Contacts of the helix formed by residues 125 - 150 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P THR* 3.5 25.6 - - - +
63P ARG* 3.0 25.4 + - - -
67P ILE* 4.3 7.4 - - - +
120P THR* 3.1 16.1 + - - +
123P GLU* 3.4 4.4 - - + -
124P GLY* 1.3 76.0 - - - +
126P ASP* 1.3 60.6 + - - +
127P VAL 3.7 1.0 + - - -
128P THR* 2.5 28.8 + - - -
129P ASN* 3.2 19.8 + - - +
136R LYS* 5.8 1.6 + - - -
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Residues in contact with ASP 126 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P GLY* 3.2 12.1 + - - +
125P ASP* 1.3 71.7 + - - +
127P VAL* 1.3 59.0 + - + +
129P ASN* 3.4 8.7 - - - +
130P ASP* 3.1 21.5 + - - +
114R LYS* 3.3 26.0 + - - -
117R ILE* 3.3 22.1 - - + +
118R GLU* 5.8 0.2 - - - +
133R ILE* 3.6 35.5 - - + +
136R LYS* 5.7 4.8 - - - +
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Residues in contact with VAL 127 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P ARG* 3.2 37.7 - - - +
125P ASP* 3.3 1.6 + - - -
126P ASP* 1.3 75.1 - - + +
128P THR* 1.3 65.6 + - - +
130P ASP* 3.4 2.6 + - - +
131P MET* 3.1 22.1 + - + +
133R ILE* 3.7 19.1 - - + +
136R LYS* 4.1 16.8 - - + +
137R ALA* 3.3 46.0 - - + +
140R ASP* 3.9 10.8 - - - +
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Residues in contact with THR 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P THR* 4.0 5.8 - - + +
12P PHE* 5.9 0.2 - - + -
13P LEU* 3.7 37.6 - - + +
63P ARG* 3.1 21.6 + - - +
67P ILE* 4.6 0.7 - - - +
120P THR* 3.6 16.2 - - - +
125P ASP* 2.5 29.6 + - - -
127P VAL* 1.3 75.0 - - - +
129P ASN* 1.3 66.1 + - - +
131P MET* 3.2 11.9 + - + +
132P LEU* 2.9 30.2 + - + +
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Residues in contact with ASN 129 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117P ILE* 3.0 39.4 + - - +
120P THR* 3.1 21.7 - - + +
121P ASP* 3.8 17.9 + - - +
125P ASP 3.2 9.1 + - - +
126P ASP* 3.4 14.9 - - - +
128P THR* 1.3 76.9 - - - +
130P ASP* 1.3 62.1 + - - +
132P LEU* 3.2 5.3 + - - +
133P ILE* 3.1 46.6 + - - +
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Residues in contact with ASP 130 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P ASP 3.1 14.9 + - - +
127P VAL 3.9 3.8 - - - +
128P THR 3.2 0.4 - - - -
129P ASN* 1.3 82.2 - - - +
131P MET* 1.3 63.6 + - - +
133P ILE* 3.3 10.9 + - - +
134P ALA* 3.1 24.9 + - - +
130R ASP* 3.5 17.0 - - - +
133R ILE* 4.2 18.4 - - + +
134R ALA* 5.9 3.5 - - - +
130X ASP* 3.5 27.5 - - - +
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Residues in contact with MET 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P LEU* 4.3 9.6 - - + -
59P GLU* 3.6 22.7 - - - +
60P VAL* 4.1 14.1 - - + -
63P ARG* 3.9 31.9 - - + -
127P VAL* 3.1 15.9 + - + +
128P THR* 3.2 7.6 + - + +
130P ASP* 1.3 77.8 - - - +
132P LEU* 1.3 74.8 + - + +
134P ALA* 3.4 6.5 + - - +
135P PHE* 3.3 56.1 + - + -
141R LYS* 4.5 6.1 - - - -
