Contacts of the helix formed by residues 94 - 124 (chain O) 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 O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O LYS* 1.3 76.0 - - - +
95O MET* 1.3 77.9 + - + +
96O ASP* 3.2 21.1 - - + +
97O GLN* 3.1 33.9 + - - -
98O LEU* 3.1 14.2 + - - +
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Residues in contact with MET 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O MET* 3.2 54.3 - - + -
35O ARG 3.6 29.7 + - - +
36O GLY* 5.8 1.1 - - - -
38O ASN* 3.6 48.2 - - + +
39O PHE* 3.8 5.8 - - - +
42O LEU* 4.6 6.1 - - + -
94O THR* 1.3 77.0 - - + +
96O ASP* 1.3 62.1 + - - +
98O LEU* 3.3 9.0 + - - +
99O MET* 2.9 46.1 + - + +
149O PHE* 4.9 6.3 - - + -
37Y HIS* 6.1 2.2 - - + -
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Residues in contact with ASP 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O THR* 3.2 13.4 - - + +
95O MET* 1.3 80.1 - - - +
97O GLN* 1.3 57.6 + - + +
99O MET* 3.2 0.9 + - - +
100O GLU* 3.0 44.1 + - - +
149O PHE* 4.7 2.3 - - - -
150O LEU* 3.9 25.8 - - + +
37Y HIS* 3.6 29.1 + - - -
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Residues in contact with GLN 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O PRO 4.5 1.8 + - - +
93O LYS* 3.6 39.7 - - + +
94O THR* 3.1 39.1 + - - +
96O ASP* 1.3 79.1 - - - +
98O LEU* 1.3 56.7 + - - +
100O GLU* 3.7 10.7 + - - +
101O ASP* 3.4 22.5 + - - +
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Residues in contact with LEU 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O GLN* 5.0 10.1 - - + +
30O ILE* 3.5 49.7 - - + +
33O TYR* 4.6 4.5 - - + +
34O MET* 4.2 27.4 - - + +
35O ARG 5.5 0.2 - - - +
89O TYR* 4.4 16.2 - - + -
93O LYS* 4.0 31.6 - - + +
94O THR 3.1 17.5 + - - +
95O MET* 3.6 9.9 - - - +
97O GLN* 1.3 73.6 - - - +
99O MET* 1.3 64.8 + - + +
100O GLU 3.2 1.6 - - - -
101O ASP* 3.4 7.6 + - + +
102O LEU 3.1 19.1 + - - -
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Residues in contact with MET 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O ILE* 3.4 33.2 - - + -
34O MET* 4.4 4.9 - - + -
42O LEU* 3.5 29.8 - - + -
46O MET* 4.1 10.1 - - + -
95O MET* 2.9 25.4 + - + +
96O ASP 3.9 0.4 - - - +
98O LEU* 1.3 79.4 - - + +
100O GLU* 1.3 59.4 + - - +
102O LEU* 3.3 21.8 + - + +
103O VAL* 2.9 35.5 + - + +
146O PHE* 4.2 11.4 - - + -
149O PHE* 4.2 18.2 - - + -
150O LEU* 3.7 23.1 - - + -
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Residues in contact with GLU 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O ASP* 3.0 28.9 + - - +
97O GLN* 4.0 10.9 - - - +
99O MET* 1.3 78.4 - - - +
101O ASP* 1.3 56.6 + - - +
103O VAL* 3.9 6.6 - - + +
104O GLY* 2.9 24.1 + - - -
150O LEU* 3.8 20.4 - - + -
152O LYS* 3.4 25.6 + - - -
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Residues in contact with ASP 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O LYS* 2.6 42.8 + - - +
29O GLN* 5.0 5.2 + - - -
30O ILE* 5.3 2.6 - - + +
97O GLN 3.4 14.3 + - - +
98O LEU* 3.4 12.1 + - + +
99O MET 3.3 0.2 - - - -
100O GLU* 1.3 76.1 - - - +
102O LEU* 1.3 61.8 + - - +
104O GLY* 4.1 1.5 - - - -
105O THR* 2.8 35.3 + - - -
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Residues in contact with LEU 102 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O PHE* 3.5 34.1 - - + -
26O LYS* 5.1 0.9 - - - -
27O ILE* 5.0 2.0 - - + -
30O ILE* 3.9 19.4 - - + +
46O MET* 4.0 6.1 - - + -
49O LEU* 4.0 16.4 - - + -
98O LEU 3.1 13.4 + - - +
99O MET* 3.3 26.0 - - + +
101O ASP* 1.3 77.1 - - - +
103O VAL* 1.3 62.1 + - - +
105O THR* 3.1 6.1 + - - -
106O LEU* 3.0 24.6 + - + +
146O PHE* 3.8 39.3 - - + -
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Residues in contact with VAL 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O MET* 2.9 21.8 + - - +
100O GLU* 3.9 7.0 - - + +
102O LEU* 1.3 73.4 - - + +
104O GLY* 1.3 68.2 + - - +
