Contacts of the helix formed by residues 125 - 150 (chain M) in PDB entry 2BKC
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 ASP 125 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M THR* 3.5 25.7 - - + +
63M ARG* 2.8 26.7 + - - -
67M ILE* 4.1 9.9 - - - +
120M THR* 3.0 13.5 + - - +
123M GLU* 3.3 6.1 - - + +
124M GLY* 1.3 72.2 - - - +
126M ASP* 1.3 57.8 + - - +
127M VAL 3.6 0.3 + - - -
128M THR* 2.6 29.9 + - - -
129M ASN* 3.2 24.7 + - - +
136Q LYS* 5.3 1.4 + - - -
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Residues in contact with ASP 126 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M ASP* 6.2 0.3 - - - -
124M GLY* 3.1 23.7 + - - +
125M ASP* 1.3 70.9 + - - +
127M VAL* 1.3 65.3 + - + +
129M ASN* 3.5 8.2 + - - +
130M ASP* 3.1 24.1 + - - +
114Q LYS* 3.2 20.3 + - - +
117Q ILE* 3.9 22.4 - - + +
133Q ILE* 3.7 29.5 - - + +
136Q LYS* 5.9 2.9 - - + +
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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
----------------------------------------------------------
63M ARG* 3.3 36.8 - - - +
125M ASP* 3.5 1.2 + - - -
126M ASP* 1.3 75.7 - - + +
128M THR* 1.3 62.9 + - - +
130M ASP* 3.3 2.8 + - - +
131M MET* 3.0 24.3 + - + +
133Q ILE* 3.7 28.0 - - + +
136Q LYS* 4.0 16.5 - - + +
137Q ALA* 3.2 38.6 - - + +
140Q ASP* 4.0 10.3 - - - +
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Residues in contact with THR 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M THR* 3.8 2.0 - - + -
13M LEU* 3.5 38.9 - - + +
63M ARG* 2.9 21.8 + - - +
67M ILE* 4.6 0.5 - - - +
120M THR* 3.8 18.2 - - + -
125M ASP* 2.6 31.6 + - - -
127M VAL* 1.3 76.4 - - - +
129M ASN* 1.3 63.6 + - - +
131M MET* 3.4 10.9 + - + +
132M LEU* 3.0 26.0 + - + +
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Residues in contact with ASN 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ILE* 2.8 42.7 + - - +
120M THR* 3.3 16.2 + - - +
121M ASP* 3.8 18.0 - - - +
125M ASP 3.2 16.3 + - - +
126M ASP* 3.6 9.5 - - - +
127M VAL 3.3 0.2 - - - -
128M THR* 1.3 77.1 - - - +
130M ASP* 1.3 61.8 + - - +
132M LEU* 3.4 4.1 + - - +
133M ILE* 3.1 41.1 + - - +
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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
----------------------------------------------------------
126M ASP 3.1 16.6 + - - +
127M VAL 3.3 3.8 + - - +
129M ASN* 1.3 79.3 + - - +
131M MET* 1.3 66.1 + - - +
133M ILE* 3.3 9.5 + - - +
134M ALA* 3.1 24.7 + - - +
130Q ASP* 3.4 21.8 - - - +
133Q ILE* 4.0 19.9 - - + +
134Q ALA* 5.7 5.2 - - - +
130U ASP* 3.5 15.2 - - - +
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Residues in contact with MET 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LEU* 4.0 26.9 - - + -
59M GLU* 3.7 35.2 - - + +
60M VAL* 4.1 16.6 - - + -
63M ARG* 3.8 23.8 - - + -
127M VAL* 3.0 20.4 + - + +
128M THR* 3.6 6.5 - - + +
129M ASN 3.4 0.2 - - - -
130M ASP* 1.3 78.0 + - - +
