Contacts of the helix formed by residues 134 - 156 (chain F) in PDB entry 1KN0
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 134 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F PHE* 3.6 1.6 - - - -
132F LEU* 3.3 3.3 - - - +
133F LYS* 1.3 79.8 - - - +
135F LYS* 1.3 61.9 + - - +
136F ALA 3.5 0.9 + - - -
137F LEU* 3.2 37.4 + - - +
138F SER* 2.8 28.4 + - - -
130G GLU* 3.1 30.8 + - - -
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Residues in contact with LYS 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F VAL* 4.2 19.1 - - + -
103F PHE* 3.4 45.1 - - + -
134F SER* 1.3 68.9 + - - +
136F ALA* 1.3 68.7 + - - +
138F SER* 2.9 13.2 + - - -
139F LEU* 3.0 20.4 + - + +
95G PHE* 3.3 39.6 - - + +
97G ASP* 2.7 36.9 + - - +
130G GLU* 5.1 1.0 + - - -
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F SER* 3.5 6.7 + - - +
135F LYS* 1.3 81.1 - - - +
137F LEU* 1.3 65.6 + - + +
139F LEU* 3.1 0.9 + - - +
140F GLU* 2.9 24.5 + - - +
95G PHE* 3.2 25.0 - - + -
105G VAL 4.4 4.0 - - - +
106G GLY* 4.5 1.8 - - - -
126G TYR* 3.7 7.7 - - - -
128G VAL* 3.5 37.0 - - + -
130G GLU* 4.1 5.8 + - - +
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F LEU* 3.8 23.9 - - + +
134F SER* 3.2 20.4 + - - +
136F ALA* 1.3 85.4 - - + +
138F SER* 1.3 61.5 + - - +
140F GLU* 3.9 18.4 - - - +
141F LYS* 3.1 24.6 + - - +
58G GLY* 5.9 6.5 - - - +
128G VAL* 4.5 9.6 - - + -
130G GLU* 3.6 23.1 - - - +
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Residues in contact with SER 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F PHE* 3.5 24.3 + - - +
105F VAL* 4.1 14.0 - - - +
129F SER* 3.3 30.0 + - - -
132F LEU* 3.2 19.6 + - - +
134F SER 2.8 21.0 + - - -
135F LYS* 2.9 6.5 + - - -
137F LEU* 1.3 77.6 - - - +
139F LEU* 1.3 60.6 + - - +
142F ALA* 3.2 19.4 + - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F VAL* 4.4 15.5 - - + -
96F VAL* 3.7 20.2 - - + -
105F VAL* 3.7 26.9 - - + -
107F VAL* 5.1 1.3 - - + -
135F LYS* 3.0 16.6 + - + +
136F ALA 3.7 2.5 - - - +
138F SER* 1.3 73.3 - - - +
140F GLU* 1.3 67.5 + - - +
142F ALA* 3.0 3.8 + - - +
143F ARG* 2.7 31.0 + - + +
94G ASP* 3.3 26.7 - - + +
95G PHE* 3.6 20.6 - - + -
126G TYR* 3.2 26.0 - - + +
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F ALA 2.9 13.8 + - - +
137F LEU* 3.9 20.9 - - - +
139F LEU* 1.3 75.6 - - - +
141F LYS* 1.3 63.4 + - - +
143F ARG* 4.8 0.2 - - - -
144F LYS* 3.0 67.3 + - + +
126G TYR* 3.6 41.8 - - + +
128G VAL* 4.8 6.5 - - + +
149G ASP* 5.2 0.5 - - - -
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Residues in contact with LYS 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F VAL* 2.8 31.2 + - - +
129F SER* 4.0 12.7 - - - +
132F LEU* 5.0 6.3 - - + -
137F LEU 3.1 15.9 + - - +
138F SER 3.7 4.3 - - - +
139F LEU 3.1 0.4 - - - -
140F GLU* 1.3 82.7 - - - +
142F ALA* 1.3 56.9 + - - +
144F LYS* 4.2 2.3 - - - +
145F GLU* 2.8 66.1 + - - +
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Residues in contact with ALA 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F VAL* 3.8 13.9 - - + +
107F VAL* 3.6 23.4 - - + +
127F GLY* 3.2 28.9 - - - +
128F VAL* 3.9 8.1 - - - +
138F SER 3.2 13.9 + - - +
139F LEU 3.0 3.2 + - - +
141F LYS* 1.3 78.4 - - - +
143F ARG* 1.3 60.2 + - - +
