Contacts of the helix formed by residues 103 - 133 (chain A) in PDB entry 5JKC
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 3.9 22.2 + - - +
44A HIS* 3.3 18.4 + - + +
101A ASP* 3.5 35.6 + - - +
102A VAL* 1.3 74.7 - - - +
104A GLY* 1.3 71.6 + - - +
106A LEU* 3.2 21.5 + - + +
107A PHE* 3.1 12.5 + - - -
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Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A HIS 2.7 18.4 + - - -
45A LEU* 4.3 12.6 - - - -
46A ASP* 5.8 1.3 - - - -
103A LYS* 1.3 74.0 - - - +
105A ASP* 1.3 64.9 + - - -
107A PHE* 3.0 3.6 + - - +
108A VAL* 3.0 25.6 + - - +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 5.5 1.7 - - - +
49A HIS* 5.9 2.3 + - - -
104A GLY* 1.3 72.4 - - - -
106A LEU* 1.3 55.9 + - - +
108A VAL* 3.7 13.9 - - - +
109A LYS* 2.9 58.6 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 3.8 18.8 - - + -
103A LYS* 3.2 17.0 - - + +
104A GLY 3.2 0.2 - - - -
105A ASP* 1.3 75.1 - - - +
107A PHE* 1.3 57.9 + - - +
109A LYS* 3.9 5.2 - - - +
110A GLU* 3.0 34.9 + - - +
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Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.4 10.8 - - + -
40A TYR* 3.8 29.6 - + - -
41A LEU* 3.7 23.6 - - + -
44A HIS* 4.3 13.7 - - + -
45A LEU* 4.4 7.9 - - + -
53A MET* 3.2 31.2 - - + -
97A ILE* 4.1 18.6 - - + -
102A VAL* 3.6 22.9 - - + +
103A LYS 3.4 13.0 - - - -
104A GLY 3.0 10.9 + - - +
106A LEU* 1.3 75.7 - - - +
108A VAL* 1.3 72.0 + - + +
110A GLU* 3.2 2.6 + - - +
111A LEU* 2.9 39.7 + - + +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.9 17.5 - - + -
53A MET* 3.9 26.2 - - + -
56A ARG* 3.8 24.9 - - - +
104A GLY 3.0 19.6 + - - +
105A ASP* 3.2 16.5 + - - +
107A PHE* 1.3 78.9 - - + +
109A LYS* 1.3 66.6 + - + +
111A LEU* 3.3 1.2 + - - +
112A PHE* 3.2 31.9 + - + -
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 2.9 42.8 + - + +
106A LEU* 3.9 5.4 - - - +
108A VAL* 1.3 81.6 - - + +
110A GLU* 1.3 62.8 + - - +
111A LEU 3.2 0.2 + - - -
112A PHE* 3.5 2.0 + - - +
113A TRP* 3.0 26.8 + - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 4.0 20.6 - - + +
100A SER* 4.4 4.9 + - - -
102A VAL* 3.9 33.5 - - + +
106A LEU* 3.0 17.3 + - - +
107A PHE* 3.2 4.7 + - - +
109A LYS* 1.3 75.7 - - - +
111A LEU* 1.3 57.9 + - - +
113A TRP* 3.5 10.6 - - + +
114A MET* 2.8 32.9 + - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 6.2 1.3 - - + -
36A LEU* 4.4 11.9 - - + -
53A MET* 3.8 31.6 - - + -
57A VAL* 4.1 11.9 - - + -
94A LEU* 4.4 14.1 - - + -
97A ILE* 3.9 10.7 - - + +
107A PHE* 2.9 31.7 + - + +
108A VAL 3.6 2.2 - - - +
109A LYS 3.2 0.2 - - - -
110A GLU* 1.3 78.0 - - - +
112A PHE* 1.3 73.1 + - + +
114A MET* 3.2 16.3 + - + +
115A LEU* 2.9 54.1 + - + +
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 3.7 23.6 - - - -
56A ARG* 3.4 80.8 - - + +
57A VAL* 3.6 25.8 - - + -
60A ALA* 4.6 7.4 - - + -
108A VAL* 3.2 19.6 + - + +
109A LYS* 4.4 1.3 - - - +
111A LEU* 1.3 84.4 - - + +
113A TRP* 1.3 65.6 + - - +
115A LEU* 3.2 15.4 + - + +
116A HIS* 3.0 24.6 + - - +
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Residues in contact with TRP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LYS 3.0 21.1 + - - +
110A GLU* 3.5 10.3 - - + +
112A PHE* 1.3 79.4 - - - +
