Contacts of the helix formed by residues 94 - 123 (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 THR 94 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93M LYS* 1.3 78.6 - - - +
95M MET* 1.3 68.2 + - + +
96M ASP* 3.2 27.1 - - + +
97M GLN* 3.2 27.2 + - + +
98M LEU* 3.1 25.3 + - - +
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Residues in contact with MET 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M MET* 3.7 35.2 - - + -
35M ARG 3.6 30.1 + - - +
36M GLY* 5.7 1.3 - - - -
38M ASN* 3.6 44.0 - - + +
39M PHE* 3.7 6.3 - - - +
42M LEU* 3.4 29.6 - - + -
94M THR* 1.3 76.5 - - + +
96M ASP* 1.3 62.3 + - - +
98M LEU* 3.4 9.1 + - - +
99M MET* 3.0 34.2 + - - +
149M PHE* 4.5 6.3 - - + -
37X HIS* 5.8 1.3 - - + -
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Residues in contact with ASP 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94M THR* 3.2 13.6 - - + +
95M MET* 1.3 80.6 - - - +
97M GLN* 1.3 57.2 + - + +
99M MET* 3.4 2.7 + - - +
100M GLU* 3.0 36.7 + - - +
149M PHE* 4.4 3.8 - - - -
150M LEU* 3.7 30.4 - - + +
37X HIS* 3.1 38.4 + - - -
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Residues in contact with GLN 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M PRO 4.7 1.9 - - - +
93M LYS* 3.9 26.2 - - + +
94M THR* 3.2 40.3 + - + +
96M ASP* 1.3 74.0 - - + +
98M LEU* 1.3 60.5 + - - +
100M GLU* 3.2 11.8 + - - +
101M ASP* 3.0 26.3 + - - +
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Residues in contact with LEU 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M GLN* 5.3 7.6 - - - +
30M ILE* 3.7 42.6 - - + +
33M TYR* 4.8 3.1 - - + +
34M MET* 4.0 34.8 - - + +
35M ARG 5.3 0.7 - - - +
89M TYR* 4.0 27.1 - - + -
93M LYS* 4.1 17.5 - - + +
94M THR 3.1 23.1 + - - +
95M MET* 3.7 7.4 - - - +
97M GLN* 1.3 76.4 - - - +
99M MET* 1.3 60.8 + - + +
101M ASP* 3.2 10.0 + - + +
102M LEU 3.0 21.5 + - - -
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Residues in contact with MET 99 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M ILE* 3.8 29.6 - - + -
34M MET* 4.9 0.4 - - + -
42M LEU* 4.0 22.2 - - + -
46M MET* 4.1 14.4 - - + -
95M MET* 3.0 22.2 + - - +
96M ASP 3.7 4.7 - - - +
97M GLN 3.3 0.2 - - - -
98M LEU* 1.3 74.9 - - + +
100M GLU* 1.3 59.8 + - - +
102M LEU* 3.4 10.5 + - + +
103M VAL* 2.8 33.9 + - + +
146M PHE* 3.6 34.8 - - + +
149M PHE* 3.8 22.0 - - + -
150M LEU* 3.9 18.6 - - + -
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Residues in contact with GLU 100 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M ASP* 3.0 22.1 + - - +
97M GLN* 3.2 14.1 + - - +
99M MET* 1.3 74.5 - - - +
101M ASP* 1.3 63.3 + - - +
103M VAL* 4.1 8.7 - - + +
104M GLY* 3.1 19.9 + - - -
147M LYS* 5.8 0.5 + - - -
150M LEU* 3.6 21.4 - - + +
152M LYS* 2.8 30.3 + - - -
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Residues in contact with ASP 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M LYS* 2.7 39.5 + - - +
29M GLN* 5.0 5.4 + - - -
30M ILE* 5.1 3.7 - - + +
97M GLN 3.0 12.8 + - - +
