ARG* 3.6 23.9 + - - +
65A LEU 3.2 0.4 - - - -
66A ALA* 1.3 74.4 - - - +
68A GLU* 1.3 65.5 + - + +
70A LEU* 3.2 2.2 + - - -
71A VAL* 3.1 20.2 + - - +
67B ARG* 3.3 37.1 + - + +
70B LEU* 3.5 27.6 - - + -
71B VAL* 3.5 25.0 - - - +
74B GLU* 2.7 45.4 + - - -
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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 ARG* 3.0 27.5 + - - +
65A LEU* 3.5 7.9 - - - +
67A ARG* 1.3 77.7 - - + +
69A GLU* 1.3 61.6 + - - +
71A VAL* 3.1 12.2 + - - +
72A HIS* 3.1 29.7 + - + +
150A SER* 5.2 4.2 - - - -
153A ARG* 5.6 1.9 - - - +
154A HIS* 2.6 40.1 + - + +
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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
----------------------------------------------------------
38A GLU* 3.0 23.6 - - - +
41A ALA* 3.7 17.5 - - + +
42A ALA* 4.0 8.7 - - + +
65A LEU* 2.7 39.9 + - + +
66A ALA* 3.8 4.3 - - - +
68A GLU* 1.3 73.3 - - - +
70A LEU* 1.3 57.9 + - - +
72A HIS* 3.0 6.4 + - - +
73A HIS* 2.9 26.9 + - - +
122A GLU* 3.1 8.0 - - - +
154A HIS* 3.2 9.6 + - - -
501A FE 2.1 28.2 - - - -
502A FE 2.2 26.0 - - - -
503A PER 3.4 1.6 + - - -
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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
----------------------------------------------------------
39A PHE* 4.7 8.1 - - + -
42A ALA* 3.9 15.7 - - + -
66A ALA* 3.0 23.7 + - + +
69A GLU* 1.3 74.5 - - - +
71A VAL* 1.3 65.3 + - - +
73A HIS* 3.2 14.4 - - + +
74A GLU* 2.9 30.2 + - - +
46B LEU* 3.7 24.7 - - + -
49B ILE* 5.0 0.9 - - + -
63B SER* 3.6 18.6 + - - +
66B ALA* 3.7 23.6 - - + -
67B ARG* 3.5 32.5 - - + +
70B LEU* 4.3 9.0 - - + -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG 3.1 16.1 + - - +
68A GLU* 3.4 11.7 - - + +
70A LEU* 1.3 74.9 - - - +
72A HIS* 1.3 61.2 + - + +
74A GLU* 3.2 12.0 + - + +
75A GLN* 2.8 52.5 + - + +
67B ARG* 3.7 24.5 - - - +
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Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 3.2 22.8 + - - +
68A GLU* 3.1 16.1 + - + +
69A GLU* 3.0 9.4 + - - +
71A VAL* 1.3 80.8 - - + +
73A HIS* 1.3 52.7 + - - +
75A GLN* 3.0 17.8 + - - +
76A VAL* 2.9 37.2 + - - +
143A PHE* 4.6 0.9 - - - -
147A LEU* 3.4 26.9 - - + +
150A SER* 3.6 31.6 + - - -
151A GLU* 3.7 7.4 + - - -
154A HIS* 4.0 11.9 - + - -
501A FE 2.5 25.5 - - - -
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Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 3.7 28.7 - - + +
38A GLU* 3.7 14.6 - - + +
39A PHE* 3.8 13.9 - + + +
69A GLU 2.9 11.6 + - - +
70A LEU* 3.2 16.6 - - + +
72A HIS* 1.3 73.0 - - - +
74A GLU* 1.3 56.2 + - - +
76A VAL* 3.1 6.9 + - - +
77A LEU* 3.0 50.1 + - + +
508A EDO 2.6 36.6 + - - -
49B ILE* 4.4 15.0 - - + -
59B ILE* 4.8 4.5 - - + -
63B SER* 3.4 28.0 + - - -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU 2.9 11.4 + - - +
71A VAL* 3.5 9.3 - - + +
73A HIS* 1.3 76.0 - - - +
75A GLN* 1.3 58.5 + - - +
77A LEU* 3.4 10.7 + - + +
78A ARG* 3.0 37.9 + - - +
60B ASN* 4.9 3.3 - - - +
