Contacts of the helix formed by residues 125 - 151 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 3.2 26.8 + - - +
63A ARG* 3.0 26.3 + - - -
67A ILE* 4.2 8.1 - - - +
120A THR* 2.9 20.8 + - - +
121A ASP* 5.9 0.4 - - - -
123A GLU* 3.3 4.6 - - + +
124A GLY* 1.3 73.6 - - - +
126A ASP* 1.3 62.1 + - - +
127A VAL 3.8 0.7 + - - -
128A THR* 2.8 25.8 + - - -
129A ASN* 3.2 22.5 + - - +
136E LYS* 5.3 1.2 + - - -
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLY* 3.2 7.7 + - - +
125A ASP* 1.3 72.0 + - - +
127A VAL* 1.3 62.6 + - + +
129A ASN* 3.5 7.3 - - - +
130A ASP* 3.1 24.9 + - - +
114E LYS* 3.6 24.6 + - - +
117E ILE* 3.4 30.7 - - + +
118E GLU* 5.9 0.2 - - - +
133E ILE* 3.7 29.7 - - + +
136E LYS* 5.8 3.2 - - + +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 3.3 37.9 - - - +
125A ASP* 3.4 1.0 + - - -
126A ASP* 1.3 72.4 - - - +
128A THR* 1.3 65.9 + - - +
130A ASP* 3.3 4.9 + - - +
131A MET* 3.0 22.2 + - + +
133E ILE* 3.8 18.8 - - + +
136E LYS* 3.8 28.9 - - + +
137E ALA* 3.6 42.8 - - + +
140E ASP* 4.0 0.9 - - - +
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 4.1 3.9 - - + +
13A LEU* 3.6 33.9 - - + +
63A ARG* 3.0 22.3 + - - +
67A ILE* 4.8 0.3 - - - +
120A THR* 3.6 19.5 - - + -
125A ASP* 2.8 30.6 + - - -
127A VAL* 1.3 73.7 - - - +
129A ASN* 1.3 66.6 + - - +
131A MET* 3.1 12.2 + - + +
132A LEU* 3.0 28.0 + - + +
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Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 2.8 40.8 + - - +
120A THR* 3.2 19.3 + - - +
121A ASP* 3.7 22.6 - - - +
125A ASP 3.2 15.8 + - - +
126A ASP* 3.5 8.7 - - - +
128A THR* 1.3 77.4 - - - +
130A ASP* 1.3 58.4 + - - +
132A LEU* 3.4 4.1 + - - +
133A ILE* 3.1 52.7 + - - +
126I ASP* 5.7 0.4 + - - -
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Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP 3.1 13.9 + - - +
127A VAL 3.7 4.8 - - - +
128A THR 3.2 0.2 - - - -
129A ASN* 1.3 80.0 + - - +
131A MET* 1.3 65.9 + - - +
133A ILE* 3.4 9.1 + - - +
134A ALA* 3.2 23.5 + - - +
130E ASP* 3.5 22.0 - - - +
133E ILE* 4.2 17.9 - - + +
134E ALA* 5.6 6.3 - - - +
130I ASP* 3.5 14.4 - - - +
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Residues in contact with MET 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.1 14.4 - - + -
59A GLU* 3.6 27.8 - - + +
60A VAL* 4.0 19.7 - - + -
63A ARG* 3.8 24.2 - - + -
127A VAL* 3.0 16.2 + - + +
128A THR* 3.1 8.7 + - + +
130A ASP* 1.3 77.8 + - - +
132A LEU* 1.3 86.9 + - + +
134A ALA* 3.4 5.2 + - - +
135A PHE* 3.1 46.1 + - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.1 20.9 - - + -
13A LEU* 4.2 9.2 - - + -
16A GLN* 6.0 0.9 - - + -
60A VAL* 5.3 2.5 - - + -
113A TYR* 4.1 16.9 - - + +
116A GLY 3.6 30.7 - - - +
117A ILE* 3.7 15.2 - - + +
120A THR* 4.0 6.1 - - + +
128A THR* 3.0 28.7 + - + +
129A ASN 3.5 4.3 - - - +
131A MET* 1.3 102.3 - - + +
133A ILE* 1.3 59.6 + - - +
135A PHE* 3.4 14.3 + - + +
136A LYS* 2.9 27.7 + - - +
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.9 26.2 - - + -
129A ASN* 3.1 41.0 + - - +
130A ASP* 3.4 8.7 + - - +
132A LEU* 1.3 75.3 - - - +
134A ALA* 1.3 57.5 + - - +
136A LYS* 3.1 5.6 + - - +
137A ALA* 2.9 25.7 + - + +
126I ASP* 3.8 41.3 - - + +
127I VAL* 3.6 15.3 - - + +
130I ASP* 4.1 21.3 - - + +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP* 3.2 14.4 + - - +
131A MET* 3.7 9.6 - - - +