114A MET* 1.3 58.5 + - - +
116A HIS* 3.1 21.0 + + + +
117A LEU* 2.7 54.5 + - + +
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Residues in contact with MET 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.1 11.4 - - + -
93A ASP* 4.1 23.6 - - + +
94A LEU* 4.0 28.3 - - + -
97A ILE* 3.7 26.7 - - + -
110A GLU 2.8 19.7 + - - +
111A LEU* 3.2 6.1 - - + +
113A TRP* 1.3 77.9 - - - +
115A LEU* 1.3 76.1 + - + +
117A LEU* 3.2 10.9 + - - +
118A GLN* 2.9 46.9 + - + +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.9 21.1 - - + -
33A LEU* 5.8 6.5 - - + -
57A VAL* 4.7 12.1 - - + -
60A ALA* 4.5 16.6 - - + -
61A VAL* 5.7 4.5 - - + -
90A LEU* 4.2 10.1 - - + -
94A LEU* 6.0 0.7 - - + -
111A LEU* 2.9 43.1 + - + +
112A PHE* 3.2 25.8 + - + +
114A MET* 1.3 95.6 - - + +
116A HIS* 1.3 59.0 + - - +
118A GLN* 3.2 4.3 + - - +
119A LYS* 2.9 35.8 + - + +
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Residues in contact with HIS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 4.0 16.8 + - - -
112A PHE 3.0 12.6 + - - +
113A TRP* 3.4 25.6 - + + +
115A LEU* 1.3 76.2 - - - +
117A LEU* 1.3 80.1 + - + +
119A LYS* 3.2 9.2 + - - +
120A GLU* 3.1 33.6 + - + +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 2.7 66.9 + - + +
114A MET* 3.5 9.4 - - - +
116A HIS* 1.3 92.3 - - + +
118A GLN* 1.3 57.8 + - + +
120A GLU* 3.1 10.8 + - + +
121A THR* 2.9 32.1 + - - +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.4 19.7 - - + -
86A GLY* 4.7 2.6 + - - -
89A SER* 3.1 35.6 + - - +
90A LEU* 3.9 19.7 - - + +
93A ASP* 3.0 24.6 - - - +
114A MET* 2.9 34.2 + - + +
115A LEU* 3.4 8.7 - - - +
117A LEU* 1.3 75.5 - - + +
119A LYS* 1.3 59.5 + - - +
121A THR* 3.1 11.9 + - - +
122A PHE* 2.8 33.0 + - - +
125A TYR* 5.8 0.4 - - - -
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.9 30.3 - - + +
60A ALA* 2.7 27.9 + - - +
63A ASP 2.2 36.4 + - - -
64A PHE* 3.6 27.6 - - + +
65A GLN* 4.6 3.0 + - - +
66A GLU* 3.7 22.8 + - - +
115A LEU* 2.9 21.1 + - - +
116A HIS* 3.5 10.1 - - - +
118A GLN* 1.3 76.6 - - - +
120A GLU* 1.3 57.8 + - - +
122A PHE* 3.3 2.7 + - - +
123A ALA* 2.8 29.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 3.4 24.0 + - + +
116A HIS* 3.1 28.1 + - + +
117A LEU* 3.4 13.2 - - + +
119A LYS* 1.3 75.3 - - - +
121A THR* 1.3 66.4 + - - +
123A ALA* 3.1 7.5 + - - +
124A THR* 3.1 24.7 + - - -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 4.7 3.6 - - - +
117A LEU* 2.9 14.6 + - - +
118A GLN* 3.1 19.0 + - - +
120A GLU* 1.3 76.2 - - - +
122A PHE* 1.3 62.5 + - - +
124A THR* 3.1 18.2 + - - -
125A TYR* 3.1 46.7 + - + +
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.4 25.6 - + + +
22A CYS* 3.8 28.0 - - + -
23A VAL* 3.2 29.6 - - + -
64A PHE* 4.2 8.7 - + - -
74A TYR* 5.8 0.2 - - - -
78A VAL* 4.7 5.4 - - + -
82A THR* 4.0 20.2 - - + -
83A LEU* 4.6 5.4 - - - -
86A GLY* 3.5 26.9 - - - -
118A GLN* 2.8 18.6 + - - +
119A LYS 3.5 3.6 - - - +
121A THR* 1.3 75.5 - - - +
123A ALA* 1.3 66.0 + - - +
125A TYR* 2.9 12.2 + + - +
126A VAL* 2.8 45.2 + - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.0 11.9 - - + -
66A GLU* 3.9 24.5 - - + -
67A LEU* 4.1 15.6 - - + +
119A LYS 2.8 13.6 + - - +
120A GLU* 3.2 17.3 - - - +
122A PHE* 1.3 76.1 - - - +