146F ALA* 3.0 27.9 + - - +
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Residues in contact with ARG 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F GLN* 2.8 62.4 + - - +
93F VAL* 3.6 30.1 - - + +
107F VAL* 4.1 12.3 - - + -
139F LEU* 2.7 27.0 + - + +
140F GLU* 4.2 3.4 - - - +
142F ALA* 1.3 70.3 - - - +
144F LYS* 1.3 68.0 + - + +
146F ALA 3.6 0.2 + - - -
147F VAL* 3.4 13.5 + - - +
92G ASN* 4.3 6.3 - - - +
94G ASP* 2.5 37.8 + - - -
108G CYS* 3.3 24.1 - - - -
110G PHE* 4.4 4.6 - - - -
124G VAL* 4.4 8.3 - - + -
126G TYR* 3.6 23.1 - - + -
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Residues in contact with LYS 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F GLU* 3.0 47.9 + - + +
141F LYS* 4.2 2.7 - - - +
143F ARG* 1.3 78.4 - - + +
145F GLU* 1.3 62.4 + - + +
147F VAL* 3.2 2.9 + - - +
148F THR* 3.1 20.0 + - - -
124G VAL* 4.3 10.1 - - + +
125G GLY 4.6 0.2 - - - -
126G TYR* 3.9 11.0 - - + +
149G ASP* 2.4 39.8 + - - -
153G ARG* 3.4 50.5 + - - +
156G ARG* 5.9 1.2 - - - +
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Residues in contact with GLU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F TYR 4.2 2.8 - - - +
127F GLY* 3.9 10.7 - - - -
128F VAL* 3.7 11.6 + - - +
141F LYS* 2.8 64.0 + - - +
144F LYS* 1.3 74.7 - - + +
146F ALA* 1.3 57.0 + - - +
148F THR* 3.3 5.2 + - - +
149F ASP* 2.7 37.6 + - - +
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Residues in contact with ALA 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F VAL* 3.7 24.0 - - + +
109F ALA* 3.8 16.1 - - + +
125F GLY* 3.2 11.1 - - - -
126F TYR* 3.4 7.4 - - - -
127F GLY* 3.2 25.5 - - - +
142F ALA 3.0 16.2 + - - +
143F ARG 3.9 2.9 - - - +
145F GLU* 1.3 75.2 - - - +
147F VAL* 1.3 57.3 + - - +
150F GLY* 2.9 22.7 + - - -
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Residues in contact with VAL 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F HIS* 5.2 7.2 - - + -
88F ILE* 3.5 28.5 - - + -
91F GLN* 3.7 12.3 - - - +
109F ALA* 4.1 12.6 - - + -
111F VAL* 3.7 7.0 - - + +
143F ARG 3.4 1.0 + - - -
144F LYS 3.2 8.0 + - - +
145F GLU 3.2 0.8 - - - -
146F ALA* 1.3 73.1 - - - +
148F THR* 1.3 64.1 + - - +
150F GLY* 2.7 19.1 + - - -
151F LEU* 2.8 13.9 + - + +
122G GLU 5.0 2.5 - - - +
123G ASP* 3.6 24.7 - - - +
124G VAL* 3.0 32.3 - - + -
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Residues in contact with THR 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F GLY* 4.1 26.7 - - - +
72F ILE* 6.6 0.4 - - + -
144F LYS 3.1 13.7 + - - -
145F GLU* 3.9 5.6 - - - -
147F VAL* 1.3 81.7 - - - +
149F ASP* 1.3 62.2 + - - +
151F LEU* 3.8 9.6 - - + +
152F LYS* 3.0 34.0 + - + +
123G ASP* 5.4 1.4 + - - -
153G ARG* 3.8 13.5 + - - -
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Residues in contact with ASP 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E GLU* 5.1 0.4 - - - -
144E LYS* 2.5 35.7 + - - -
125F GLY* 3.4 2.3 - - - -
126F TYR 2.9 26.8 + - - +
145F GLU* 2.7 21.7 + - + +
146F ALA 3.6 4.0 - - - +
148F THR* 1.3 74.1 - - - +
150F GLY* 1.3 62.5 + - - +
152F LYS* 3.6 18.3 + - - +
153F ARG* 3.2 29.0 + - - +
156F ARG* 5.0 4.7 + - - -
