Contacts of the helix formed by residues 103 - 133 (chain C) in PDB entry 5JKE
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 LYS 103 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLY 3.7 21.3 + - - +
44C HIS* 3.3 19.0 - - + +
101C ASP* 3.6 22.0 + - - +
102C VAL* 1.3 80.9 - - - +
104C GLY* 1.3 69.4 + - - +
105C ASP 3.7 0.2 + - - -
106C LEU* 3.5 11.6 + - - +
107C PHE* 3.2 13.2 + - - -
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C HIS 2.9 16.2 + - - -
45C LEU* 4.4 13.0 - - - -
103C LYS* 1.3 73.1 - - - +
105C ASP* 1.3 63.5 + - - -
107C PHE* 3.0 13.1 + - - +
108C VAL* 3.0 19.5 + - - +
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.6 17.1 - - + +
104C GLY* 1.3 69.7 - - - -
106C LEU* 1.3 64.3 + - - +
108C VAL* 3.8 7.9 - - - +
109C LYS* 2.9 57.7 + - - +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 4.7 8.3 - - + +
106A LEU* 4.4 37.1 - - + +
109A LYS* 4.4 22.7 - - + +
110A GLU* 6.5 0.7 - - + -
102C VAL* 2.8 32.8 - - + -
103C LYS 3.5 9.8 + - - +
104C GLY 3.2 0.6 + - - -
105C ASP* 1.3 77.8 - - - +
107C PHE* 1.3 57.4 + - - +
109C LYS* 4.0 0.7 - - - +
110C GLU* 2.9 55.7 + - + +
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Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 4.5 11.0 - - + -
40C TYR* 3.8 28.9 - + - -
41C LEU* 3.6 32.5 - - + -
44C HIS 4.3 13.5 - - - -
45C LEU* 4.7 7.4 - - + -
53C MET* 3.9 22.2 - - + -
97C ILE* 4.1 22.9 - - + -
102C VAL* 3.7 21.1 - - + +
103C LYS 3.2 13.8 + - - -
104C GLY 3.0 10.5 + - - +
106C LEU* 1.3 77.3 - - - +
108C VAL* 1.3 72.9 + - + +
110C GLU* 3.3 2.2 + - - +
111C LEU* 2.9 34.0 + - + +
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 4.0 22.2 - - + -
53C MET* 4.2 15.3 - - - -
104C GLY 3.0 15.9 + - - +
105C ASP* 3.8 9.9 - - - +
107C PHE* 1.3 81.2 - - + +
109C LYS* 1.3 73.7 + - + +
111C LEU* 3.2 3.4 + - - +
112C PHE* 3.1 46.7 + - + -
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 6.4 0.4 - - + -
106A LEU* 4.6 9.4 - - + +
110A GLU* 3.9 24.9 - - - +
105C ASP* 2.9 44.1 + - - +
106C LEU 4.3 1.1 - - - +
108C VAL* 1.3 85.0 - - + +
110C GLU* 1.3 63.1 + - - +
112C PHE* 4.0 3.4 - - - +
113C TRP* 3.0 27.2 + - - +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LYS* 3.9 16.2 - - - +
110A GLU* 5.0 15.8 - - + +
113A TRP* 3.5 30.4 + - + +
97C ILE* 4.2 20.6 - - + +
100C SER* 4.8 4.2 + - - -
102C VAL* 4.1 13.7 - - + +
106C LEU* 2.9 47.9 + - + +
107C PHE* 3.8 4.5 - - - +
109C LYS* 1.3 75.8 - - - +
111C LEU* 1.3 53.9 + - - +
113C TRP* 3.6 4.7 - - - +
114C MET* 2.8 35.9 + - - +
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 4.3 11.0 - - + -
53C MET* 3.1 33.2 - - + -
57C VAL* 4.0 17.5 - - + -
94C LEU* 3.9 27.6 - - + -
97C ILE* 4.0 10.9 - - + +
107C PHE* 2.9 32.7 + - + +
108C VAL* 3.4 4.3 - - - +
110C GLU* 1.3 77.1 - - - +
112C PHE* 1.3 62.0 + - + +
114C MET* 3.1 15.5 + - + +