98M LEU* 3.2 13.2 + - + +
100M GLU* 1.3 75.5 - - - +
102M LEU* 1.3 64.7 + - - +
104M GLY* 3.5 0.9 + - - -
105M THR* 3.1 28.9 + - - -
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Residues in contact with LEU 102 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M PHE* 3.4 37.2 - - + -
26M LYS* 5.3 1.3 - - - -
27M ILE* 4.6 7.4 - - + -
30M ILE* 4.1 18.3 - - + +
46M MET* 4.6 7.9 - - + -
49M LEU* 3.8 25.8 - - + -
98M LEU 3.0 12.1 + - - +
99M MET* 3.4 13.5 - - + +
101M ASP* 1.3 76.3 - - - +
103M VAL* 1.3 57.3 + - - +
105M THR* 3.1 7.6 + - - -
106M LEU* 3.0 38.0 + - + +
146M PHE* 3.9 37.2 - - + -
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Residues in contact with VAL 103 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M MET 2.8 21.6 + - - +
100M GLU* 4.1 9.4 - - + +
101M ASP 3.3 0.2 - - - -
102M LEU* 1.3 71.9 - - + +
104M GLY* 1.3 61.1 + - - +
106M LEU* 3.1 12.7 + - + +
107M GLU* 2.9 49.8 + - + +
143M ILE* 4.5 6.4 - - + +
146M PHE* 3.6 33.0 - - + -
147M LYS* 4.1 31.0 - - + +
150M LEU* 4.3 8.3 - - + -
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Residues in contact with GLY 104 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M GLU 3.1 16.7 + - - -
101M ASP 4.0 1.6 - - - -
103M VAL* 1.3 77.0 - - - +
105M THR* 1.3 56.6 + - - +
107M GLU* 3.3 16.7 + - - +
108M LEU* 3.0 28.4 + - - +
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Residues in contact with THR 105 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M PHE* 3.2 35.0 - - + -
26M LYS* 3.4 17.9 - - - -
84M VAL* 3.5 33.3 - - + +
85M GLU 5.1 0.3 + - - -
101M ASP* 3.1 14.8 + - - -
102M LEU* 3.1 10.1 + - - -
104M GLY* 1.3 76.5 - - - +
106M LEU* 1.3 61.5 + - - +
108M LEU* 3.4 7.4 + - + +
109M LEU* 3.1 25.8 + - + +
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Residues in contact with LEU 106 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M PHE* 3.7 25.8 - - + -
49M LEU* 5.4 1.8 - - + -
53M PHE* 3.9 25.1 - - + -
102M LEU* 3.0 35.8 + - + +
103M VAL* 3.1 11.4 + - + +
105M THR* 1.3 74.3 - - - +
107M GLU* 1.3 59.8 + - - +
109M LEU* 3.3 5.1 + - + +
110M ARG* 3.0 29.5 + - - +
139M ILE* 3.5 15.4 - - + +
142M HIS* 3.8 31.0 - - + +
143M ILE* 3.7 20.9 - - + -
146M PHE* 4.4 3.4 - - + -
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Residues in contact with GLU 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M VAL* 2.9 21.7 + - - +
104M GLY* 3.5 18.7 - - - +
106M LEU* 1.3 76.5 - - - +
108M LEU* 1.3 62.1 + - - +
110M ARG* 3.2 31.0 + - - +
111M ASP* 3.0 30.7 + - - +
143M ILE* 3.9 12.4 - - + +
147M LYS* 3.3 32.8 + - - -
154M PRO 4.5 2.8 - - - +
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Residues in contact with LEU 108 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ASN* 4.3 0.2 - - - +
83M SER* 3.8 31.6 - - - +
84M VAL* 3.9 25.6 - - + +
104M GLY 3.0 16.3 + - - +
105M THR* 3.6 5.6 - - - +
107M GLU* 1.3 77.2 - - - +
109M LEU* 1.3 65.8 + - + +
111M ASP* 3.3 8.3 + - - +
112M GLU* 2.9 57.6 + - + +
