Contacts of the helix formed by residues 125 - 150 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LYS* 5.0 2.1 + - - -
9J THR* 3.8 19.4 - - - +
63J ARG* 3.1 26.1 + - - -
67J ILE* 4.2 10.6 - - - +
120J THR* 3.0 20.0 + - - +
123J GLU* 3.3 4.9 + - + -
124J GLY* 1.3 75.3 - - - +
126J ASP* 1.3 62.8 + - - +
127J VAL 3.6 1.0 + - - -
128J THR* 2.8 29.1 + - - -
129J ASN* 3.2 22.9 + - - +
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Residues in contact with ASP 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LYS* 2.9 35.7 + - - +
117C ILE* 3.3 20.9 - - + +
133C ILE* 3.7 28.6 - - + +
136C LYS* 5.9 2.8 - - + +
124J GLY* 3.2 9.9 + - - +
125J ASP* 1.3 73.0 + - - +
127J VAL* 1.3 66.2 + - + +
129J ASN* 3.4 7.6 + - - +
130J ASP* 3.0 23.7 + - - +
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Residues in contact with VAL 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 6.0 0.2 - - + -
133C ILE* 3.6 28.7 - - + +
136C LYS* 3.9 30.0 - - + +
137C ALA* 3.4 37.0 - - + +
140C ASP* 4.2 0.4 - - - +
63J ARG* 3.5 33.0 - - - +
125J ASP* 3.5 1.2 + - - -
126J ASP* 1.3 76.9 - - + +
128J THR* 1.3 57.1 + - - +
130J ASP* 3.1 5.0 + - - +
131J MET* 2.9 30.0 + - + +
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Residues in contact with THR 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J THR* 3.7 16.1 - - + +
13J LEU* 3.7 34.1 - - + +
63J ARG* 3.0 22.4 + - - +
67J ILE* 4.8 0.9 - - - +
120J THR* 3.6 5.8 - - - +
125J ASP* 2.8 31.0 + - - -
127J VAL* 1.3 75.9 - - - +
129J ASN* 1.3 62.8 + - - +
131J MET* 3.5 13.4 + - + +
132J LEU* 3.1 30.2 + - + +
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Residues in contact with ASN 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J ILE* 3.0 37.1 + - - +
120J THR* 3.3 17.8 + - + +
121J ASP* 3.5 17.2 + - - +
125J ASP 3.2 19.8 + - - +
126J ASP* 3.4 8.5 - - - +
127J VAL 3.3 0.2 - - - -
128J THR* 1.3 77.0 - - - +
130J ASP* 1.3 62.5 + - - +
132J LEU* 3.3 3.9 + - - +
133J ILE* 3.1 46.5 + - - +
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Residues in contact with ASP 130 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP* 3.8 17.9 - - - +
133C ILE* 3.9 20.4 - - + +
134C ALA* 5.8 3.7 - - - +
130H ASP* 3.9 13.2 - - - +
126J ASP 3.0 13.2 + - - +
127J VAL* 3.5 8.0 - - - +
129J ASN* 1.3 77.3 + - - +
131J MET* 1.3 68.5 + - - +
132J LEU 3.2 0.2 + - - -
133J ILE* 3.3 9.6 + - - +
134J ALA* 3.2 23.7 + - - +
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Residues in contact with MET 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LEU* 4.3 8.1 - - + -
59J GLU* 3.7 37.5 - - - +
60J VAL* 4.4 13.0 - - + -
63J ARG* 3.8 27.1 - - + -
127J VAL* 2.9 18.0 + - + +
128J THR* 3.7 13.7 - - + +
129J ASN 3.4 0.2 - - - -
130J ASP* 1.3 80.6 + - - +
132J LEU* 1.3 85.0 + - + +
134J ALA* 3.4 6.1 + - - +
135J PHE* 3.4 41.3 + - + -
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Residues in contact with LEU 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J PHE* 3.7 34.3 - - + -
13J LEU* 4.4 4.7 - - + -
16J GLN* 5.8 1.3 - - + -
60J VAL* 5.2 4.0 - - + -
113J TYR* 4.2 20.3 - - + +
116J GLY 3.9 21.3 - - - +
117J ILE* 3.6 17.4 - - + +
120J THR* 4.3 6.7 - - + -
128J THR* 3.1 25.6 + - + +
129J ASN 3.3 0.9 + - - +
130J ASP 3.2 0.2 - - - -
131J MET* 1.3 96.7 - - + +
133J ILE* 1.3 66.9 + - - +
135J PHE* 3.5 14.6 + - + +
136J LYS* 3.1 22.7 + - - +
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Residues in contact with ILE 133 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H ASP* 3.6 47.1 - - + +
127H VAL* 3.5 12.2 - - + +
130H ASP* 4.0 20.9 - - + -
117J ILE* 3.8 25.1 - - + -
129J ASN* 3.1 40.6 + - - +
130J ASP* 3.3 9.6 + - - +
132J LEU* 1.3 77.8 - - - +
134J ALA* 1.3 62.2 + - - +
