Contacts of the helix formed by residues 55 - 84 (chain B) in PDB entry 2XQL
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 55 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.7 5.5 - - - +
78A ILE 3.0 14.0 + - - +
79A ILE* 3.7 22.2 - - - +
80A PRO* 3.7 2.9 - - - +
54B ILE* 1.3 76.1 - - - +
56B SER* 1.3 54.1 + - - +
57B LYS* 3.9 5.9 + - - +
58B ALA* 3.0 25.0 + - - +
59B MET* 2.7 34.3 + - - +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE 3.9 0.4 + - - -
55B SER* 1.3 73.0 - - - +
57B LYS* 1.3 58.6 + - - +
59B MET* 3.1 11.6 + - - +
60B GLY* 2.9 23.7 + - - -
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 4.1 17.0 - - + -
103A ALA* 5.2 4.5 - - + +
104A GLN* 3.0 38.0 - - + +
55B SER* 4.1 7.1 - - - +
56B SER* 1.3 77.7 - - - +
58B ALA* 1.3 61.7 + - - +
60B GLY* 3.2 10.7 + - - +
61B ILE* 3.3 16.0 + - + +
64I GLU* 4.3 1.6 + - - -
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE 3.2 18.6 - - - +
79A ILE* 4.0 0.9 - - - -
80A PRO* 3.7 21.7 - - + +
83A LEU* 3.6 13.7 - - + +
54B ILE* 3.7 11.4 - - + -
55B SER* 3.0 24.3 + - - +
57B LYS* 1.3 74.9 - - - +
59B MET* 1.3 65.5 + - - +
61B ILE* 3.2 6.0 + - - +
62B MET* 3.1 20.1 + - - +
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Residues in contact with MET 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 3.5 43.3 - - - +
41B VAL* 3.2 44.2 - - + -
42B TYR* 3.8 11.4 - - + +
54B ILE* 4.0 27.3 - - + +
55B SER 2.7 15.6 + - - +
56B SER* 3.2 14.6 - - - +
58B ALA* 1.3 76.1 - - - +
60B GLY* 1.3 65.7 + - - +
62B MET* 3.3 5.2 + - - +
63B ASN* 3.0 31.4 + - - +
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER 2.9 13.5 + - - -
57B LYS* 3.2 6.6 + - - -
58B ALA 3.1 0.6 - - - -
59B MET* 1.3 76.4 - - - +
61B ILE* 1.3 62.6 + - - +
63B ASN* 3.2 10.3 + - - +
64B SER* 3.0 22.6 + - - -
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 3.4 25.1 - - + -
83A LEU* 3.5 17.7 - - + -
87A ILE* 5.9 1.1 - - + -
102A ILE* 3.2 48.5 - - + -
103A ALA* 3.4 27.8 - - + +
57B LYS* 3.3 8.1 + - + +
58B ALA 3.2 7.5 + - - +
59B MET 3.2 0.2 - - - -
60B GLY* 1.3 74.7 - - - +
62B MET* 1.3 61.7 + - - +
64B SER* 2.8 26.6 + - - -
65B PHE* 2.9 14.6 + - + +
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Residues in contact with MET 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 3.7 32.8 - - + +
62A ILE* 3.4 39.3 - - + -
63A LEU* 4.1 20.0 - - + -
83A LEU* 4.0 17.5 - - + -
41B VAL* 4.0 20.9 - - + -
54B ILE* 4.2 7.4 - - + -
58B ALA 3.1 13.6 + - - +
59B MET* 3.3 9.8 + - - +
61B ILE* 1.3 78.4 - - - +
63B ASN* 1.3 58.3 + - - +
65B PHE* 3.1 11.7 + - + +
66B VAL* 2.9 33.6 + - + +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 3.6 10.4 - - - +
37B TYR* 2.7 41.7 + - - +
38B SER* 3.1 28.7 + - - +
41B VAL* 4.8 0.6 - - - +
59B MET* 3.0 28.1 + - - +
60B GLY* 3.4 10.6 - - - +
61B ILE 3.1 0.2 - - - -
62B MET* 1.3 76.8 - - - +
64B SER* 1.3 63.2 + - - +
66B VAL* 3.3 6.0 + - - +
67B ASN* 3.1 33.5 + - - +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLY 3.0 13.0 + - - -
61B ILE* 2.8 13.9 + - - -
63B ASN* 1.3 75.9 - - - +
65B PHE* 1.3 58.0 + - - +
67B ASN* 3.8 4.9 - - - +
68B ASP* 2.8 31.8 + - - +
105J GLU* 4.7 15.4 + - - -
109J HIS* 6.0 0.5 - - - -
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.9 1.6 - - - -