63B SER* 2.6 44.1 + - - +
64B ARG* 3.3 34.1 + - - +
67B ARG* 2.8 44.4 + - - -
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 2.8 32.2 + - + +
72A HIS* 3.0 31.0 + - - +
74A GLU* 1.3 73.4 - - - +
76A VAL* 1.3 61.8 + - - +
78A ARG* 3.4 24.1 + - - +
79A LEU* 3.2 22.3 + - - +
143A PHE* 3.6 30.8 - - + -
147A LEU* 4.4 1.9 - - - +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.5 38.1 - - + +
34A HIS* 3.7 35.2 - - + +
35A LYS* 3.6 22.0 - - + -
38A GLU* 4.5 1.6 - - + +
72A HIS 2.9 19.3 + - - +
73A HIS 3.1 6.3 + - - +
75A GLN* 1.3 73.4 - - - +
77A LEU* 1.3 60.6 + - - +
79A LEU* 3.1 7.1 + - - +
80A MSE 2.8 32.4 + - - +
143A PHE* 4.1 10.3 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 3.5 28.3 - - + -
73A HIS* 3.0 51.3 + - + +
74A GLU* 3.7 7.9 - - + +
76A VAL* 1.3 75.2 - - - +
78A ARG* 1.3 57.4 + - - +
80A MSE 3.3 10.7 + - + +
81A LYS* 2.9 29.8 + - - +
87A LEU* 3.8 21.1 - - + -
56B LEU* 4.6 11.7 - - + +
59B ILE* 4.0 17.5 - - + -
60B ASN* 4.2 21.8 - - - +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.0 20.5 + - - +
75A GLN* 3.5 29.2 - - - +
77A LEU* 1.3 76.6 - - - +
79A LEU* 1.3 57.3 + - - +
81A LYS* 3.5 7.9 - - - +
82A ARG* 3.1 45.8 + - + +
64B ARG* 4.9 14.9 - - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 5.0 11.4 - - + -
75A GLN 3.2 13.5 + - - +
76A VAL* 3.1 11.1 + - - +
78A ARG* 1.3 75.4 - - - +
80A MSE 1.3 65.7 + - - +
81A LYS 3.2 0.2 - - - -
82A ARG* 3.2 11.0 + - - +
83A ARG* 3.0 50.1 + - - +
139A GLU* 4.9 14.6 - - + +
140A LEU* 5.4 7.4 - - + -
143A PHE* 5.0 18.6 - - + -
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Residues in contact with MSE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.0 20.8 - - + +
32A ILE* 3.7 26.0 - - + -
35A LYS* 4.1 15.7 - - - -
76A VAL* 2.8 35.8 + - - +
77A LEU* 3.5 16.6 - - + +
79A LEU* 1.3 72.0 - - - +
81A LYS* 1.3 57.6 + - - +
83A ARG* 3.3 1.4 + - - -
84A GLY 3.0 8.7 + - - -
85A VAL* 2.7 53.1 + - + +
86A PRO 3.2 29.6 - - - +
87A LEU* 4.0 16.2 - - + -
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 2.9 13.6 + - - +
78A ARG* 3.5 12.6 - - - +
80A MSE 1.3 77.0 - - - +
82A ARG* 1.3 65.2 + - + +
84A GLY* 3.0 14.2 + - - -
85A VAL 5.1 1.6 - - - -
56B LEU* 4.4 22.9 - - + -
----------------------------------------------------------
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 3.1 35.2 + - + +
79A LEU* 3.2 10.4 + - - +
81A LYS* 1.3 82.2 - - + +
83A ARG* 1.3 62.0 + - + +
84A GLY 3.7 0.2 + - - -
139A GLU* 4.1 22.8 + - - +
----------------------------------------------------------
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 5.2 5.3 + - - -
31A LEU* 4.5 14.1 - - - +
79A LEU* 3.0 30.7 + - - +
82A ARG* 1.3 81.1 - - + +
84A GLY* 1.3 62.1 + - - +
85A VAL* 3.3 17.3 + - + +
137A ASP* 2.8 43.2 + - - -
139A GLU* 3.1 36.5 + - - +
140A LEU* 3.7 14.7 - - - +
----------------------------------------------------------
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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