Contacts of the helix formed by residues 125 - 150 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 3.5 21.2 - - - +
63C ARG* 3.0 25.4 + - - -
67C ILE* 4.5 7.3 - - - +
120C THR* 3.0 19.5 + - - +
121C ASP* 5.9 0.2 - - - -
123C GLU* 3.3 6.9 - - + +
124C GLY* 1.3 74.0 - - - +
126C ASP* 1.3 62.3 + - - +
127C VAL 3.8 0.7 + - - -
128C THR* 2.6 28.4 + - - -
129C ASN* 3.2 20.0 + - - +
136H LYS* 5.4 1.9 + - - -
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ASP* 5.7 1.4 - - - +
124C GLY* 3.2 19.8 + - - +
125C ASP* 1.3 69.1 + - - +
127C VAL* 1.3 61.4 + - + +
129C ASN* 3.6 8.2 - - - +
130C ASP* 3.0 29.8 + - - +
114H LYS* 4.1 12.6 + - - -
117H ILE* 3.9 21.3 - - + +
133H ILE* 3.6 37.0 - - + +
136H LYS* 5.9 6.1 - - - +
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 3.4 37.9 - - - +
125C ASP* 3.4 1.4 + - - -
126C ASP* 1.3 73.2 - - + +
128C THR* 1.3 60.0 + - - +
130C ASP* 3.3 4.4 + - - +
131C MET* 2.9 29.3 + - + +
133H ILE* 3.7 17.9 - - + +
136H LYS* 3.9 21.9 - - + +
137H ALA* 3.5 45.8 - - + +
140H ASP* 4.0 4.7 - - - +
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Residues in contact with THR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 3.9 4.9 - - + +
13C LEU* 3.5 40.1 - - + +
63C ARG* 3.0 22.0 + - - +
67C ILE* 4.7 1.0 - - - +
120C THR* 3.8 14.4 - - - +
125C ASP* 2.6 30.0 + - - -
127C VAL* 1.3 77.7 - - - +
129C ASN* 1.3 63.2 + - - +
131C MET* 3.2 10.9 + - + +
132C LEU* 2.9 29.7 + - + +
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Residues in contact with ASN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 3.0 40.4 + - - +
120C THR* 3.1 24.4 - - + +
121C ASP* 3.7 16.2 - - - +
125C ASP 3.2 14.9 + - - +
126C ASP* 3.6 9.3 - - - +
128C THR* 1.3 78.4 - - - +
130C ASP* 1.3 56.8 + - - +
132C LEU* 3.2 3.9 + - - +
133C ILE* 3.0 47.1 + - - +
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASP 3.0 19.0 + - - +
127C VAL* 3.6 5.1 - - - +
129C ASN* 1.3 76.0 + - - +
131C MET* 1.3 65.5 + - - +
133C ILE* 3.3 9.7 + - - +
134C ALA* 3.2 22.1 + - - +
130H ASP* 3.8 12.6 - - - +
133H ILE* 4.0 19.0 - - + +
134H ALA* 5.3 8.1 - - - +
130J ASP* 3.8 18.4 - - - +
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Residues in contact with MET 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.8 28.5 - - + -
59C GLU* 3.6 35.2 - - + +
60C VAL* 4.3 10.3 - - + -
63C ARG* 3.8 23.8 - - + -
127C VAL* 2.9 21.9 + - + +
128C THR* 3.6 6.1 - - + +
130C ASP* 1.3 72.6 + - - +
132C LEU* 1.3 78.9 + - + +
134C ALA* 3.3 6.7 + - - +
135C PHE* 3.2 43.3 + - + -
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 3.9 22.7 - - + -
13C LEU* 4.0 10.5 - - + -
16C GLN* 6.0 0.4 - - + -
60C VAL* 5.1 2.2 - - + -
113C TYR* 4.1 25.7 - - + +
116C GLY 3.9 26.5 - - - +
117C ILE* 3.7 16.1 - - + +
120C THR* 4.2 4.3 - - + +
128C THR* 2.9 34.9 + - + +
129C ASN 3.5 4.0 - - - +
131C MET* 1.3 99.1 - - + +
133C ILE* 1.3 56.1 + - - +
135C PHE* 3.5 8.8 + - + +
136C LYS* 3.1 27.5 + - - +
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 3.8 23.3 - - + -
129C ASN* 3.0 41.1 + - - +
130C ASP* 3.8 9.2 - - - +
131C MET 3.3 0.4 - - - -
132C LEU* 1.3 73.6 - - - +
134C ALA* 1.3 61.0 + - - +
136C LYS* 3.4 1.5 + - - -
137C ALA* 3.0 24.8 + - + +
126J ASP* 3.7 34.1 - - + +
127J VAL* 3.6 15.3 - - + +
130J ASP* 3.9 32.8 - - + +
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Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP* 3.2 12.3 + - - +
131C MET* 3.3 10.3 + - - +