132A LEU 3.4 0.2 - - - -
133A ILE* 1.3 76.9 - - - +
135A PHE* 1.3 67.2 + - + +
137A ALA* 3.4 16.9 + - - +
138A SER* 3.5 12.6 + - - -
130I ASP* 5.9 4.0 - - - +
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 3.2 48.3 + - + +
59A GLU* 4.0 23.3 - - + -
60A VAL* 3.8 20.4 - - + -
113A TYR* 3.6 25.1 - + + -
131A MET* 3.1 39.5 + - + -
132A LEU* 3.6 8.3 - - + +
133A ILE 3.3 0.2 - - - -
134A ALA* 1.3 78.8 - - + +
136A LYS* 1.3 65.9 + - - +
138A SER* 3.4 6.4 + - - -
139A ILE* 3.0 28.8 + - - +
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 4.0 31.9 - - + +
113A TYR* 4.4 5.1 - - + -
114A LYS* 4.2 25.4 - - + +
117A ILE* 4.0 22.4 - - + -
132A LEU 2.9 14.7 + - - +
133A ILE 3.1 8.5 + - - +
135A PHE* 1.3 76.3 - - - +
137A ALA* 1.3 57.7 + - - +
139A ILE* 4.3 8.3 - - - -
140A ASP* 2.7 61.2 + - - +
63I ARG* 4.2 10.3 - - - +
125I ASP* 5.6 0.4 + - - -
126I ASP* 6.1 2.2 - - + -
127I VAL* 3.9 11.2 - - + +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 2.9 11.9 + - + +
134A ALA* 3.5 13.2 - - - +
135A PHE 3.3 0.4 - - - -
136A LYS* 1.3 75.1 - - - +
138A SER* 1.3 61.5 + - - +
140A ASP* 3.9 3.7 - - - +
141A LYS* 3.2 26.5 + - - +
63I ARG* 4.9 1.6 + - - -
127I VAL* 3.5 31.1 - - + +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 2.4 33.4 + - - -
53A PHE* 5.3 0.5 - - - -
56A GLN* 5.3 2.7 - - - -
134A ALA 3.5 8.4 + - - -
135A PHE* 3.4 9.6 + - - -
136A LYS 3.2 0.4 - - - -
137A ALA* 1.3 77.5 - - - +
139A ILE* 1.3 60.5 + - - +
141A LYS* 3.1 9.6 + - - +
142A HIS* 2.8 39.6 + - - -
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 4.2 22.4 - - + -
56A GLN* 4.3 7.0 - - - +
106A LEU* 3.6 29.8 - - + +
109A LEU* 4.3 16.4 - - + -
110A ARG* 3.7 15.3 - - + +
113A TYR* 3.9 30.3 - - + -
135A PHE 3.0 22.3 + - - +
136A LYS* 3.7 5.8 - - - +
138A SER* 1.3 75.6 - - - +
140A ASP* 1.3 64.0 + - - +
142A HIS* 3.2 9.0 + - - +
143A ILE* 3.0 35.1 + - + +
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 3.1 34.8 + - - +
136A LYS* 2.7 45.3 + - - +
137A ALA 3.9 2.0 - - - +
139A ILE* 1.3 76.6 - - - +
141A LYS* 1.3 57.8 + - - +
143A ILE* 3.4 7.0 + - - +
144A TRP* 3.1 27.0 + - - +
154A PRO* 5.9 0.2 - - - +
63I ARG* 3.0 32.6 + - - +
66I ALA* 4.0 14.8 - - + +
67I ILE* 6.0 0.4 - - - -
127I VAL* 4.1 1.4 - - - +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA* 3.2 16.1 + - - +
138A SER* 3.1 9.5 + - - +
140A ASP* 1.3 78.2 - - - +
142A HIS* 1.3 62.3 + - - +
144A TRP* 3.6 19.2 + - + +
145A MET* 3.2 42.2 + - + +
59I GLU* 4.3 19.0 + - - +
62I GLU* 2.5 46.2 + - - +
63I ARG* 5.6 1.3 - - - +
66I ALA* 4.6 5.4 - - + +
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Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.3 12.4 + - - -
49A LEU* 3.5 27.5 - - + +
52A GLU* 2.8 24.6 + - - -
53A PHE* 4.2 10.8 - + - -
106A LEU* 4.2 11.2 - - + -
138A SER* 2.8 37.5 + - - +
139A ILE* 3.7 6.1 - - - +
141A LYS* 1.3 70.9 - - - +
143A ILE* 1.3 60.1 + - - +
145A MET* 3.7 20.7 - - + +
146A PHE* 2.8 53.2 + - + +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 4.8 5.8 - - + +
106A LEU* 3.9 30.7 - - + +
107A GLU* 4.3 8.3 - - + -
110A ARG* 3.9 33.4 - - + +
139A ILE* 3.0 39.7 + - + +
140A ASP* 3.7 7.0 - - - +
141A LYS 3.4 0.2 - - - -
142A HIS* 1.3 73.6 - - - +
144A TRP* 1.3 68.8 + - - +
146A PHE* 5.0 2.2 - - - -
147A LYS* 3.0 54.2 + - + +
154A PRO* 3.8 13.0 - - + +
155A LEU* 6.0 0.2 - - + -