58A LEU* 3.7 35.0 - - + -
59A THR* 4.2 11.4 - - - -
62A ILE* 3.9 35.4 - - + -
87A ILE* 5.9 0.7 - - + -
96A LEU* 4.6 4.5 - - + -
97A LEU* 3.9 34.8 - - + -
61B ILE* 2.9 14.4 + - + +
62B MET* 3.1 15.0 + - + +
64B SER* 1.3 75.5 - - - +
66B VAL* 1.3 78.8 + - + +
68B ASP* 3.2 5.0 + - + +
69B ILE* 3.1 51.1 + - + +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.8 16.4 - - + -
55A LEU* 4.2 13.4 - - + +
59A THR* 3.7 23.6 - - + +
37B TYR* 3.4 50.3 - - + +
41B VAL* 5.7 2.0 - - + -
62B MET* 2.9 25.1 + - + +
63B ASN 3.3 4.7 + - - +
65B PHE* 1.3 83.7 - - + +
67B ASN* 1.3 62.3 + - - +
69B ILE* 3.8 4.3 + - - +
70B PHE* 3.2 21.7 + - - +
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.2 6.9 - - - +
36B SER* 4.9 5.9 + - - -
37B TYR* 3.4 32.5 + - - -
63B ASN* 3.1 24.6 + - - +
64B SER* 3.9 4.7 - - - +
66B VAL* 1.3 75.7 - - - +
68B ASP* 1.3 63.2 + - - +
70B PHE* 3.3 7.8 + - - +
71B GLU* 2.9 38.3 + - + +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 5.0 2.1 - - - +
100A VAL* 4.3 11.1 - - - +
64B SER 2.8 18.4 + - - +
65B PHE* 3.2 7.9 + - - +
67B ASN* 1.3 75.7 - - - +
69B ILE* 1.3 61.8 + - + +
71B GLU* 2.9 31.5 + - - +
72B ARG* 2.9 50.2 + - - +
108J LYS* 5.4 6.4 + - - -
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.7 0.4 - - + -
55A LEU* 3.3 24.0 - - + -
58A LEU* 3.4 26.0 - - + -
96A LEU* 4.9 8.5 - - + -
97A LEU* 4.8 7.0 - - + -
65B PHE* 3.1 46.8 + - + +
66B VAL 4.3 1.6 - - - +
68B ASP* 1.3 80.8 - - - +
70B PHE* 1.3 58.2 + - - +
72B ARG* 3.7 16.8 - - + +
73B ILE* 3.0 69.7 + - + +
102B LEU* 5.1 3.1 - - + -
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.0 10.5 - - + -
33A LEU* 3.4 40.8 - - + -
34A LEU* 3.7 28.9 - - + -
39A TYR* 4.5 14.8 - + - -
51A LEU* 3.8 16.6 - - + +
55A LEU* 4.0 25.1 - - + -
37B TYR* 4.6 10.8 - - - +
66B VAL 3.2 19.0 + - - +
67B ASN* 3.3 12.1 - - - +
68B ASP 3.0 0.6 + - - -
69B ILE* 1.3 78.2 - - - +
71B GLU* 1.3 68.0 + - + +
73B ILE* 3.3 1.7 + - - +
74B ALA* 2.9 39.3 + - + +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.1 20.0 + - - +
67B ASN* 2.9 24.0 + - + +
68B ASP* 2.9 16.5 + - - +
70B PHE* 1.3 86.2 - - + +
72B ARG* 1.3 56.8 + - + +
74B ALA* 4.0 0.7 - - - +
75B GLY* 3.0 26.5 + - - -
108J LYS* 5.3 6.6 + - - -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.0 46.0 + - - +
97A LEU* 4.0 11.1 - - - +
99A LYS 6.1 0.2 - - - +
100A VAL* 4.1 10.7 - - - +
68B ASP* 2.9 47.9 + - - +
69B ILE* 3.7 14.3 - - + +
71B GLU* 1.3 78.5 - - + +
73B ILE* 1.3 62.0 + - + +
75B GLY* 3.3 2.0 + - - -
76B GLU* 3.1 19.2 + - - +
79B ARG* 5.5 0.2 + - - -
101B LEU* 3.3 32.5 + - + +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.3 19.1 - - + -
54A VAL* 4.2 9.9 - - + -
69B ILE* 3.0 41.8 + - + +
70B PHE 3.9 2.0 - - - +
72B ARG* 1.3 77.5 - - + +
74B ALA* 1.3 63.2 + - - +
76B GLU 3.5 0.5 + - - -
77B ALA* 2.9 27.0 + - - +
94B ILE* 4.1 26.5 - - + +
97B ALA* 3.6 16.3 - - + +
98B VAL* 3.9 20.9 - - + -
101B LEU* 3.5 17.9 - - + -
102B LEU* 4.8 9.2 - - + -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.0 22.7 - - + -
39A TYR* 3.3 28.8 - - + +
51A LEU* 4.7 4.7 - - + +
70B PHE* 2.9 26.3 + - + +
73B ILE* 1.3 74.4 - - - +
75B GLY* 1.3 62.0 + - - +
77B ALA* 3.7 7.1 - - - +
78B SER* 3.0 30.1 + - - -
89B ILE* 4.5 0.7 - - - +