133C ILE* 1.3 75.2 - - - +
135C PHE* 1.3 72.5 + - + +
137C ALA* 3.3 15.5 + - - +
138C SER* 3.4 12.8 + - - -
130J ASP* 5.8 3.3 - - - +
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Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLN* 3.4 67.4 + - + +
59C GLU* 3.3 29.8 - - + -
60C VAL* 3.7 15.5 - - + -
113C TYR* 3.4 26.9 - + + -
131C MET* 3.2 32.5 + - + -
132C LEU* 3.8 7.0 - - + +
134C ALA* 1.3 77.8 - - + +
136C LYS* 1.3 67.7 + - - +
138C SER* 3.1 6.5 + - - -
139C ILE* 2.9 27.9 + - - +
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Residues in contact with LYS 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 3.8 40.6 - - + +
113C TYR* 4.4 5.1 - - + -
114C LYS* 4.5 23.9 - - + +
117C ILE* 4.3 18.6 - - + -
132C LEU 3.1 17.8 + - - +
133C ILE 3.4 5.4 + - - +
135C PHE* 1.3 76.6 - - - +
137C ALA* 1.3 63.7 + - - +
139C ILE* 3.3 8.8 + - - -
140C ASP* 2.8 47.5 + - - +
63J ARG* 3.9 13.5 - - - +
125J ASP* 5.0 2.0 + - - -
126J ASP* 5.9 3.2 - - + +
127J VAL* 3.9 13.2 - - + +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 3.0 11.5 + - + +
134C ALA* 3.4 13.2 - - - +
135C PHE 3.1 0.6 - - - -
136C LYS* 1.3 76.1 - - - +
138C SER* 1.3 60.9 + - - +
140C ASP* 3.5 4.9 + - - +
141C LYS* 3.2 21.8 + - - +
63J ARG* 5.0 1.7 + - - -
127J VAL* 3.4 31.6 - - + +
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Residues in contact with SER 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLU* 2.5 32.1 + - - -
53C PHE* 5.5 0.2 - - - -
56C GLN* 4.9 3.3 + - - -
134C ALA 3.4 8.0 + - - -
135C PHE* 3.1 10.1 + - - -
137C ALA* 1.3 78.8 - - - +
139C ILE* 1.3 65.7 + - - +
141C LYS* 3.4 6.9 + - - +
142C HIS* 3.0 32.3 + - - -
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Residues in contact with ILE 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PHE* 3.9 28.7 - - + -
56C GLN* 4.3 2.9 - - - +
106C LEU* 3.4 33.2 - - + +
109C LEU* 4.3 17.9 - - + -
110C ARG* 4.0 11.2 - - + +
113C TYR* 4.1 28.5 - - + -
135C PHE 2.9 22.8 + - - +
136C LYS* 3.8 7.4 - - - +
138C SER* 1.3 77.5 - - - +
140C ASP* 1.3 56.3 + - - +
142C HIS* 3.2 8.3 + - - +
143C ILE* 2.8 37.4 + - + +
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Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 3.2 35.0 + - - +
136C LYS* 2.8 45.5 + - - +
137C ALA 3.7 2.7 - - - +
139C ILE* 1.3 72.9 - - - +
141C LYS* 1.3 66.1 + - - +
143C ILE* 3.2 8.0 + - - +
144C TRP* 3.0 23.2 + - - +
63J ARG* 2.9 29.4 + - - +
66J ALA* 4.0 14.8 - - + +
127J VAL* 4.2 1.4 - - - +
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Residues in contact with LYS 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ALA 3.2 11.5 + - - +
138C SER* 3.7 10.8 - - - +
140C ASP* 1.3 77.6 - - - +
142C HIS* 1.3 66.8 + - + +
144C TRP* 3.4 22.0 + - + +
145C MET* 3.1 47.1 + - + +
62J GLU* 3.1 33.8 + - + +
66J ALA* 4.5 6.0 - - + +
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Residues in contact with HIS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 5.7 3.4 - - - -
48C ASP* 6.5 0.9 - - + -
49C LEU* 3.4 31.2 - - + +
52C GLU* 2.7 27.9 + - - -
53C PHE* 4.0 13.0 - + - -
106C LEU* 3.9 16.2 - - + -
138C SER* 3.0 31.7 + - - -
139C ILE* 3.4 8.7 - - - +
141C LYS* 1.3 78.6 - - + +
143C ILE* 1.3 57.7 + - - +
145C MET* 3.4 23.8 + - + +
146C PHE* 2.9 42.3 + + + +
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 5.0 3.6 - - + +
106C LEU* 3.9 33.9 - - + +
107C GLU* 4.2 9.2 - - + +
110C ARG* 4.0 35.9 - - + +
