Contacts of the helix formed by residues 120 - 148 (chain M) in PDB entry 2FJC
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 ILE 120 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M ILE* 4.1 22.4 - - + -
61M TYR 3.4 23.8 + - - +
62M GLY* 4.0 2.7 - - - -
64M GLU* 3.3 36.6 - - + +
65M PHE* 3.5 30.5 - - - +
68M VAL* 3.7 21.8 - - + -
119M THR* 1.3 71.2 + - - +
121M VAL* 1.3 71.8 + - + +
123M ALA* 3.3 1.6 + - - +
124M LEU* 2.9 35.2 + - + +
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Residues in contact with VAL 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M THR* 3.2 14.8 - - + +
120M ILE* 1.3 82.8 - - + +
122M SER* 1.3 62.0 + - - +
124M LEU* 6.1 0.2 - - + -
125M ALA* 3.0 30.8 + - - +
174M THR 6.1 0.9 - - - +
175M LEU* 3.7 23.8 - - + +
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Residues in contact with SER 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M ILE* 3.9 9.1 - - - +
119M THR* 2.9 28.3 - - - +
121M VAL* 1.3 81.0 - - - +
123M ALA* 1.3 61.5 + - - +
125M ALA* 3.5 5.1 + - - +
126M ARG* 3.1 54.9 + - - +
129M ARG* 5.2 0.2 + - - -
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Residues in contact with ALA 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M TYR* 3.7 26.1 - - + -
60M ILE* 3.6 24.9 - - + -
72M LEU* 5.5 1.1 - - + -
118M ILE* 3.7 10.5 - - + +
119M THR 2.9 17.9 + - - +
120M ILE 3.7 2.7 - - - +
122M SER* 1.3 75.9 - - - +
124M LEU* 1.3 66.2 + - + +
126M ARG* 3.1 4.6 + - - +
127M VAL* 3.0 27.9 + - - +
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Residues in contact with LEU 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M VAL* 3.9 26.9 - - + -
71M LEU* 4.4 13.0 - - + -
72M LEU* 4.4 13.5 - - + -
120M ILE* 2.9 36.8 + - + +
121M VAL* 5.1 0.7 - - + -
123M ALA* 1.3 77.4 - - + +
125M ALA* 1.3 58.9 + - - +
127M VAL* 3.3 8.1 + - + +
128M LYS* 2.9 30.1 + - - +
171M LEU* 3.9 24.3 - - + +
174M THR* 3.8 21.5 - - + +
175M LEU* 3.8 17.7 - - + +
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Residues in contact with ALA 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M VAL 3.0 19.0 + - - +
122M SER* 3.8 7.2 - - - +
124M LEU* 1.3 77.0 - - - +
126M ARG* 1.3 57.5 + - - +
128M LYS* 3.4 3.9 + - - +
129M ARG* 3.0 44.0 + - - +
175M LEU* 3.5 17.9 - - + +
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Residues in contact with ARG 126 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M LYS* 5.4 3.6 - - - +
56M TYR* 3.3 25.1 - - - +
113M GLU* 2.7 40.0 + - - -
115M GLU* 3.4 25.2 + - - -
118M ILE* 3.2 20.0 - - - +
122M SER* 3.1 30.6 + - - +
123M ALA 3.1 7.2 + - - +
125M ALA* 1.3 74.5 - - - +
127M VAL* 1.3 65.6 + - - +
129M ARG* 3.2 32.8 + - - +
130M ASP* 3.0 26.5 + - - -
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Residues in contact with VAL 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M LEU* 5.6 1.3 - - + -
53M LEU* 3.8 21.8 - - + -
56M TYR* 3.5 27.4 - - + -
72M LEU* 4.4 7.9 - - + -
75M TYR* 4.2 13.0 - - + -
123M ALA 3.0 15.5 + - - +
124M LEU* 3.3 15.5 - - + +
126M ARG* 1.3 72.2 - - - +
128M LYS* 1.3 65.1 + - - +
130M ASP* 3.2 7.5 + - - +
131M PHE* 2.7 39.3 + - + -
171M LEU* 3.3 23.3 - - + -
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Residues in contact with LYS 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M LEU 2.9 17.0 + - - +
125M ALA* 3.6 6.7 - - - +
127M VAL* 1.3 77.6 - - - +
129M ARG* 1.3 57.7 + - - +
131M PHE* 3.2 4.2 + - - +
132M GLU* 2.9 67.1 + - + +
168M ILE* 3.7 16.3 - - + +
171M LEU* 3.6 22.2 - - + -
172M GLY* 3.5 38.8 - - - +
175M LEU* 4.2 10.5 - - + -
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Residues in contact with ARG 129 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125M ALA* 3.0 27.7 + - - +