136J LYS* 3.2 1.3 + - - -
137J ALA* 3.1 18.4 + - - +
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Residues in contact with ALA 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H ASP* 5.5 8.1 - - - +
130J ASP* 3.2 15.6 + - - +
131J MET* 3.8 9.9 - - - +
132J LEU 3.2 0.2 - - - -
133J ILE* 1.3 78.5 - - - +
135J PHE* 1.3 67.5 + - + +
137J ALA* 3.2 22.2 + - - +
138J SER* 3.3 6.8 + - - -
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Residues in contact with PHE 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J GLN* 3.3 51.3 + - + +
59J GLU* 3.7 35.2 - - + -
60J VAL* 4.1 18.6 - - + -
113J TYR* 3.6 25.8 - + + -
131J MET* 3.4 34.4 + - + -
132J LEU* 4.0 8.1 - - + +
133J ILE 3.4 0.2 - - - -
134J ALA* 1.3 81.8 - - + +
136J LYS* 1.3 58.7 + - - +
138J SER* 3.1 5.7 + - - +
139J ILE* 2.8 35.1 + - - +
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Residues in contact with LYS 136 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ARG* 4.4 6.3 - - - +
125H ASP* 5.6 0.4 + - - -
126H ASP* 5.6 6.1 - - - +
127H VAL* 4.0 16.1 - - + +
110J ARG* 4.1 32.3 - - + +
113J TYR* 4.4 6.2 - - + -
114J LYS* 4.7 17.3 - - + +
117J ILE* 4.4 17.9 - - + -
132J LEU 3.1 14.0 + - - +
133J ILE 3.2 8.5 + - - +
135J PHE* 1.3 78.6 - - - +
137J ALA* 1.3 58.1 + - - +
139J ILE* 4.2 8.3 - - - -
140J ASP* 2.8 63.6 + - - +
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Residues in contact with ALA 137 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ARG* 5.0 0.4 + - - +
127H VAL* 3.5 28.8 - - + +
133J ILE* 3.1 11.0 + - + +
134J ALA* 3.3 13.9 - - - +
136J LYS* 1.3 75.6 - - - +
138J SER* 1.3 63.3 + - - +
140J ASP* 3.8 3.2 - - - +
141J LYS* 3.1 22.7 + - - +
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Residues in contact with SER 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J GLU* 2.2 34.8 + - - -
53J PHE* 5.1 0.3 - - - -
56J GLN* 4.8 3.7 + - - -
134J ALA 3.3 7.0 + - - -
135J PHE* 3.1 12.3 + - - -
137J ALA* 1.3 80.5 - - - +
139J ILE* 1.3 58.4 + - - +
141J LYS* 3.1 11.5 + - - +
142J HIS* 2.9 39.3 + - - -
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Residues in contact with ILE 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J PHE* 3.8 25.8 - - + -
56J GLN* 4.1 7.9 - - - +
106J LEU* 3.6 30.9 - - + +
109J LEU* 4.3 12.3 - - + -
110J ARG* 3.8 19.3 - - + +
113J TYR* 3.5 36.6 - - + -
135J PHE 2.8 20.9 + - - +
136J LYS* 3.8 4.9 - - - +
138J SER* 1.3 76.7 - - - +
140J ASP* 1.3 56.8 + - - +
142J HIS* 3.1 11.7 + - - +
143J ILE* 2.9 32.5 + - + +
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Residues in contact with ASP 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ARG* 2.8 33.7 + - - +
66H ALA* 3.8 21.0 - - + +
127H VAL* 4.2 1.0 - - - +
110J ARG* 3.2 32.1 + - - +
136J LYS* 2.8 46.0 + - - +
137J ALA 3.8 2.7 - - - +
139J ILE* 1.3 72.4 - - - +
141J LYS* 1.3 64.9 + - - +
143J ILE* 3.4 8.4 + - - +
144J TRP* 3.2 17.3 + - - +
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Residues in contact with LYS 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H GLU* 3.5 29.0 + - + +
66H ALA* 4.7 5.6 - - + +
137J ALA 3.1 11.3 + - - +
138J SER* 3.3 12.1 - - - +
140J ASP* 1.3 76.0 - - - +
142J HIS* 1.3 67.3 + - + +
143J ILE 3.2 0.2 + - - -
144J TRP* 3.4 23.5 + - + +
145J MET* 3.1 46.6 + - + +
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Residues in contact with HIS 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J LYS* 4.8 7.3 + - - -
48J ASP* 6.4 0.9 - - + -
49J LEU* 4.3 17.0 - - + +
52J GLU* 2.7 28.4 + - - -
53J PHE* 4.1 16.9 - + - -
106J LEU* 3.8 19.1 - - + -
138J SER* 2.9 37.6 + - - -
139J ILE* 3.1 8.7 + - - +
141J LYS* 1.3 76.3 - - + +
143J ILE* 1.3 57.5 + - - +
145J MET* 4.0 21.6 - - + +
146J PHE* 2.9 51.7 + + + +