139C ILE* 2.8 38.9 + - + +
140C ASP* 3.2 9.8 + - - +
142C HIS* 1.3 73.8 - - - +
144C TRP* 1.3 69.0 + - - +
146C PHE* 5.3 1.1 - - - -
147C LYS* 3.0 39.7 + - + +
154C PRO* 3.8 25.6 - - + +
155C LEU* 5.2 1.6 - - + -
66J ALA 6.1 0.4 - - - +
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Residues in contact with TRP 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ASP 3.0 11.7 + - - +
141C LYS* 3.8 20.9 - - + +
143C ILE* 1.3 75.9 - - - +
145C MET* 1.3 80.1 + - + +
147C LYS* 3.8 1.6 - - - +
148C ALA* 2.8 39.4 + - + +
152C LYS 5.1 0.3 - - - +
154C PRO* 3.9 34.4 - - + +
62J GLU* 3.8 49.8 - - + -
65J LEU* 4.0 33.4 - - + +
66J ALA* 4.0 10.3 - - - -
31L HIS* 4.9 9.0 - + - -
32L TRP* 4.2 19.4 + + - -
34L MET 5.7 0.4 + - - -
39L PHE* 4.1 19.6 - + - -
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Residues in contact with MET 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 4.1 13.7 - - - +
141C LYS* 3.1 40.1 + - + +
142C HIS* 3.7 28.9 - - + +
144C TRP* 1.3 92.9 - - + +
146C PHE* 1.3 64.0 + - + +
148C ALA* 3.3 2.6 + - - +
149C PHE* 3.0 26.9 + - - +
39L PHE* 3.9 33.1 - - + -
40L PHE* 4.0 20.8 - - + -
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Residues in contact with PHE 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 5.2 1.8 - - + -
45C LYS* 4.0 19.7 - - + -
46C MET* 3.9 14.4 - - + -
49C LEU* 3.9 30.5 - - + -
99C MET* 4.0 17.7 - - + +
102C LEU* 3.7 22.0 - - + -
103C VAL* 3.6 23.8 - - + -
106C LEU* 4.5 4.0 - - + -
142C HIS* 2.9 53.8 + + + +
143C ILE* 4.5 0.4 - - - +
145C MET* 1.3 73.3 - - + +
147C LYS* 1.3 65.6 + - - +
149C PHE* 3.2 9.8 + + + +
150C LEU* 3.1 24.3 + - - +
40L PHE* 3.7 27.1 - + - -
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Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 3.4 26.0 - - + -
107C GLU* 3.1 29.3 + - - -
143C ILE* 3.0 24.9 + - + +
144C TRP 3.8 2.7 - - - +
146C PHE* 1.3 75.6 - - - +
148C ALA* 1.3 56.7 + - - +
150C LEU* 2.9 25.4 + - + +
151C GLY 3.2 0.2 + - - -
152C LYS* 3.2 32.6 + - + +
153C ALA 3.7 19.7 - - - +
154C PRO* 3.6 19.3 + - + +
155C LEU 5.0 0.4 - - - -
156C GLU* 3.1 37.2 + - - +
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TRP* 2.8 29.1 + - + +
145C MET 3.7 4.0 - - - +
147C LYS* 1.3 73.0 - - - +
149C PHE* 1.3 65.0 + - - +
151C GLY 3.0 6.9 + - - -
152C LYS 3.5 10.4 + - - +
34L MET 4.0 9.2 - - - +
35L ARG* 3.6 11.0 - - + +
36L GLY 3.0 20.8 + - - -
39L PHE* 3.8 26.7 - - + -
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Residues in contact with PHE 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 3.8 20.2 - - - -
41C THR* 5.0 0.4 - - + -
42C LEU* 3.6 38.8 - - + -
95C MET* 4.5 6.3 - - + -
96C ASP* 5.1 1.6 - - - -
99C MET* 4.2 15.9 - - + -
145C MET 3.0 13.3 + - - +
146C PHE* 3.4 13.0 - + - +
148C ALA* 1.3 74.5 - - - +
150C LEU* 1.3 73.9 + - + +
36L GLY* 3.2 28.4 - - - -
37L HIS* 3.3 48.1 + + - -
39L PHE* 4.1 7.0 - - + +
40L PHE* 3.8 30.1 - + + -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASP* 3.5 48.3 - - - +
99C MET* 4.2 12.1 - - + -
100C GLU* 3.4 36.3 - - + +
103C VAL* 4.3 21.1 - - + -
146C PHE 3.1 14.1 + - - +
147C LYS* 2.9 15.2 + - + +
149C PHE* 1.3 82.3 - - + +
151C GLY* 1.3 59.8 + - - +
152C LYS* 3.4 21.3 + - + +
36L GLY* 5.4 0.2 - - - -
37L HIS* 6.0 2.2 - - - -
----------------------------------------------------------
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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