126M ARG* 3.3 39.9 - - - +
128M LYS* 1.3 76.5 - - - +
130M ASP* 1.3 60.0 + - - +
132M GLU* 3.2 15.5 + - - +
133M TYR* 2.9 27.5 + - - +
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Residues in contact with ASP 130 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M LEU* 4.2 19.6 - - + +
52M LYS* 2.7 43.6 + - - +
56M TYR* 5.4 0.7 - - - -
110M ILE* 3.8 20.9 - - + +
111M ALA 5.4 0.3 + - - -
126M ARG 3.0 17.0 + - - +
127M VAL* 3.7 9.2 - - - +
129M ARG* 1.3 76.3 - - - +
131M PHE* 1.3 62.0 + - - +
133M TYR* 3.2 10.2 + - - +
134M LEU* 2.9 33.8 + - - +
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Residues in contact with PHE 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M LEU* 3.8 30.1 - - + -
53M LEU* 4.9 3.4 - - + -
75M TYR* 3.8 46.0 - + + -
79M VAL* 4.5 10.1 - - + -
127M VAL* 2.7 23.9 + - + +
128M LYS 3.5 5.4 - - - +
130M ASP* 1.3 73.5 - - + +
132M GLU* 1.3 58.2 + - - +
134M LEU* 3.3 4.7 + - + +
135M SER* 2.8 28.9 + - - -
164M LEU* 3.8 23.4 - - + +
167M ALA* 3.8 28.9 - - + -
168M ILE* 3.6 17.7 - - + +
171M LEU* 3.7 19.1 - - + -
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Residues in contact with GLU 132 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M LYS* 2.9 54.2 + - - +
129M ARG* 3.5 17.3 - - - +
130M ASP 3.2 0.2 - - - -
131M PHE* 1.3 75.0 - - - +
133M TYR* 1.3 63.3 + - - +
135M SER* 3.2 3.5 + - - -
136M THR* 3.1 31.2 + - + +
168M ILE* 3.8 28.4 - - + +
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Residues in contact with TYR 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M GLN* 3.9 10.9 + - - -
45M ASP* 3.1 29.9 + - - -
109M GLY* 3.3 31.3 + - - -
110M ILE* 3.7 25.1 - - + -
129M ARG 2.9 14.2 + - - +
130M ASP* 3.6 10.8 - - - +
132M GLU* 1.3 76.3 - - - +
134M LEU* 1.3 68.5 + - + +
136M THR* 3.0 24.5 + - - -
137M ARG* 3.1 36.1 + - + +
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Residues in contact with LEU 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M HIS* 5.2 3.4 - - - +
45M ASP* 3.8 33.2 - - + +
46M LEU* 3.6 21.3 - - + -
49M LEU* 3.6 31.9 - - + -
79M VAL* 5.7 0.7 - - + -
110M ILE* 4.3 7.6 - - + -
130M ASP 2.9 17.4 + - - +
131M PHE* 3.6 5.2 - - + +
133M TYR* 1.3 78.5 - - + +
135M SER* 1.3 53.5 + - - +
137M ARG* 3.2 6.3 + - + +
138M PHE* 2.7 63.8 + - + -
164M LEU* 4.0 13.5 - - + -
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Residues in contact with SER 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131M PHE 2.8 17.9 + - - -
132M GLU* 3.2 6.9 + - - -
134M LEU* 1.3 77.7 - - - +
136M THR* 1.3 58.1 + - - +
139M SER* 2.9 35.1 + - - -
161M LEU* 3.7 15.5 + - - +
164M LEU* 4.0 14.7 - - - +
165M GLY* 5.6 1.7 + - - -
168M ILE* 4.0 17.5 - - - +
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Residues in contact with THR 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132M GLU* 3.1 15.8 + - + +
133M TYR* 3.0 15.5 + - - -
135M SER* 1.3 77.3 - - - +
137M ARG* 1.3 70.7 + - - +
139M SER* 3.3 7.0 + - - -
140M GLN* 3.1 29.9 + - - +
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Residues in contact with ARG 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M GLN* 3.5 25.0 - - - +
41M GLN* 3.3 29.5 + - - +
42M HIS* 3.7 13.9 - - + +
45M ASP* 4.9 1.6 - - - +
133M TYR* 3.1 44.5 + - + +
134M LEU* 3.5 12.1 - - + +
136M THR* 1.3 85.8 + - - +
138M PHE* 1.3 62.2 + - - +
140M GLN* 3.1 44.4 + - - +
141M THR* 3.4 14.0 + - - -
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Residues in contact with PHE 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M HIS* 3.3 39.9 - + + -
46M LEU* 3.9 20.4 - - + -
86M ILE* 3.4 24.9 - - + -
134M LEU* 2.7 51.3 + - + +
137M ARG* 1.3 72.3 - - - +
139M SER* 1.3 58.0 + - - +
141M THR* 3.0 3.5 + - - -
142M GLN 2.9 24.1 + - - -
