Contacts of the helix formed by residues 55 - 84 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ARG* 4.7 5.5 - - - +
78E ILE 3.0 13.4 + - - +
79E ILE* 3.7 22.0 - - - +
80E PRO* 3.7 3.5 - - - +
54F ILE* 1.3 76.1 - - - +
56F SER* 1.3 54.1 + - - +
57F LYS* 3.9 5.2 + - - +
58F ALA* 3.0 25.9 + - - +
59F MET* 2.7 33.9 + - - +
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Residues in contact with SER 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ILE 3.9 0.4 + - - -
55F SER* 1.3 74.3 - - - +
57F LYS* 1.3 56.7 + - - +
59F MET* 3.1 10.6 + - - +
60F GLY* 2.9 24.4 + - - -
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Residues in contact with LYS 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLU* 4.3 1.4 + - - -
80E PRO* 4.1 17.0 - - + -
103E ALA* 5.2 4.3 - - + +
104E GLN* 3.0 39.3 - - + +
55F SER* 3.9 7.1 + - - +
56F SER* 1.3 78.3 - - - +
58F ALA* 1.3 62.8 + - - +
60F GLY* 3.2 10.3 + - - -
61F ILE* 3.3 16.7 + - + +
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Residues in contact with ALA 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ILE 3.2 18.6 - - - +
79E ILE 4.0 1.3 - - - -
80E PRO* 3.7 22.0 - - + +
83E LEU* 3.6 13.6 - - + +
54F ILE* 3.7 11.4 - - + -
55F SER* 3.0 23.8 + - - +
57F LYS* 1.3 73.5 - - - +
59F MET* 1.3 65.7 + - - +
61F ILE* 3.2 5.5 + - - +
62F MET* 3.1 20.1 + - - +
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Residues in contact with MET 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F SER* 3.5 44.9 - - - +
41F VAL* 3.2 42.4 - - + -
42F TYR* 3.8 11.0 - - + +
54F ILE* 4.0 27.3 - - + +
55F SER 2.7 14.4 + - - +
56F SER* 3.2 14.6 - - - +
58F ALA* 1.3 76.8 - - - +
60F GLY* 1.3 64.4 + - - +
62F MET* 3.3 4.4 + - - +
63F ASN* 3.0 32.4 + - - +
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Residues in contact with GLY 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F SER 2.9 13.0 + - - -
57F LYS* 3.2 6.7 + - - -
58F ALA 3.1 0.4 - - - -
59F MET* 1.3 76.0 - - - +
61F ILE* 1.3 61.6 + - - +
63F ASN* 3.2 10.6 + - - +
64F SER* 3.0 23.3 + - - -
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Residues in contact with ILE 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E PRO* 3.4 25.4 - - + -
83E LEU* 3.5 17.0 - - + -
87E ILE* 5.9 1.3 - - + -
102E ILE* 3.2 50.3 - - + -
103E ALA* 3.4 26.5 - - + +
57F LYS* 3.3 7.9 + - + +
58F ALA 3.2 7.1 + - - +
59F MET 3.2 0.2 - - - -
60F GLY* 1.3 75.9 - - - +
62F MET* 1.3 60.7 + - - +
64F SER* 2.8 26.2 + - - -
65F PHE* 2.9 14.3 + - + +
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Residues in contact with MET 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E THR* 3.7 33.2 - - + +
62E ILE* 3.4 41.1 - - + -
63E LEU* 4.1 19.3 - - + -
83E LEU* 4.0 15.7 - - + -
41F VAL* 4.0 20.6 - - + -
54F ILE* 4.2 7.9 - - + -
58F ALA 3.1 13.5 + - - +
59F MET* 3.3 9.4 + - - +
61F ILE* 1.3 79.4 - - - +
63F ASN* 1.3 57.9 + - - +
65F PHE* 3.1 11.1 + - + +
66F VAL* 2.9 35.1 + - + +
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Residues in contact with ASN 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F SER* 3.6 11.5 - - - +
37F TYR* 2.7 40.4 + - - +
38F SER* 3.1 28.5 + - - +
41F VAL* 4.8 0.8 - - - +
59F MET* 3.0 27.3 + - - -
60F GLY* 3.4 10.8 - - - +
62F MET* 1.3 75.8 - - - +
64F SER* 1.3 63.2 + - - +
66F VAL* 3.3 6.0 + - - +
67F ASN* 3.1 32.8 + - - +
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Residues in contact with SER 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D GLU* 4.7 15.9 + - - -
109D HIS* 6.0 0.3 - - - -
60F GLY 3.0 12.6 + - - -
61F ILE* 2.8 14.3 + - - -
63F ASN* 1.3 75.5 - - - +
65F PHE* 1.3 57.9 + - - +
67F ASN* 3.4 5.2 + - - +
68F ASP* 2.8 32.4 + - - +
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Residues in contact with PHE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E LEU* 4.9 1.6 - - - -