115C LEU* 2.9 41.2 + - + +
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Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C MET* 3.7 29.4 - - + -
56C ARG* 3.8 35.2 - - + -
57C VAL* 3.6 33.0 - - + -
60C ALA* 4.5 7.2 - - + -
108C VAL* 3.1 35.5 + - + +
109C LYS* 4.3 3.6 - - - +
111C LEU* 1.3 75.7 - - + +
113C TRP* 1.3 66.4 + - - +
115C LEU* 3.3 16.5 + - + +
116C HIS* 2.9 24.4 + - - +
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ASP* 3.7 26.7 - - + -
96A ARG* 3.6 39.7 - - + -
97A ILE* 3.8 18.9 - - + +
110A GLU* 3.7 30.8 + - + +
113A TRP* 4.4 13.5 - + - -
114A MET* 3.4 34.1 - - + +
109C LYS 3.0 19.3 + - - +
110C GLU* 3.6 3.8 - - - +
112C PHE* 1.3 77.1 - - - +
114C MET* 1.3 61.9 + - - +
116C HIS* 3.3 18.1 - + + +
117C LEU* 3.0 35.8 + - + +
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Residues in contact with MET 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 3.4 30.8 - - + +
117A LEU* 4.6 6.0 - - + +
90C LEU* 3.8 25.4 - - + -
93C ASP* 4.1 11.4 - - + +
94C LEU* 3.7 42.8 - - + +
97C ILE* 3.7 14.8 - - + -
110C GLU 2.8 18.3 + - - +
111C LEU* 3.2 16.8 - - + +
113C TRP* 1.3 74.4 - - - +
115C LEU* 1.3 62.6 + - + +
117C LEU* 3.1 5.7 + - - +
118C GLN* 2.8 40.6 + - + +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.9 22.8 - - + -
33C LEU* 5.8 7.4 - - + -
57C VAL* 4.8 11.7 - - + -
60C ALA* 4.3 17.9 - - + -
61C VAL* 5.5 5.2 - - + -
90C LEU* 4.2 10.5 - - + -
94C LEU* 6.2 1.1 - - + -
111C LEU* 2.9 38.2 + - + +
112C PHE* 3.3 31.4 + - + +
114C MET* 1.3 90.1 - - + +
116C HIS* 1.3 63.8 + - - +
118C GLN* 3.5 4.1 - - - +
119C LYS* 2.9 33.1 + - - +
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Residues in contact with HIS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 3.0 17.6 + - - -
96A ARG* 3.4 22.2 + - - -
66C GLU* 4.0 14.6 + - - -
112C PHE 2.9 13.4 + - - +
113C TRP* 3.3 24.0 - + + +
115C LEU* 1.3 75.0 - - - +
117C LEU* 1.3 87.6 + - + +
119C LYS* 3.2 13.0 + - - +
120C GLU* 2.7 46.5 + - - +
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ASP* 3.1 25.4 - - - +
114A MET* 4.7 5.8 - - + +
117A LEU* 3.3 39.0 - - + -
118A GLN* 3.7 21.3 - - + +
121A THR* 3.8 3.5 + - - +
113C TRP* 3.0 50.5 + - + +
114C MET 3.1 0.4 + - - +
116C HIS* 1.3 96.6 - - + +
118C GLN* 1.3 58.0 + - - +
120C GLU* 3.0 15.2 + - - +
121C THR* 2.9 32.5 + - - -
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.8 4.8 - - + +
120A GLU* 3.6 3.8 - - - +
21C TRP* 3.6 17.9 - - + -
86C GLY* 4.2 6.1 + - - -
89C SER* 2.7 35.5 + - - -
90C LEU* 3.8 20.9 - - + +
93C ASP* 2.9 20.7 - - - +
114C MET* 2.8 36.7 + - - +
115C LEU* 3.5 5.4 - - - +
117C LEU* 1.3 72.7 - - - +
119C LYS* 1.3 59.5 + - - +
121C THR* 3.3 11.5 + - - +
122C PHE* 2.7 34.6 + - - +
125C TYR* 5.7 0.2 - - - -
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.7 30.3 - - + +