157M ILE* 3.3 25.3 - - + +
160M ILE* 3.8 18.2 - - + -
161M LEU* 3.4 16.6 - - + -
164M LEU* 3.5 22.4 - - + -
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Residues in contact with SER 139 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135M SER* 2.9 23.6 + - - -
136M THR* 3.6 8.9 - - - -
137M ARG 3.3 0.2 - - - -
138M PHE* 1.3 76.2 - - - +
140M GLN* 1.3 62.8 + - - +
142M GLN* 3.2 5.4 + - - +
143M VAL* 3.0 30.6 + - - +
161M LEU* 4.0 20.6 - - - +
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Residues in contact with GLN 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M GLN* 3.7 12.5 + - - +
136M THR* 3.1 19.8 + - - +
137M ARG* 3.1 49.2 + - - +
138M PHE 3.2 0.6 - - - -
139M SER* 1.3 76.4 - - - +
141M THR* 1.3 63.4 + - - +
143M VAL* 3.2 8.9 + - - +
144M LEU* 3.0 29.1 + - + +
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Residues in contact with THR 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ILE* 4.6 7.6 - - + -
38M GLN* 3.1 24.1 + - + +
39M LEU* 3.7 28.5 - - + -
42M HIS* 2.6 27.4 + - - +
137M ARG 3.4 0.4 + - - -
138M PHE 3.0 9.3 + - - -
140M GLN* 1.3 78.2 - - - +
142M GLN* 1.3 56.9 + - - +
144M LEU* 3.1 9.1 + - - +
145M ALA* 2.8 28.4 + - - +
153M THR* 4.4 7.4 - - + -
157M ILE* 4.0 14.1 - - + -
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Residues in contact with GLN 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138M PHE 2.9 8.0 + - - +
139M SER* 3.2 9.8 + - - +
141M THR* 1.3 76.4 - - - +
143M VAL* 1.3 75.8 + - + +
145M ALA* 3.4 6.6 + - - +
146M ALA* 2.8 33.3 + - - +
154M ASP* 2.9 32.1 - - - +
157M ILE* 3.7 26.6 - - + +
158M THR* 3.9 9.3 + - - +
161M LEU* 4.2 14.6 - - + -
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Residues in contact with VAL 143 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M SER* 3.0 20.2 + - - +
140M GLN* 3.5 10.3 - - - +
141M THR 3.2 0.2 - - - -
142M GLN* 1.3 92.7 - - + +
144M LEU* 1.3 59.2 + - + +
146M ALA* 3.3 2.4 + - - +
147M GLU* 2.9 60.7 + - + +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M ALA* 4.0 31.2 - - + +
35M ILE* 4.1 13.6 - - + +
38M GLN* 4.2 24.5 - - + -
140M GLN* 3.0 18.7 + - + +
141M THR* 3.1 7.6 + - - +
143M VAL* 1.3 80.2 - - + +
145M ALA* 1.3 61.7 + - - +
147M GLU* 3.9 11.9 - - - +
148M SER* 3.0 27.6 + - - -
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Residues in contact with ALA 145 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ILE* 3.7 8.4 - - + +
141M THR 2.8 17.7 + - - +
142M GLN* 3.8 4.0 - - - +
144M LEU* 1.3 73.9 - - - +
146M ALA* 1.3 62.4 + - - +
148M SER* 3.4 6.0 + - - -
149M GLY 3.1 3.8 + - - -
150M ASP* 2.8 51.9 + - + +
153M THR* 4.0 12.8 - - + -
154M ASP* 3.8 17.0 - - - +
----------------------------------------------------------
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Residues in contact with ALA 146 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M GLN* 2.8 29.3 + - - +
143M VAL* 3.3 5.1 + - - +
145M ALA* 1.3 77.2 - - - +
147M GLU* 1.3 63.9 - - + +
149M GLY* 3.3 11.7 + - - -
154M ASP* 3.5 20.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 147 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M VAL* 2.9 41.7 + - + +
144M LEU* 4.0 11.5 - - - +
146M ALA* 1.3 78.3 - - + +
148M SER* 1.3 59.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 148 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ASP* 5.6 0.7 - - - -
31M ALA* 3.6 28.9 - - - +
35M ILE* 3.6 17.2 - - - +
144M LEU 3.0 18.3 + - - -
145M ALA 3.4 5.2 + - - -
146M ALA 3.2 0.2 - - - -
147M GLU* 1.3 76.3 - - - +
149M GLY* 1.3 60.2 + - - +
150M ASP* 3.4 4.9 + - - +
----------------------------------------------------------
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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