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Residues in contact with ILE 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J VAL* 4.8 6.7 - - + +
106J LEU* 4.1 18.8 - - + +
107J GLU* 4.1 23.1 - - + +
110J ARG* 3.6 38.8 - - - +
139J ILE* 2.9 36.9 + - + +
140J ASP* 3.8 7.0 - - - +
141J LYS 3.1 0.6 - - - -
142J HIS* 1.3 73.1 - - - +
144J TRP* 1.3 68.4 + - - +
146J PHE* 5.1 1.6 - - - -
147J LYS* 3.0 33.0 + - + +
154J PRO* 3.7 23.6 - - + +
155J LEU* 5.3 0.9 - - + -
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Residues in contact with TRP 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F HIS* 5.1 13.9 - + - -
32F TRP* 4.7 8.0 + - - -
39F PHE* 4.1 26.9 - + - -
62H GLU* 3.9 44.6 - - + -
65H LEU* 3.8 35.6 - - + +
66H ALA* 4.0 18.4 - - + -
140J ASP 3.2 10.9 + - - +
141J LYS* 3.7 22.0 - - + +
143J ILE* 1.3 79.4 - - - +
145J MET* 1.3 85.2 + - + +
147J LYS* 3.9 0.9 - - - +
148J ALA* 2.9 30.3 + - + +
154J PRO* 4.0 29.6 - - + +
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Residues in contact with MET 145 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F PHE* 3.8 30.0 - - + -
40F PHE* 4.1 20.8 - - + -
45J LYS* 4.4 13.0 - - - +
141J LYS* 3.1 43.5 + - + +
142J HIS* 3.8 26.5 - - + +
143J ILE 3.2 0.2 - - - -
144J TRP* 1.3 111.1 - - + +
146J PHE* 1.3 57.9 + - + +
148J ALA* 3.4 4.2 + - - +
149J PHE* 3.1 24.4 + - - +
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Residues in contact with PHE 146 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F PHE* 3.7 32.3 - + - -
42J LEU* 4.8 3.1 - - + -
45J LYS* 4.4 9.2 - - + -
46J MET* 3.8 23.6 - - + -
49J LEU* 4.0 23.6 - - + -
99J MET* 3.9 31.1 - - + +
102J LEU* 4.0 15.9 - - + -
103J VAL* 3.5 22.9 - - + -
106J LEU* 4.3 2.7 - - + -
142J HIS* 2.9 42.6 + - + +
143J ILE 4.4 0.2 - - - +
145J MET* 1.3 74.3 - - + +
147J LYS* 1.3 66.3 + - - +
149J PHE* 3.2 9.1 + + + +
150J LEU* 3.1 24.5 + - + +
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Residues in contact with LYS 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J VAL* 3.7 24.6 - - + +
107J GLU* 2.9 30.9 + - - -
143J ILE* 3.0 24.7 + - + +
144J TRP 4.1 1.8 - - - +
146J PHE* 1.3 71.9 - - - +
148J ALA* 1.3 65.7 + - - +
150J LEU* 3.1 18.6 + - + +
151J GLY 3.3 0.2 + - - -
152J LYS* 3.0 45.1 + - + +
153J ALA 3.7 21.3 - - - +
154J PRO* 3.7 16.2 - - + -
155J LEU* 5.3 0.4 - - - +
156J GLU 3.8 21.1 + - - +
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Residues in contact with ALA 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F MET 4.1 7.9 - - - +
35F ARG* 3.7 9.8 - - + +
36F GLY 3.1 16.4 + - - -
39F PHE* 3.4 33.2 - - + -
144J TRP* 2.9 27.1 + - + +
145J MET 3.5 1.3 - - - +
147J LYS* 1.3 75.0 - - - +
149J PHE* 1.3 63.6 + - - +
151J GLY* 3.0 12.0 + - - -
152J LYS 3.7 10.2 + - - +
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Residues in contact with PHE 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F GLY* 3.3 27.7 - - - -
37F HIS* 3.3 47.9 + + - -
39F PHE* 4.1 4.6 - - + +
40F PHE* 4.0 27.8 - + + -
38J ASN* 3.9 20.4 - - - -
41J THR* 6.0 0.2 - - - -
42J LEU* 3.5 30.7 - - + -
95J MET* 4.4 4.9 - - + -
96J ASP* 4.3 16.8 - - - -
99J MET* 4.0 23.3 - - + -
145J MET 3.1 13.4 + - - +
146J PHE* 3.2 10.3 + + - +
148J ALA* 1.3 75.9 - - - +
150J LEU* 1.3 67.9 + - + +
151J GLY 3.4 2.1 + - - -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F HIS* 5.4 1.8 - - - -
96J ASP* 3.9 34.3 - - + +
99J MET* 3.9 24.2 - - + +
100J GLU* 4.2 22.2 - - + +
103J VAL* 4.2 21.5 - - + -
146J PHE 3.1 15.7 + - - +
147J LYS* 3.1 19.1 + - + +
149J PHE* 1.3 81.7 - - + +
151J GLY* 1.3 61.2 + - - -
152J LYS* 3.5 23.3 + - + +
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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