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Residues in contact with TRP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP 3.1 17.4 + - - +
141A LYS* 3.8 14.6 - - + +
143A ILE* 1.3 76.9 - - - +
145A MET* 1.3 82.9 + - + +
147A LYS* 3.7 1.4 - - - +
148A ALA* 2.8 38.1 + - + +
152A LYS 4.9 0.6 - - - +
154A PRO* 4.2 30.2 - - + +
62I GLU* 3.9 46.9 - - + -
65I LEU* 4.0 33.0 - - + +
66I ALA* 4.0 19.1 - - + -
31K HIS* 5.0 13.7 - + - -
32K TRP* 4.4 11.6 + + - -
39K PHE* 3.9 22.6 - + - -
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Residues in contact with MET 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.6 7.2 - - - +
141A LYS* 3.2 39.2 + - + +
142A HIS* 3.7 30.5 - - + +
144A TRP* 1.3 101.7 - - + +
146A PHE* 1.3 59.3 + - + +
148A ALA* 3.3 2.6 + - - +
149A PHE* 2.9 27.7 + - - +
39K PHE* 3.7 30.7 - - + -
40K PHE* 4.0 21.3 - - + -
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.9 3.4 - - + -
45A LYS* 4.2 20.9 - - + -
46A MET* 3.7 29.2 - - + -
49A LEU* 4.1 15.3 - - + -
99A MET* 4.5 13.0 - - + -
102A LEU* 3.9 15.9 - - + -
103A VAL* 3.7 20.4 - - + -
106A LEU* 3.9 14.4 - - + -
142A HIS* 2.8 48.2 + - + +
143A ILE 4.6 0.2 - - - +
145A MET* 1.3 74.0 - - + +
147A LYS* 1.3 61.5 + - - +
149A PHE* 3.3 9.6 - + + +
150A LEU* 3.1 25.9 + - + +
40K PHE* 3.6 29.2 - + - -
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.8 23.1 - - + -
107A GLU* 2.7 30.6 + - - -
110A ARG* 5.3 1.2 - - - +
143A ILE* 3.0 29.8 + - + +
144A TRP 3.8 1.6 - - - +
146A PHE* 1.3 74.4 - - - +
148A ALA* 1.3 66.0 + - - +
150A LEU* 2.9 20.0 + - + +
151A GLY 3.1 0.2 + - - -
152A LYS* 3.1 38.7 + - + +
153A ALA 3.7 9.4 - - - +
154A PRO* 2.8 30.8 + - + +
155A LEU* 4.5 2.4 - - - +
156A GLU 3.8 22.4 + - - +
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 2.8 32.6 + - + +
145A MET 3.3 5.1 + - - +
147A LYS* 1.3 71.3 - - - +
149A PHE* 1.3 62.3 + - - +
151A GLY 3.1 7.4 + - - -
152A LYS 3.5 11.6 + - - +
34K MET 4.0 7.4 - - - +
35K ARG* 3.4 12.2 - - + +
36K GLY 3.0 19.2 + - - -
39K PHE* 3.7 27.4 - - + -
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 3.8 18.2 - - - -
41A THR* 4.9 1.3 - - + -
42A LEU* 3.5 41.5 - - + -
95A MET* 3.8 20.4 - - + -
99A MET* 4.5 6.3 - - + -
145A MET 2.9 13.2 + - - +
146A PHE* 3.3 12.1 - + - +
147A LYS 3.1 0.2 - - - -
148A ALA* 1.3 76.1 - - - +
150A LEU* 1.3 73.5 + - + +
151A GLY 3.4 0.3 + - - -
36K GLY* 3.4 35.7 - - - -
37K HIS* 3.3 38.7 + + - -
39K PHE* 4.0 6.8 - - + +
40K PHE* 4.0 26.9 - + + -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET* 4.4 2.0 - - + -
96A ASP* 3.5 29.9 - - - +
99A MET* 3.9 29.6 - - + +
100A GLU* 4.2 18.8 - - - +
103A VAL* 4.2 21.1 - - + -
146A PHE* 3.1 15.4 + - + +
147A LYS* 2.9 14.2 + - + +
149A PHE* 1.3 93.4 - - + +
151A GLY* 1.3 60.0 + - - +
152A LYS* 3.8 23.0 + - + +
36K GLY* 5.6 0.2 - - - -
37K HIS* 5.8 2.7 - - - +
----------------------------------------------------------
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Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS 3.1 1.8 + - - -
148A ALA 3.1 11.5 + - - -
149A PHE 3.3 1.8 + - - -
150A LEU* 1.3 77.5 - - - +
152A LYS* 1.3 62.2 + - - +
156A GLU* 4.9 1.2 - - - +
35K ARG* 4.0 23.3 + - - -
36K GLY* 4.7 4.3 - - - -
----------------------------------------------------------
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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