60C ALA* 2.6 44.7 + - - +
63C ASP 2.7 16.2 + - - -
64C PHE* 3.6 28.4 - - + +
65C GLN* 5.0 3.2 - - - +
66C GLU* 3.9 23.4 + - - +
115C LEU* 2.9 24.8 + - - +
116C HIS* 3.2 10.7 + - - +
118C GLN* 1.3 75.5 - - - +
120C GLU* 1.3 52.8 + - - +
122C PHE 3.4 0.3 + - - -
123C ALA* 2.8 33.4 + - - +
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 3.2 24.3 + - - -
93A ASP* 3.9 7.7 - - - +
96A ARG* 4.4 2.6 + - - -
118A GLN* 3.8 6.9 - - - +
121A THR* 4.4 13.1 - - + +
125A TYR* 5.1 4.7 + - - +
66C GLU* 4.1 19.7 - - + +
116C HIS* 2.7 47.6 + - + +
117C LEU* 3.0 14.6 + - - +
119C LYS* 1.3 72.5 - - - +
121C THR* 1.3 67.8 + - - +
123C ALA* 3.2 9.9 + - - +
124C THR* 3.2 21.4 + - - -
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Residues in contact with THR 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.9 6.9 + - - +
120A GLU* 4.3 9.0 - - + +
121A THR* 2.6 34.7 + - - +
124A THR* 4.0 8.7 - - - +
89C SER* 4.8 4.0 - - - +
117C LEU 2.9 12.0 + - - -
118C GLN* 3.5 19.6 - - - +
120C GLU* 1.3 76.4 - - - +
122C PHE* 1.3 57.5 + - - +
124C THR* 2.9 26.2 + - - -
125C TYR* 3.1 41.9 + - + +
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Residues in contact with PHE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.5 29.8 - + + +
22C CYS* 3.8 30.3 - - + -
23C VAL* 3.6 17.3 - - + -
64C PHE* 4.2 7.9 - + - -
78C VAL* 4.6 6.3 - - + -
82C THR* 3.8 30.1 - - + -
83C LEU* 4.5 5.6 - - - -
86C GLY* 3.6 20.4 - - - -
118C GLN* 2.7 23.4 + - - +
119C LYS 3.7 2.2 - - - +
121C THR* 1.3 69.8 - - - +
123C ALA* 1.3 68.3 + - - +
125C TYR* 2.9 11.8 + + + -
126C VAL* 2.8 46.6 + - + +
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 4.1 12.1 - - + -
66C GLU* 3.9 23.1 - - + +
67C LEU* 4.1 15.4 - - + +
119C LYS 2.8 17.8 + - - +
120C GLU* 3.2 11.4 + - - +
122C PHE* 1.3 72.1 - - - +
124C THR* 1.3 62.6 + - - +
126C VAL* 3.2 6.0 + - - +
127C ALA* 2.9 24.9 + - - +
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Residues in contact with THR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 4.3 2.1 - - - +
124A THR* 3.0 38.9 + - + -
125A TYR* 3.4 35.1 - - + -
128A ARG* 4.5 20.2 - - - +
120C GLU 3.2 8.2 + - - -
121C THR* 2.9 14.0 + - - -
123C ALA* 1.3 78.2 - - - +
125C TYR* 1.3 64.9 + - - +
127C ALA* 3.1 5.0 + - - -
128C ARG* 2.9 22.5 + - - +
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Residues in contact with TYR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 5.1 4.2 + - - +
124A THR* 3.4 31.5 + - + -
82C THR* 3.9 19.9 + - + +
85C LYS* 3.7 44.7 - - + +
86C GLY* 3.9 29.8 - - - -
89C SER* 4.7 9.7 + - - -
118C GLN* 5.7 0.4 - - - -
121C THR* 3.1 26.6 + - + +
122C PHE* 2.9 17.7 + + + +
124C THR* 1.3 76.7 - - - +
126C VAL* 1.3 57.1 + - - +
128C ARG* 3.6 10.8 + - - +
129C PHE* 2.9 28.8 + - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 4.8 5.4 - - + -