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Residues in contact with LEU 132 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 3.9 33.2 - - + -
13P LEU* 4.3 6.1 - - + -
16P GLN* 5.9 1.1 - - + -
60P VAL* 5.3 2.9 - - + -
113P TYR* 4.1 19.9 - - + +
116P GLY 3.9 19.3 - - - +
117P ILE* 3.7 16.6 - - + +
120P THR* 4.4 4.9 - - + +
128P THR* 2.9 37.1 + - + +
129P ASN 3.8 1.1 - - - +
130P ASP 3.2 0.2 - - - -
131P MET* 1.3 95.1 - - + +
133P ILE* 1.3 58.9 + - - +
135P PHE* 3.3 16.7 + - + +
136P LYS* 3.0 27.0 + - - +
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Residues in contact with ILE 133 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117P ILE* 3.5 24.5 - - + -
129P ASN* 3.1 38.4 + - - +
130P ASP* 3.7 11.4 - - - +
132P LEU* 1.3 75.9 - - - +
134P ALA* 1.3 59.1 + - - +
136P LYS* 3.8 2.0 - - - -
137P ALA* 3.2 22.3 + - - +
126X ASP* 3.7 50.0 - - + +
127X VAL* 3.4 13.0 - - + +
130X ASP* 4.2 16.6 - - + +
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Residues in contact with ALA 134 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P ASP* 3.1 18.6 + - - +
131P MET* 3.7 8.5 - - - +
132P LEU 3.3 0.2 - - - -
133P ILE* 1.3 77.5 - - - +
135P PHE* 1.3 67.1 + - + +
137P ALA* 3.4 14.3 + - - +
138P SER* 3.5 11.4 + - - -
130X ASP* 5.7 5.2 - - - +
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Residues in contact with PHE 135 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P GLN* 3.2 57.4 + - + +
59P GLU* 3.9 24.0 - - + -
60P VAL* 3.6 24.7 - - + -
113P TYR* 3.5 28.5 - + + -
131P MET* 3.3 38.5 + - + -
132P LEU* 3.3 10.6 + - + +
134P ALA* 1.3 79.8 - - + +
136P LYS* 1.3 60.7 + - - +
138P SER* 3.2 3.0 + - - -
139P ILE* 3.0 33.8 + - - +
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Residues in contact with LYS 136 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P ARG* 4.1 31.6 - - + +
113P TYR* 4.4 6.2 - - + -
114P LYS* 4.6 20.1 - - + +
117P ILE* 4.2 18.8 - - + -
132P LEU 3.0 16.1 + - - +
133P ILE* 3.8 7.0 - - - +
134P ALA 3.3 0.2 - - - -
135P PHE* 1.3 75.5 - - - +
137P ALA* 1.3 60.3 + - - +
139P ILE* 3.7 8.9 - - - +
140P ASP* 2.9 65.9 + - - +
63X ARG* 4.1 7.9 - - - +
125X ASP* 4.9 4.0 + - - +
126X ASP* 5.9 3.7 - - + +
127X VAL* 3.9 16.2 - - + +
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Residues in contact with ALA 137 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P ILE 3.2 11.7 + - - +
134P ALA* 3.6 11.0 - - - +
135P PHE 3.2 0.4 - - - -
136P LYS* 1.3 77.9 - - - +
138P SER* 1.3 61.2 + - - +
140P ASP* 3.7 3.0 + - - +
141P LYS* 3.2 24.3 + - - +
63X ARG* 5.0 1.2 + - - -
127X VAL* 3.5 30.0 - - + +
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Residues in contact with SER 138 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P GLU* 2.4 30.7 + - - -
53P PHE* 5.5 0.2 - - - -
56P GLN* 4.9 1.8 - - - -
134P ALA 3.5 7.6 + - - -
135P PHE* 3.2 10.1 + - - -
137P ALA* 1.3 74.8 - - - +
139P ILE* 1.3 65.9 + - - +
141P LYS* 3.3 8.4 + - - +
142P HIS* 3.0 38.7 + - - -