124A THR* 1.3 64.5 + - - +
126A VAL* 3.1 5.9 + - - +
127A ALA* 3.0 23.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 3.1 15.2 + - - -
121A THR* 3.3 11.3 + - - -
122A PHE 3.1 0.2 - - - -
123A ALA* 1.3 82.7 - - - +
125A TYR* 1.3 67.8 + - + +
127A ALA* 3.2 7.0 + - + +
128A ARG* 3.1 25.7 + - + +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 3.9 17.3 - - + +
85A LYS* 3.8 55.5 + - + +
86A GLY* 4.0 19.5 - - - -
89A SER* 4.7 10.2 + - - -
118A GLN* 5.8 0.4 - - - -
121A THR* 3.1 37.5 + - + +
122A PHE* 2.9 16.0 + + + +
124A THR* 1.3 82.5 - - + +
126A VAL* 1.3 63.2 + - - +
128A ARG* 3.5 13.9 + - - +
129A PHE* 3.0 22.5 + - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.9 2.2 - - + -
67A LEU* 3.6 21.1 - - + -
74A TYR* 4.0 17.3 - - + -
77A VAL 4.9 6.7 - - - +
78A VAL* 4.6 11.4 - - + -
82A THR* 4.5 4.0 - - + -
122A PHE* 2.8 47.7 + - + +
123A ALA* 3.1 8.0 + - - +
125A TYR* 1.3 76.6 - - - +
127A ALA* 1.3 54.7 + - - +
129A PHE* 2.8 10.9 + - + +
130A GLN* 2.8 50.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.4 13.6 - - + +
72A ASP* 4.6 10.9 - - + +
123A ALA 3.0 12.8 + - - +
124A THR* 3.8 10.1 - - + +
126A VAL* 1.3 76.2 - - - +
128A ARG* 1.3 61.5 + - - +
130A GLN* 3.5 10.4 + - - +
131A LYS* 3.0 26.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 3.7 25.2 - - - +
124A THR* 3.1 16.5 + - + +
125A TYR* 3.6 18.3 - - - +
127A ALA* 1.3 74.2 - - - +
129A PHE* 1.3 66.9 + - - +
131A LYS* 3.3 2.2 + - - -
132A GLU* 2.9 66.2 + - - +
----------------------------------------------------------
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 5.2 0.2 - - + -
77A VAL* 3.8 31.6 - - + -
78A VAL* 4.0 3.8 - - + -
79A ASP* 3.3 44.6 - - + -
82A THR* 3.4 19.7 - - + +
125A TYR 3.0 11.4 + - - +
126A VAL* 2.8 13.4 + - + +
128A ARG* 1.3 75.1 - - - +
130A GLN* 1.3 68.1 + - + +
132A GLU* 5.1 0.2 - - - -
133A ALA* 2.8 41.4 + - + +
134A TYR* 3.0 41.8 + + + -
144A GLN* 4.3 2.5 - - - -
146A LEU* 3.8 22.9 - - + -
----------------------------------------------------------
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Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.8 1.8 - - - +
72A ASP* 3.3 24.8 + - - +
73A ALA 3.2 20.0 + - - -
74A TYR* 3.4 18.3 - - - -
75A MET* 3.3 43.8 + - + +
77A VAL* 5.4 2.5 - - - +
126A VAL* 2.8 31.4 + - + +
127A ALA* 3.7 8.1 - - - +
129A PHE* 1.3 85.2 - - + +
131A LYS* 1.3 59.3 + - - +
134A TYR* 3.6 26.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 5.0 6.3 - - - +
127A ALA 3.0 15.0 + - - +
128A ARG* 4.2 1.8 - - - +
130A GLN* 1.3 79.6 - - + +
132A GLU* 1.3 64.2 + - + +
134A TYR 5.7 0.9 - - - -
----------------------------------------------------------
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 2.9 58.9 + - - +
131A LYS* 1.3 89.4 - - + +
133A ALA* 1.3 62.3 + - + +
134A TYR 3.8 1.6 - - - -
136A PRO* 4.4 12.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP* 3.8 11.0 - - - +
129A PHE* 2.8 35.4 + - + +
132A GLU* 1.3 75.6 - - + +
134A TYR* 1.3 60.4 + - - +
136A PRO* 3.3 15.0 - - - +
142A MET* 5.7 0.2 - - - +
144A GLN* 3.1 18.2 + - - -
----------------------------------------------------------
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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