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Residues in contact with LEU 109 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M GLN* 3.5 22.9 - - - +
19M ASN* 3.8 23.6 - - + +
20M LEU* 4.3 16.8 - - + -
23M PHE* 4.1 33.4 - - + -
53M PHE* 4.6 8.7 - - + -
84M VAL* 4.2 7.9 - - + -
105M THR* 3.1 22.3 + - + +
106M LEU* 3.8 7.9 - - + +
107M GLU 3.3 0.2 - - - -
108M LEU* 1.3 77.1 - - + +
110M ARG* 1.3 60.5 + - - +
112M GLU* 4.4 2.2 - - - +
113M TYR* 2.9 37.3 + - + +
139M ILE* 4.1 12.6 - - + -
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Residues in contact with ARG 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M LEU 3.0 14.1 + - - +
107M GLU* 3.2 36.1 + - - +
109M LEU* 1.3 77.1 - - - +
111M ASP* 1.3 81.9 + - - +
113M TYR* 3.6 5.2 + - - +
114M LYS* 3.0 28.0 + - + +
136M LYS* 4.0 21.6 - - + +
139M ILE* 4.0 15.9 - - + +
140M ASP* 3.1 27.6 - - - +
143M ILE* 4.2 19.9 - - + +
154M PRO 5.2 0.4 + - - -
155M LEU* 3.6 29.0 - - - +
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Residues in contact with ASP 111 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M GLU* 3.0 21.9 + - - +
108M LEU* 3.7 6.4 - - - +
109M LEU 3.2 0.2 - - - -
110M ARG* 1.3 104.1 + - - +
112M GLU* 1.3 63.4 + - + +
114M LYS* 3.3 19.7 + - - +
115M GLN* 3.4 14.7 + - - +
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Residues in contact with GLU 112 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 3.3 12.3 - - + -
15M HIS* 2.7 28.8 - - - -
16M GLN* 2.9 17.0 + - - +
19M ASN* 3.0 3.8 + - - -
83M SER* 2.4 28.0 + - - -
108M LEU* 2.9 34.9 + - + +
109M LEU* 4.1 4.9 - - - +
111M ASP* 1.3 75.3 - - + +
113M TYR* 1.3 59.7 + - - +
115M GLN* 3.1 20.0 + - - +
116M GLY 2.9 22.3 + - - -
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Residues in contact with TYR 113 (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 10.1 - + - -
16M GLN* 3.4 38.1 - - + +
20M LEU* 3.4 25.4 - - + +
56M GLN* 2.9 19.7 + - - -
60M VAL* 4.7 1.9 - - + +
109M LEU* 2.9 27.8 + - + +
110M ARG 3.9 3.4 - - - +
112M GLU* 1.3 74.6 - - - +
114M LYS* 1.3 52.6 + - - +
116M GLY* 3.1 0.9 + - - -
117M ILE* 2.7 45.5 + - + +
132M LEU* 3.9 21.3 - - + +
135M PHE* 3.4 41.6 - + + -
136M LYS* 4.2 8.5 - - + -
139M ILE* 3.9 17.3 - - + -
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Residues in contact with LYS 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M ARG* 3.0 13.5 + - + +
111M ASP* 3.3 13.9 - - - +
112M GLU 3.1 0.4 - - - -
113M TYR* 1.3 74.1 - - - +
115M GLN* 1.3 64.3 - - + +
117M ILE* 3.0 18.9 + - + +
118M GLU* 3.0 42.6 + - - +
136M LYS* 4.1 23.1 - - - +
124U GLY* 3.6 18.7 + - - +
126U ASP* 3.0 27.9 + - - +
----------------------------------------------------------
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Residues in contact with GLN 115 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 4.7 3.9 - - + -
111M ASP* 3.4 9.8 + - - +
112M GLU* 3.1 26.8 + - - +
114M LYS* 1.3 77.3 - - + +
116M GLY* 1.3 56.9 + - - +