58E LEU* 3.7 35.4 - - + -
59E THR* 4.2 10.5 - - - -
62E ILE* 3.9 36.6 - - + -
87E ILE* 5.9 0.7 - - + -
96E LEU* 4.6 4.5 - - + -
97E LEU* 3.9 35.4 - - + -
61F ILE* 2.9 13.6 + - + +
62F MET* 3.3 15.0 - - + +
64F SER* 1.3 75.0 - - - +
66F VAL* 1.3 78.0 - - + +
68F ASP* 3.2 5.0 + - + -
69F ILE* 3.1 51.6 + - + +
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Residues in contact with VAL 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 3.8 17.3 - - + -
55E LEU* 4.2 13.5 - - + +
59E THR* 3.7 22.4 - - + +
37F TYR* 3.4 49.1 - - + +
41F VAL* 5.7 2.2 - - + -
62F MET* 2.9 25.1 + - + +
63F ASN 3.9 3.8 - - - +
65F PHE* 1.3 82.8 - - + +
67F ASN* 1.3 62.8 + - - +
69F ILE* 4.2 4.4 - - - +
70F PHE* 3.2 21.1 + - - +
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Residues in contact with ASN 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LEU* 5.2 6.7 - - - +
36F SER* 4.9 5.9 + - - -
37F TYR* 3.4 31.8 + - - -
63F ASN* 3.1 23.6 + - - +
64F SER* 3.9 4.7 - - - +
66F VAL* 1.3 75.9 - - - +
68F ASP* 1.3 63.8 + - - +
70F PHE* 3.3 8.0 + - - +
71F GLU* 2.9 38.6 + - + +
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Residues in contact with ASP 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS* 5.4 6.9 + - - -
97E LEU* 5.0 1.9 - - - +
100E VAL* 4.3 11.0 - - - +
64F SER 2.8 19.7 + - - +
65F PHE* 3.2 8.0 + - - +
67F ASN* 1.3 76.1 - - - +
69F ILE* 1.3 61.2 + - - +
71F GLU* 2.9 31.9 + - - +
72F ARG* 2.9 48.4 + - - +
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Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E VAL* 4.7 0.2 - - + -
55E LEU* 3.3 22.4 - - + -
58E LEU* 3.4 27.6 - - + -
96E LEU* 4.9 8.7 - - + -
97E LEU* 4.8 7.0 - - + -
65F PHE* 3.1 47.3 + - + +
66F VAL* 4.3 1.8 - - - +
68F ASP* 1.3 81.4 - - - +
70F PHE* 1.3 58.7 + - - +
72F ARG* 3.7 15.9 - - + +
73F ILE* 3.0 70.2 + - + +
102F LEU* 5.1 3.6 - - + -
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Residues in contact with PHE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E VAL* 4.0 10.1 - - + -
33E LEU* 3.4 40.8 - - + -
34E LEU* 3.7 28.5 - - + -
39E TYR* 4.5 14.1 - + - -
51E LEU* 3.8 18.4 - - + +
55E LEU* 4.0 24.7 - - + -
37F TYR* 4.6 9.9 - - - +
66F VAL 3.2 19.9 + - - +
67F ASN* 3.3 10.5 - - - +
68F ASP 3.0 0.6 + - - -
69F ILE* 1.3 78.2 - - - +
71F GLU* 1.3 69.0 + - + +
73F ILE* 3.3 1.6 + - - +
74F ALA* 2.9 40.4 + - + +
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Residues in contact with GLU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS* 5.3 6.6 + - - -
39E TYR* 4.1 18.5 + - - +
67F ASN* 2.9 25.1 + - + +
68F ASP* 2.9 16.1 + - - +
70F PHE* 1.3 86.6 - - + +
72F ARG* 1.3 57.4 + - + +
74F ALA* 4.0 1.0 - - - +
75F GLY* 3.0 25.6 + - - -
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Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LEU* 3.0 47.4 + - - +
97E LEU* 4.0 11.4 - - - +
100E VAL* 4.1 10.3 - - - +
68F ASP* 2.9 50.0 + - - +
69F ILE* 3.7 12.9 - - + +
70F PHE 3.2 0.2 - - - -
71F GLU* 1.3 77.4 - - + +
73F ILE* 1.3 61.9 + - + +
75F GLY* 3.3 1.8 + - - -
76F GLU* 3.1 19.8 + - - +
79F ARG* 5.5 0.3 + - - -
101F LEU* 3.3 32.3 + - + +
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Residues in contact with ILE 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E LEU* 4.3 17.9 - - + -
54E VAL* 4.2 9.2 - - + -
69F ILE* 3.0 42.6 + - + +
70F PHE 3.9 1.8 - - - +
72F ARG* 1.3 77.8 - - + +
74F ALA* 1.3 61.3 + - - +
76F GLU 3.5 0.3 + - - -
77F ALA* 2.9 26.9 + - - +
94F ILE* 4.1 25.6 - - + +
97F ALA* 3.6 16.7 - - + +
98F VAL* 3.9 20.6 - - + -
101F LEU* 3.5 17.9 - - + -
102F LEU* 4.8 8.5 - - + -
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 4.0 23.3 - - + -
39E TYR* 3.3 28.9 - - + +
51E LEU* 4.7 4.5 - - + +
70F PHE* 2.9 25.4 + - + +
73F ILE* 1.3 76.0 - - - +