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Residues in contact with ILE 139 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P PHE* 4.1 27.4 - - + -
56P GLN* 4.3 1.3 - - - +
106P LEU* 3.5 29.2 - - + +
109P LEU* 4.2 18.2 - - + -
110P ARG* 3.8 20.0 - - + +
113P TYR* 3.8 30.1 - - + -
135P PHE 3.0 21.1 + - - +
136P LYS* 3.7 6.3 - - - +
138P SER* 1.3 76.3 + - - +
140P ASP* 1.3 57.3 + - - +
142P HIS* 3.2 10.1 + - - +
143P ILE* 2.9 33.7 + - + +
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Residues in contact with ASP 140 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P ARG* 3.2 33.8 - - - +
136P LYS* 2.9 49.1 + - - +
137P ALA 3.9 1.8 - - - +
139P ILE* 1.3 73.0 - - - +
141P LYS* 1.3 63.4 + - - +
143P ILE* 3.3 7.4 + - - +
144P TRP* 3.0 21.8 + - - +
154P PRO* 5.8 0.2 - - - +
63X ARG* 3.1 33.3 + - - +
66X ALA* 4.0 15.3 - - + +
67X ILE* 6.1 0.2 - - - -
127X VAL* 4.1 1.7 - - - +
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Residues in contact with LYS 141 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P ALA 3.2 13.6 + - - +
138P SER* 3.6 10.3 - - - +
139P ILE 3.3 0.2 - - - -
140P ASP* 1.3 78.5 - - - +
142P HIS* 1.3 56.6 + - + +
144P TRP* 3.2 22.2 + - + +
145P MET* 3.0 45.1 + - + +
59X GLU* 4.7 17.0 + - - +
62X GLU* 2.7 45.1 + - - +
63X ARG* 5.6 1.1 - - - +
66X ALA* 4.5 6.4 - - + +
----------------------------------------------------------
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Residues in contact with HIS 142 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P LYS* 5.4 4.5 - - - -
48P ASP* 6.4 0.2 - - + -
49P LEU* 3.2 32.3 - - + +
52P GLU* 2.8 25.0 + - - -
53P PHE* 4.6 8.1 - + - -
106P LEU* 4.3 17.7 - - + +
138P SER* 3.0 35.2 + - - -
139P ILE* 3.2 11.0 + - - +
141P LYS* 1.3 74.9 - - + +
143P ILE* 1.3 60.9 + - - +
145P MET* 3.8 24.0 - - + +
146P PHE* 3.0 43.2 + + + +
----------------------------------------------------------
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Residues in contact with ILE 143 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P VAL* 4.8 8.7 - - + +
106P LEU* 3.7 33.2 - - + +
107P GLU* 4.0 21.1 - - + +
110P ARG* 4.0 27.6 - - - +
139P ILE* 2.9 37.1 + - + +
140P ASP* 3.3 5.8 + - - +
142P HIS* 1.3 72.6 - - - +
144P TRP* 1.3 70.4 + - - +
146P PHE 4.7 0.2 - - - +
147P LYS* 3.1 35.3 + - + +
154P PRO* 3.8 24.7 - - + +
155P LEU* 5.7 0.7 - - + -
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Residues in contact with TRP 144 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P ASP 3.0 14.5 + - - +
141P LYS* 3.2 18.1 + - + +
143P ILE* 1.3 80.0 - - - +
145P MET* 1.3 82.6 + - + +
147P LYS* 3.7 1.9 - - - +
148P ALA* 3.0 28.5 + - + +
152P LYS 6.1 0.4 - - - -
154P PRO* 4.0 27.9 - - + +
31U HIS* 4.9 11.2 - + - -
32U TRP* 4.4 13.0 + + - -
39U PHE* 4.0 23.8 - + - -
62X GLU* 3.6 51.8 - - + -
65X LEU* 3.8 37.2 - - + +
66X ALA* 4.0 15.9 - - + -