132M LEU* 1.3 72.4 + - + +
134M ALA* 3.4 6.8 + - - +
135M PHE* 3.2 45.0 + - + -
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Residues in contact with LEU 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 3.8 29.4 - - + -
13M LEU* 4.4 4.7 - - + -
16M GLN* 5.7 0.7 - - + -
60M VAL* 5.2 2.9 - - + -
113M TYR* 3.9 28.4 - - + +
116M GLY 3.7 30.1 - - - +
117M ILE* 3.7 11.5 - - + +
120M THR* 4.2 11.7 - - + +
128M THR* 3.0 21.8 + - + +
129M ASN 3.7 4.0 - - - +
131M MET* 1.3 95.3 - - + +
133M ILE* 1.3 62.7 + - - +
135M PHE* 3.4 10.6 + - + +
136M LYS* 3.1 23.6 + - - +
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Residues in contact with ILE 133 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ILE* 3.7 24.0 - - + -
129M ASN* 3.1 38.2 + - - +
130M ASP* 3.5 12.1 - - - +
132M LEU* 1.3 74.6 - - - +
134M ALA* 1.3 65.4 + - - +
136M LYS* 3.3 1.9 + - - -
137M ALA* 3.1 21.8 + - + +
126U ASP* 3.7 40.4 - - + +
127U VAL* 3.7 12.3 - - + +
130U ASP* 3.9 24.0 - - + +
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Residues in contact with ALA 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ASP* 3.1 17.0 + - - +
131M MET* 3.4 9.2 + - - +
133M ILE* 1.3 75.9 - - - +
135M PHE* 1.3 67.7 + - + +
137M ALA* 3.3 19.8 - - - +
138M SER* 3.4 7.8 + - - -
130U ASP* 5.7 5.6 - - - +
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Residues in contact with PHE 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M GLN* 3.3 48.8 + - + +
59M GLU* 3.9 26.2 - - + -
60M VAL* 3.8 22.9 - - + -
113M TYR* 3.4 28.9 - + + -
131M MET* 3.2 41.4 + - + -
132M LEU* 3.7 7.2 - - + +
133M ILE 3.2 0.8 - - - -
134M ALA* 1.3 80.6 - - + +
136M LYS* 1.3 64.5 + - - +
138M SER* 3.3 6.1 + - - -
139M ILE* 3.0 27.2 + - - +
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Residues in contact with LYS 136 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M ARG* 4.0 29.4 - - + +
113M TYR* 4.2 7.4 - - + -
114M LYS* 4.1 26.5 - - + +
117M ILE* 4.2 19.1 - - + -
132M LEU 3.1 16.5 + - - +
133M ILE 3.3 4.2 + - - +
135M PHE* 1.3 75.2 - - - +
137M ALA* 1.3 54.2 + - - +
139M ILE* 3.6 10.9 - - + +
140M ASP* 2.6 71.5 + - - +
63U ARG* 4.4 5.7 - - - +
125U ASP* 5.5 1.0 + - - -
126U ASP* 5.7 4.3 - - - +
127U VAL* 3.7 15.4 - - + +
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Residues in contact with ALA 137 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ILE* 3.1 11.7 + - + +
134M ALA* 3.3 15.7 - - - +
136M LYS* 1.3 78.0 - - - +
138M SER* 1.3 61.3 + - - +
140M ASP* 3.4 3.6 + - - +
141M LYS* 3.3 20.3 + - - +
63U ARG* 5.0 0.9 + - - -
127U VAL* 3.4 31.9 - - + +
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Residues in contact with SER 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M GLU* 2.4 33.0 + - - -
53M PHE* 5.1 0.7 - - - -
56M GLN* 4.8 5.5 + - - -
134M ALA 3.4 6.9 + - - -
135M PHE* 3.3 9.2 + - - -
137M ALA* 1.3 77.2 - - - +