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Residues in contact with GLY 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F VAL* 3.8 16.3 - - - +
123F ASP* 4.4 3.8 - - - +
124F VAL 4.0 4.0 - - - -
125F GLY* 3.3 22.8 - - - -
146F ALA 2.9 7.5 + - - -
147F VAL 2.7 8.9 + - - -
149F ASP* 1.3 75.9 - - - +
151F LEU* 1.3 62.5 + - - -
153F ARG* 3.2 3.8 + - - +
154F ALA* 3.0 23.6 + - - +
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F VAL* 5.6 0.9 - - + -
72F ILE* 4.7 19.5 - - + -
84F TRP* 3.8 21.8 - - + -
86F HIS* 3.5 34.5 - - + +
111F VAL* 3.7 16.5 - - + +
113F VAL* 3.6 19.5 - - + -
147F VAL* 2.8 15.6 + - + +
148F THR* 3.8 12.8 - - + +
150F GLY* 1.3 70.5 - - - +
152F LYS* 1.3 64.9 + - + +
154F ALA* 3.3 1.8 + - - +
155F LEU* 3.1 39.2 + - + +
157G SER* 5.0 0.7 - - - +
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Residues in contact with LYS 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ARG* 6.1 0.6 - - - +
65F TYR* 4.3 15.8 - - - +
66F ILE* 3.0 31.8 + - + +
67F GLU* 4.9 0.2 - - - +
68F GLY* 4.2 12.2 - - - +
71F VAL* 3.8 33.7 - - + -
148F THR* 3.0 32.1 + - + +
149F ASP* 3.9 19.1 + - - +
151F LEU* 1.3 78.3 - - + +
153F ARG* 1.3 64.9 + - + +
154F ALA 3.0 1.0 + - - -
155F LEU* 3.2 3.6 + - - +
156F ARG* 3.0 37.0 + - + +
162F LEU 4.8 1.6 - - - +
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Residues in contact with ARG 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E LYS* 3.3 67.3 + - - +
147E VAL* 4.8 0.2 - - - +
148E THR* 3.7 12.9 + - - -
123F ASP* 3.1 39.4 + - + +
124F VAL 2.8 26.9 + - - +
149F ASP* 3.2 19.5 + - - +
150F GLY 3.8 4.0 - - - +
152F LYS* 1.3 79.0 - - - +
154F ALA* 1.3 60.6 + - - +
156F ARG* 3.6 52.2 - - - +
157F SER* 3.8 5.2 + - - -
167F LEU* 6.0 0.2 - - - +
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F VAL 4.1 16.4 - - - +
113F VAL* 3.2 28.9 - - + -
121F HIS* 3.7 15.8 - - - +
122F GLU 5.0 0.9 - - - -
123F ASP* 3.9 10.5 - - - +
150F GLY 3.0 16.1 + - - +
151F LEU* 3.5 3.1 - - - +
152F LYS 3.0 0.2 - - - -
153F ARG* 1.3 75.6 - - - +
155F LEU* 1.3 65.3 + - - +
156F ARG 3.2 0.2 - - - -
157F SER* 3.2 23.2 + - - -
158F PHE* 4.4 1.9 + - - -
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Residues in contact with LEU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F VAL* 3.3 35.7 - - + +
72F ILE* 5.4 0.7 - - - +
75F ALA* 4.4 12.1 - - + -
79F PHE* 4.6 3.8 - - + -
84F TRP* 4.0 18.2 - - + -
113F VAL* 3.6 25.4 - - + -
151F LEU* 3.1 35.4 + - + +
152F LYS 3.2 3.1 + - - +
154F ALA* 1.3 74.5 - - - +
156F ARG* 1.3 65.0 + - - +
157F SER 3.0 2.5 - - - -
158F PHE* 2.9 35.0 + - + +
162F LEU* 3.5 24.4 - - + +
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Residues in contact with ARG 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ILE* 4.8 5.4 - - + -
144E LYS* 6.0 0.6 - - - +
65F TYR* 6.4 0.6 - - - +
149F ASP* 5.0 6.1 + - - -
152F LYS* 3.0 26.3 + - - +
153F ARG* 3.6 51.5 - - - +
154F ALA 3.2 0.4 - - - -
155F LEU* 1.3 76.4 - - - +
157F SER* 1.3 62.1 + - - +
158F PHE 3.1 1.2 + - - -
159F GLY 3.1 17.1 + - - +
162F LEU 4.0 11.2 + - - +
163F GLY* 3.6 24.4 - - - +
164F ASN* 3.3 23.0 - - + +
166F ILE* 4.0 16.4 - - - +
167F LEU* 3.2 37.1 - - - +
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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