118M GLU* 3.5 20.1 + - - +
119M LEU* 3.0 33.0 + - + +
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Residues in contact with GLY 116 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 3.5 35.8 - - - -
112M GLU 2.9 11.1 + - - -
113M TYR 3.5 3.8 - - - -
115M GLN* 1.3 75.9 - - - +
117M ILE* 1.3 60.4 + - - +
119M LEU* 3.7 4.1 - - - +
120M THR* 2.9 33.3 + - - +
132M LEU* 3.7 6.3 - - - -
----------------------------------------------------------
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Residues in contact with ILE 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M TYR 2.7 24.6 + - - +
114M LYS* 3.0 13.7 + - + +
116M GLY* 1.3 78.1 - - - +
118M GLU* 1.3 63.6 + - - +
120M THR* 3.1 9.5 + - - -
121M ASP* 3.2 5.5 + - + +
129M ASN* 2.8 33.0 + - - +
132M LEU* 3.7 27.1 - - + +
133M ILE* 3.7 28.0 - - + -
136M LYS* 4.2 17.0 - - + -
126U ASP* 3.3 38.1 - - + +
127U VAL* 6.0 0.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 118 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M LYS* 3.0 39.7 + - - +
115M GLN* 3.7 22.8 - - - +
117M ILE* 1.3 76.1 - - - +
119M LEU* 1.3 61.8 + - - +
121M ASP* 3.4 9.6 - - - +
122M LYS* 3.1 28.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M VAL* 3.7 37.5 - - + +
8M ASP 4.4 0.2 - - - +
9M THR* 4.0 8.5 - - - +
12M PHE* 4.0 33.0 - - + -
115M GLN* 3.0 20.1 + - + +
116M GLY* 3.7 2.9 - - - +
118M GLU* 1.3 77.4 - - - +
120M THR* 1.3 58.0 + - + +
122M LYS* 3.2 9.2 + - - +
123M GLU* 3.0 62.1 + - + +
----------------------------------------------------------
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Residues in contact with THR 120 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M THR* 3.5 40.2 - - + +
12M PHE* 5.7 2.9 - - + -
116M GLY* 2.9 23.7 + - - +
117M ILE* 3.1 11.4 + - - -
119M LEU* 1.3 75.7 - - + +
121M ASP* 1.3 60.3 + - - +
123M GLU* 4.4 1.1 - - - -
124M GLY* 3.1 8.0 + - - -
125M ASP* 3.0 43.9 + - - +
128M THR* 3.8 16.6 - - + -
129M ASN* 3.3 17.9 - - - +
132M LEU* 4.2 5.1 - - + +
----------------------------------------------------------
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Residues in contact with ASP 121 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ILE* 3.2 18.5 + - + +
118M GLU* 3.4 9.5 - - - +
120M THR* 1.3 75.7 + - - +
122M LYS* 1.3 63.1 + - - +
124M GLY* 3.3 12.2 + - - -
126M ASP* 6.2 0.2 - - - -
129M ASN* 3.8 14.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M GLU* 3.1 20.2 + - + +
119M LEU* 3.2 9.6 + - - +
121M ASP* 1.3 77.8 - - + +
123M GLU* 1.3 60.9 + - + +
124M GLY 3.2 1.0 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M VAL 4.2 1.0 - - - +
8M ASP* 3.2 21.7 - - - +
9M THR* 2.8 37.2 + - - +
119M LEU* 3.0 33.5 + - + +
120M THR* 3.6 2.4 + - - +
121M ASP 3.4 0.2 - - - -
122M LYS* 1.3 75.5 - - + +
124M GLY* 1.3 62.6 + - - +
125M ASP* 3.3 4.5 + - + +
----------------------------------------------------------
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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