139M ILE* 1.3 57.5 + - - +
141M LYS* 3.2 10.9 + - - +
142M HIS* 2.9 37.7 + - - -
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Residues in contact with ILE 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M PHE* 3.9 29.6 - - + -
56M GLN* 4.5 2.2 - - - +
106M LEU* 3.5 30.7 - - + +
109M LEU* 4.1 21.8 - - + -
110M ARG* 4.0 9.9 - - + +
113M TYR* 3.9 29.8 - - + -
135M PHE 3.0 21.5 + - - +
136M LYS* 3.6 6.7 - - - +
138M SER* 1.3 75.8 - - - +
140M ASP* 1.3 56.3 + - - +
142M HIS* 3.4 8.4 + - - +
143M ILE* 3.0 37.2 + - + +
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Residues in contact with ASP 140 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M ARG* 3.1 33.3 + - - +
136M LYS* 2.6 51.3 + - - +
137M ALA 3.7 2.7 - - - +
138M SER 3.3 0.2 - - - -
139M ILE* 1.3 71.8 - - - +
141M LYS* 1.3 60.5 + - - +
143M ILE* 3.4 8.3 + - - +
144M TRP* 3.2 17.8 + - - +
63U ARG* 3.0 34.4 + - - +
66U ALA* 3.8 22.5 - - + +
67U ILE* 6.1 0.4 - - - -
127U VAL* 3.9 1.7 - - - +
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Residues in contact with LYS 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M ALA 3.3 10.4 + - - +
138M SER* 3.4 12.6 - - - +
140M ASP* 1.3 76.3 - - - +
142M HIS* 1.3 64.3 + - + +
143M ILE 3.3 0.3 + - - -
144M TRP* 3.3 19.2 + - + +
145M MET* 3.1 42.3 + - + +
59U GLU* 4.8 19.4 + - - +
62U GLU* 3.4 40.3 + - - +
63U ARG* 5.5 1.1 - - - +
66U ALA* 4.5 5.1 - - + +
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Residues in contact with HIS 142 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M LYS* 4.6 5.1 + - - -
48M ASP* 6.5 0.7 - - + -
49M LEU* 3.8 24.9 - - + +
52M GLU* 2.6 28.3 + - - -
53M PHE* 4.0 19.5 - + - -
106M LEU* 3.8 19.1 - - + -
138M SER* 2.9 38.4 + - - +
139M ILE* 3.4 4.0 + - - +
141M LYS* 1.3 71.9 - - + +
143M ILE* 1.3 61.7 + - - +
145M MET* 3.5 23.3 - - + +
146M PHE* 2.9 39.4 + - + +
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Residues in contact with ILE 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M VAL* 4.5 8.1 - - + +
106M LEU* 3.7 34.3 - - + +
107M GLU* 3.9 16.2 - - + +
110M ARG* 4.2 28.3 - - - +
139M ILE* 3.0 40.4 + - + +
140M ASP* 3.8 7.0 - - - +
141M LYS 3.2 0.4 - - - -
142M HIS* 1.3 76.6 - - - +
144M TRP* 1.3 64.7 + - - +
146M PHE* 5.1 0.9 - - - -
147M LYS* 3.0 30.8 + - + +
154M PRO* 3.6 27.1 - - + +
155M LEU* 5.6 0.9 - - + -
66U ALA 6.1 0.4 - - - +
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Residues in contact with TRP 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M ASP 3.2 11.6 + - - +
141M LYS* 3.5 15.0 - - + +
143M ILE* 1.3 76.9 - - - +
145M MET* 1.3 79.5 + - + +
147M LYS* 3.8 1.4 - - - +
148M ALA* 2.9 34.4 + - + +
152M LYS 5.1 0.4 - - - +
154M PRO* 4.0 28.4 - - + +
62U GLU* 3.5 50.0 - - + -
65U LEU* 3.6 37.3 - - + +
66U ALA* 4.2 14.8 - - + -
31X HIS* 4.6 15.9 - + - -
32X TRP* 4.1 12.2 + - - -
34X MET 5.5 0.4 + - - -
39X PHE* 3.8 25.1 - + - -