94B ILE* 5.6 0.2 - - - -
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.8 11.4 - - - -
71B GLU 3.0 18.6 + - - -
72B ARG 3.7 2.0 - - - -
73B ILE 3.2 0.2 - - - -
74B ALA* 1.3 77.5 - - - +
76B GLU* 1.3 56.6 + - - +
78B SER* 3.3 5.0 + - - -
79B ARG* 2.9 45.3 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG 3.1 11.8 + - - +
75B GLY* 1.3 71.3 - - - +
77B ALA* 1.3 56.8 + - - +
79B ARG* 2.6 40.8 + - - +
80B LEU* 2.7 40.7 + - - +
83B TYR* 5.6 2.4 - - - -
97B ALA* 3.9 17.7 - - + -
100B LEU* 3.9 25.7 - - + +
101B LEU* 3.7 30.4 - - + +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 6.1 0.2 - - + -
73B ILE 2.9 19.0 + - - +
74B ALA* 3.7 7.2 - - - +
76B GLU* 1.3 76.9 - - - +
78B SER* 1.3 63.5 + - - +
80B LEU* 3.2 5.6 + - - +
81B ALA* 3.1 22.2 + - - +
89B ILE* 4.2 10.3 - - + -
93B GLU* 3.9 23.2 - - + +
94B ILE* 4.0 25.8 - - + -
97B ALA* 3.7 7.1 - - + +
----------------------------------------------------------
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 2.6 44.9 + - - -
74B ALA 3.0 19.1 + - - -
75B GLY* 3.5 4.7 - - - -
77B ALA* 1.3 77.7 - - - +
79B ARG* 1.3 62.7 + - - +
81B ALA* 3.4 2.5 + - - +
82B HIS* 3.2 36.9 + - - -
89B ILE* 3.9 10.2 - - - +
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG 5.7 0.2 + - - -
75B GLY* 2.9 27.7 + - - +
76B GLU* 2.6 60.4 + - - +
78B SER* 1.3 77.5 - - - +
80B LEU* 1.3 61.8 + - - +
82B HIS* 3.3 8.6 + - - +
83B TYR* 3.1 71.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 2.7 24.9 + - - +
77B ALA* 3.3 8.1 - - - +
79B ARG* 1.3 74.4 - - - +
81B ALA* 1.3 61.2 + - - +
83B TYR* 3.5 13.9 + - + +
84B ASN* 3.1 38.9 + - - +
93B GLU* 3.6 28.8 - - + +
96B THR* 3.5 41.3 - - + -
97B ALA* 3.7 9.9 - - - +
100B LEU* 4.4 10.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA 3.1 12.5 + - - +
78B SER* 3.7 8.7 - - - +
79B ARG 3.2 0.4 - - - -
80B LEU* 1.3 74.3 - - - +
82B HIS* 1.3 67.3 + - + +
84B ASN* 3.3 2.8 + - - -
85B LYS 3.2 3.6 + - - -
86B ARG* 2.9 47.3 + - + +
88B THR 4.2 16.4 - - - +
89B ILE* 4.5 10.8 - - + -
93B GLU* 4.3 11.2 - - + +
----------------------------------------------------------
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Residues in contact with HIS 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN 6.0 0.2 - - - -
39A TYR 3.8 15.3 + - - -
40A ALA* 5.5 1.4 - - - -
78B SER* 3.2 27.6 + - - -
79B ARG* 3.3 8.4 + - - +
81B ALA* 1.3 81.7 - - + +
83B TYR* 1.3 68.1 + - + +
85B LYS* 2.9 22.0 + - - +
86B ARG 4.6 6.7 - - - -
----------------------------------------------------------
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 5.6 2.7 - - - -
79B ARG* 3.1 52.2 + - + +
80B LEU* 3.7 18.8 - - + +
81B ALA 3.3 0.2 - - - -
82B HIS* 1.3 81.0 - - + +
84B ASN* 1.3 65.9 + - - +
85B LYS* 3.4 8.1 + - - +
----------------------------------------------------------
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Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.1 31.9 + - - +
81B ALA* 4.2 1.6 - - - +
82B HIS 3.2 0.6 - - - -
83B TYR* 1.3 83.1 + - - +
85B LYS* 1.3 69.6 + - - +
86B ARG* 3.0 23.5 + - + +
93B GLU* 5.7 3.8 - - - +
----------------------------------------------------------
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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