75F GLY* 1.3 59.8 + - - +
77F ALA* 3.7 6.9 - - - +
78F SER* 3.0 30.0 + - - -
89F ILE* 4.5 1.0 - - - +
94F ILE* 5.6 0.7 - - - -
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Residues in contact with GLY 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E TYR* 3.8 10.5 - - - -
71F GLU 3.0 19.1 + - - -
72F ARG* 3.3 2.2 + - - -
73F ILE 3.2 0.2 - - - -
74F ALA* 1.3 76.7 - - - +
76F GLU* 1.3 56.6 + - - +
78F SER* 3.3 5.2 + - - -
79F ARG* 2.9 44.8 + - - +
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Residues in contact with GLU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ARG 3.1 13.7 + - - +
75F GLY* 1.3 71.3 - - - +
77F ALA* 1.3 57.7 + - - +
79F ARG* 2.6 40.5 + - - +
80F LEU* 2.7 40.4 + - - +
83F TYR* 5.6 2.8 - - - -
97F ALA* 3.9 18.4 - - + -
100F LEU* 3.9 25.5 - - + +
101F LEU* 3.7 30.2 - - + +
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Residues in contact with ALA 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ILE 2.9 19.2 + - - +
74F ALA* 3.7 7.2 - - - +
76F GLU* 1.3 76.5 - - - +
78F SER* 1.3 63.3 + - - +
80F LEU* 3.2 5.0 + - - +
81F ALA* 3.1 21.8 + - - +
89F ILE* 4.2 10.3 - - + -
93F GLU* 3.9 24.1 - - + +
94F ILE* 4.0 25.4 - - + -
97F ALA* 3.7 6.8 - - + +
----------------------------------------------------------
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Residues in contact with SER 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E TYR* 2.6 45.1 + - - -
74F ALA 3.0 20.1 + - - -
75F GLY* 3.5 6.1 - - - -
77F ALA* 1.3 75.6 - - - +
79F ARG* 1.3 61.1 + - - +
81F ALA* 3.4 2.3 + - - +
82F HIS* 3.2 37.5 + - - -
89F ILE* 3.9 10.3 - - - +
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Residues in contact with ARG 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ARG 5.5 0.2 + - - -
75F GLY* 2.9 28.5 + - - +
76F GLU* 2.6 61.7 + - - +
78F SER* 1.3 76.1 - - - +
80F LEU* 1.3 62.5 + - - +
82F HIS* 3.3 8.1 + - - +
83F TYR* 3.1 69.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F GLU* 2.7 25.3 + - - +
77F ALA* 3.3 7.9 - - - +
79F ARG* 1.3 74.4 - - - +
81F ALA* 1.3 60.2 + - - +
83F TYR* 3.5 14.1 + - + +
84F ASN* 3.1 38.5 + - - +
93F GLU* 3.6 28.7 - - + +
96F THR* 3.5 42.2 - - + -
97F ALA* 3.7 9.6 - - + +
100F LEU* 4.4 9.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ALA 3.1 11.9 + - - +
78F SER* 3.7 8.5 - - - +
79F ARG 3.2 0.2 - - - -
80F LEU* 1.3 74.9 - - - +
82F HIS* 1.3 66.6 + - + +
84F ASN* 3.3 3.1 + - - -
85F LYS 3.2 3.5 + - - -
86F ARG* 2.9 46.3 + - + +
87F SER 5.7 0.2 - - - -
88F THR 4.2 16.4 - - - +
89F ILE* 4.5 10.5 - - + -
93F GLU* 4.3 11.9 - - + +
----------------------------------------------------------
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Residues in contact with HIS 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ASN 6.0 0.2 - - - -
39E TYR 3.8 15.6 + - - -
40E ALA* 5.5 1.8 - - - -
78F SER* 3.2 27.6 + - - -
79F ARG* 3.3 7.6 + - - +
81F ALA* 1.3 82.1 - - + +
83F TYR* 1.3 68.5 + - + +
85F LYS* 2.9 21.6 + - - +
86F ARG 4.6 6.7 - - - -
87F SER* 6.3 0.2 - - - -
----------------------------------------------------------
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Residues in contact with TYR 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F GLU* 5.6 3.1 - - - -
79F ARG* 3.1 53.5 + - + +
80F LEU* 3.7 18.8 - - + +
81F ALA 3.3 0.2 - - - -
82F HIS* 1.3 80.4 - - + +
84F ASN* 1.3 64.6 + - - +
85F LYS* 3.2 8.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LEU* 3.1 32.2 + - - +
81F ALA* 3.4 2.2 - - - +
82F HIS 3.2 0.4 - - - -
83F TYR* 1.3 83.4 + - - +
85F LYS* 1.3 68.0 + - - +
86F ARG* 3.0 23.8 + - + +
93F GLU* 5.7 3.5 - - - +
----------------------------------------------------------
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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