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Residues in contact with MET 145 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M LYS* 4.7 8.5 - - - +
141M LYS* 3.1 33.2 + - + +
142M HIS* 3.5 35.4 - - + +
144M TRP* 1.3 99.9 - - + +
146M PHE* 1.3 58.5 + - + +
148M ALA* 3.3 3.5 + - - +
149M PHE* 2.8 27.0 + - - +
62U GLU* 5.7 0.7 - - - +
39X PHE* 3.6 33.1 - - + -
40X PHE* 3.8 18.6 - - + -
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Residues in contact with PHE 146 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M LEU* 4.6 2.0 - - + -
45M LYS* 3.9 24.0 - - + -
46M MET* 3.9 19.1 - - + -
49M LEU* 4.0 22.7 - - + -
99M MET* 3.6 32.5 - - + -
102M LEU* 3.9 17.0 - - + -
103M VAL* 3.6 23.1 - - + -
106M LEU* 4.4 1.6 - - + -
142M HIS* 2.9 44.1 + - + +
143M ILE* 5.1 0.2 - - - -
145M MET* 1.3 72.4 - - + +
147M LYS* 1.3 66.4 + - - +
149M PHE* 3.3 8.8 + - + +
150M LEU* 3.1 25.8 + - + +
40X PHE* 3.8 25.8 - + - -
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Residues in contact with LYS 147 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M GLU* 5.8 0.4 + - - -
103M VAL* 4.1 21.5 - - + +
107M GLU* 3.3 22.7 + - - -
143M ILE* 3.0 27.8 + - + +
144M TRP 3.8 2.5 - - - +
146M PHE* 1.3 76.1 - - - +
148M ALA* 1.3 56.8 + - - +
150M LEU* 2.8 26.5 + - + +
151M GLY 3.1 8.8 + - - -
152M LYS* 3.1 32.4 + - + +
153M ALA 3.6 21.8 - - - +
154M PRO* 3.2 30.7 - - + +
155M LEU* 5.0 0.7 - - - +
156M GLU 3.7 20.5 + - - +
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Residues in contact with ALA 148 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M TRP* 2.9 27.1 + - + +
145M MET 3.5 4.0 - - - +
146M PHE 3.3 0.2 - - - -
147M LYS* 1.3 76.2 - - - +
149M PHE* 1.3 60.1 + - - +
151M GLY 3.0 6.4 + - - -
152M LYS 3.5 13.1 + - - +
34X MET 3.9 8.3 - - - +
35X ARG* 3.4 9.8 - - + +
36X GLY 2.8 24.2 + - - -
39X PHE* 3.7 26.9 - - + -
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Residues in contact with PHE 149 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ASN* 3.9 20.2 - - - -
41M THR* 5.9 1.1 - - - -
42M LEU* 3.4 29.6 - - + -
95M MET* 4.5 3.6 - - + -
96M ASP* 4.4 9.6 - - - -
99M MET* 3.8 29.6 - - + -
145M MET 2.8 14.5 + - - +
146M PHE* 3.4 9.0 - - - +
147M LYS 3.2 0.2 - - - -
148M ALA* 1.3 74.6 - - - +
150M LEU* 1.3 72.5 + - + +
36X GLY* 3.2 27.0 - - - +
37X HIS* 3.2 47.7 + + - -
39X PHE* 4.1 5.1 - - + +
40X PHE* 3.8 29.4 - + + -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M ASP* 3.7 48.5 - - + +
99M MET* 3.9 23.1 - - + -
100M GLU* 3.6 32.3 - - + +
103M VAL* 4.3 14.4 - - + -
146M PHE 3.1 15.6 + - - +
147M LYS* 2.8 15.2 + - + +
149M PHE* 1.3 82.2 - - + +
151M GLY* 1.3 61.3 + - - +
152M LYS* 3.7 15.2 + - + +
36X GLY* 5.4 0.2 - - - -
37X HIS* 5.4 1.8 - - - -
----------------------------------------------------------
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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