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Residues in contact with MET 145 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P LYS* 3.9 21.8 - - - +
141P LYS* 3.0 29.3 + - + +
142P HIS* 3.8 34.8 - - + +
144P TRP* 1.3 95.1 - - + +
146P PHE* 1.3 60.7 + - + +
148P ALA* 3.3 3.6 + - - +
149P PHE* 3.0 25.5 + - - +
39U PHE* 3.8 34.9 - - + -
40U PHE* 3.8 15.0 - - + -
----------------------------------------------------------
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Residues in contact with PHE 146 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P LEU* 4.0 9.6 - - + -
45P LYS* 4.4 11.2 - - + -
46P MET* 3.9 24.9 - - + -
49P LEU* 4.2 14.4 - - + -
99P MET* 4.0 19.5 - - + +
102P LEU* 3.9 17.0 - - + -
103P VAL* 3.7 17.7 - - + -
106P LEU* 4.5 5.2 - - + -
142P HIS* 3.0 53.0 + - + +
145P MET* 1.3 77.0 - - + +
147P LYS* 1.3 64.8 + - - +
149P PHE* 3.5 7.4 + - + +
150P LEU* 3.2 28.8 + - + +
40U PHE* 3.6 31.0 - + - -
----------------------------------------------------------
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Residues in contact with LYS 147 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100P GLU* 5.1 5.1 + - - -
103P VAL* 4.3 19.3 - - + +
107P GLU* 4.1 18.2 + - - -
143P ILE* 3.1 34.7 + - + +
144P TRP 3.7 2.5 - - - +
146P PHE* 1.3 76.9 - - - +
148P ALA* 1.3 58.8 + - - +
150P LEU* 3.0 22.8 + - + +
151P GLY 3.3 0.3 + - - -
152P LYS* 3.0 47.3 + - + +
153P ALA 3.6 9.6 - - - +
154P PRO* 3.4 22.9 - - + +
156P GLU 3.1 32.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 148 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P TRP* 3.0 26.2 + - + +
145P MET 3.3 5.4 + - - +
147P LYS* 1.3 75.3 - - - +
149P PHE* 1.3 58.1 + - - +
150P LEU 3.2 0.2 - - - -
151P GLY 3.3 4.9 + - - -
152P LYS 3.5 12.3 + - - +
34U MET 4.2 7.4 - - - +
35U ARG* 3.4 11.1 - - + +
36U GLY 2.9 25.0 + - - -
39U PHE* 3.8 28.3 - - + -
----------------------------------------------------------
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Residues in contact with PHE 149 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ASN* 3.9 15.3 - - - -
41P THR* 5.8 0.7 - - - -
42P LEU* 3.3 30.3 - - + -
95P MET* 4.2 5.2 - - + -
96P ASP* 3.5 22.2 - - - -
99P MET* 4.1 19.1 - - + -
145P MET 3.0 13.9 + - - +
146P PHE* 3.5 11.2 - + - +
147P LYS 3.2 0.2 - - - -
148P ALA* 1.3 78.2 - - - +
150P LEU* 1.3 69.3 + - + +
151P GLY 3.3 1.1 - - - -
36U GLY* 3.1 28.0 - - - +
37U HIS* 3.3 41.9 + + - -
39U PHE* 4.1 4.2 - - + +
40U PHE* 3.7 30.1 - + + -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P ASP* 3.7 49.9 - - + +
99P MET* 3.9 25.1 - - + +
100P GLU* 3.9 26.9 - - + +
103P VAL* 4.5 7.2 - - + -
146P PHE 3.2 20.0 - - - +
147P LYS* 3.0 16.8 + - + +
149P PHE* 1.3 82.5 - - + +
151P GLY* 1.3 60.3 + - - +
152P LYS* 3.5 19.3 - - + +
36U GLY* 5.5 0.2 - - - -
37U HIS* 5.6 1.3 - - - -
----------------------------------------------------------
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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