67C LEU* 3.8 16.6 - - + -
74C TYR* 4.0 14.8 - - + -
77C VAL 4.8 2.9 - - - +
78C VAL* 4.4 15.3 - - + -
82C THR* 4.4 2.5 - - + -
122C PHE* 2.8 53.6 + - + +
123C ALA* 3.5 8.5 - - - +
125C TYR* 1.3 73.0 - - - +
127C ALA* 1.3 59.2 + - - +
129C PHE* 3.0 9.7 + - + +
130C GLN* 2.9 47.8 + - + +
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 3.5 31.7 + - - +
67C LEU* 4.7 12.1 - - + +
123C ALA 2.9 19.7 + - - +
124C THR* 3.1 3.1 + - - +
126C VAL* 1.3 73.1 - - - +
128C ARG* 1.3 62.0 + - - +
130C GLN* 3.3 9.6 + - - +
131C LYS* 3.1 24.9 + - - +
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Residues in contact with ARG 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR* 4.7 14.3 - - - +
127A ALA* 3.6 34.1 + - - +
128A ARG* 4.2 30.2 - - + +
131A LYS* 4.8 8.3 - - - +
132A GLU* 4.1 4.7 - - - +
85C LYS* 4.7 15.8 - - - +
124C THR* 2.9 16.0 + - + +
125C TYR* 3.7 11.4 - - - +
127C ALA* 1.3 76.6 - - - +
129C PHE* 1.3 62.8 + - - +
131C LYS 3.2 1.4 + - - -
132C GLU* 2.9 65.1 + - - +
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Residues in contact with PHE 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL* 3.9 25.8 - - + -
78C VAL* 4.1 5.6 - - + -
79C ASP* 3.3 47.6 - - + -
82C THR* 3.5 17.5 - - + +
125C TYR 2.9 12.7 + - - +
126C VAL* 3.3 12.6 - - + +
128C ARG* 1.3 74.6 - - - +
130C GLN* 1.3 74.0 + - + +
133C ALA* 2.9 34.3 + - + +
134C TYR* 3.0 48.0 + + + -
144C GLN* 4.5 0.9 - - - -
146C LEU* 3.8 24.0 - - + -
----------------------------------------------------------
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Residues in contact with GLN 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 4.6 3.6 - - - +
73C ALA 2.8 24.0 + - - -
74C TYR* 3.3 24.5 + - - +
75C MET* 4.0 19.0 - - - +
77C VAL* 5.6 2.5 - - - +
126C VAL* 2.9 41.0 + - + +
127C ALA* 3.3 7.8 + - - +
129C PHE* 1.3 86.6 - - + +
131C LYS* 1.3 61.1 + - - +
134C TYR* 3.8 26.9 + - + +
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 5.1 7.6 - - - +
132A GLU* 3.5 44.9 - - - +
127C ALA 3.1 16.0 + - - +
128C ARG 4.0 0.2 - - - +
130C GLN* 1.3 79.5 - - - +
132C GLU* 1.3 58.4 + - + +
134C TYR 5.8 0.4 - - - -
----------------------------------------------------------
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 4.2 0.7 - - - +
131A LYS* 3.3 41.3 - - + +
132A GLU* 2.4 44.4 - - + +
128C ARG* 2.9 45.9 + - - +
131C LYS* 1.3 80.7 - - + +
133C ALA* 1.3 59.3 + - + +
134C TYR 3.9 1.1 - - - -
136C PRO* 4.2 14.1 - - - +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ASP* 3.8 11.0 - - - +
129C PHE* 2.9 29.6 + - + +
132C GLU* 1.3 79.5 - - + +
134C TYR* 1.3 62.8 + - - +
136C PRO* 3.4 12.7 - - - +
144C GLN* 3.0 21.7 + - - +
----------------------------------------------------------
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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