106O LEU* 3.0 21.2 + - + +
107O GLU* 3.2 32.6 + - + +
143O ILE* 5.3 7.0 - - + +
146O PHE* 3.7 33.4 - - + -
147O LYS* 4.3 22.9 - - + +
150O LEU* 4.3 13.9 - - + -
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Residues in contact with GLY 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O GLU 2.9 18.5 + - - -
101O ASP* 4.1 1.3 - - - -
102O LEU 3.3 0.2 - - - -
103O VAL* 1.3 75.7 - - - +
105O THR* 1.3 61.9 + - - +
107O GLU* 3.3 18.1 + - - +
108O LEU* 3.2 21.5 + - - +
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Residues in contact with THR 105 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O PHE* 3.6 33.2 - - + -
26O LYS* 3.4 16.9 - - - -
84O VAL* 3.9 31.5 - - + +
85O GLU 5.7 0.5 + - - -
101O ASP* 2.8 26.4 + - - -
102O LEU 3.3 4.7 - - - -
104O GLY* 1.3 78.8 - - - +
106O LEU* 1.3 60.9 + - - +
108O LEU* 3.7 7.6 + - + +
109O LEU* 3.2 22.8 + - + +
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Residues in contact with LEU 106 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O PHE* 4.0 13.5 - - + -
49O LEU* 5.5 2.2 - - + -
53O PHE* 4.0 29.8 - - + -
102O LEU* 3.0 32.4 + - + +
103O VAL* 3.0 13.8 + - - +
105O THR* 1.3 75.3 - - - +
107O GLU* 1.3 52.8 + - - +
109O LEU* 3.1 6.5 + - + +
110O ARG 2.7 29.8 + - - -
139O ILE* 3.3 23.9 - - + +
142O HIS* 4.2 24.5 - - + -
143O ILE* 3.8 20.2 - - + -
146O PHE* 4.2 16.2 - - + -
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Residues in contact with GLU 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O VAL* 3.2 21.4 + - - +
104O GLY* 3.5 20.2 - - - +
105O THR 3.2 0.2 - - - -
106O LEU* 1.3 72.7 - - - +
108O LEU* 1.3 61.1 + - - +
109O LEU 3.1 1.1 - - - -
110O ARG* 3.3 36.9 + - - +
111O ASP* 2.8 37.8 + - - +
143O ILE* 4.1 14.0 - - + +
147O LYS* 4.0 20.1 + - - -
154O PRO 4.7 1.9 - - - +
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Residues in contact with LEU 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O ASN* 4.4 2.2 - - - +
83O SER* 3.9 23.3 - - - +
84O VAL* 3.8 29.4 - - + -
85O GLU* 5.6 3.1 - - + +
104O GLY 3.2 10.1 + - - +
105O THR* 3.9 9.2 - - + +
107O GLU* 1.3 78.4 - - - +
109O LEU* 1.3 60.1 + - - +
111O ASP* 3.9 6.5 - - - +
112O GLU* 2.9 62.2 + - + +
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Residues in contact with LEU 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O GLN* 3.7 22.4 - - - +
19O ASN* 3.9 23.8 - - + +
20O LEU* 4.1 17.5 - - + -
23O PHE* 3.7 37.9 - - + -
53O PHE* 4.4 9.9 - - + -
84O VAL* 4.2 10.3 - - + -
105O THR 3.2 16.4 + - - +
106O LEU* 3.1 13.2 + - + +
108O LEU* 1.3 75.5 - - + +
110O ARG* 1.3 66.6 + - - +
112O GLU* 3.8 1.5 - - - +
113O TYR* 2.9 35.1 + - + +
139O ILE* 4.3 11.7 - - + -
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Residues in contact with ARG 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O LEU 2.7 16.7 + - - +
107O GLU* 3.4 35.7 + - - +
109O LEU* 1.3 73.4 - - - +
111O ASP* 1.3 79.2 + - - +
113O TYR* 3.3 7.5 + - - +
114O LYS* 3.0 27.1 + - + +
136O LYS* 4.3 19.6 - - + +
139O ILE* 3.9 14.9 - - + +
140O ASP* 3.3 26.2 - - - +
143O ILE* 3.8 22.8 - - - +
154O PRO 5.0 0.4 + - - -
155O LEU* 4.0 24.5 - - - +
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Residues in contact with ASP 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107O GLU* 2.8 27.9 + - - +
108O LEU* 4.0 6.7 + - - +
109O LEU 3.2 0.2 - - - -
110O ARG* 1.3 100.2 + - - +
112O GLU* 1.3 65.9 + - + +
114O LYS* 3.5 8.4 + - - +
115O GLN* 3.3 18.7 + - - +
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Residues in contact with GLU 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O PHE* 2.9 25.5 - - + -
15O HIS* 3.1 11.2 - - - -
16O GLN* 2.9 30.7 + - - +
19O ASN* 3.0 12.8 + - - -
83O SER* 2.4 28.5 + - - -
108O LEU* 2.9 32.9 + - + +
109O LEU* 4.0 3.1 - - - +
111O ASP* 1.3 76.2 - - + +
113O TYR* 1.3 62.6 + - - +
115O GLN* 3.3 8.4 + - - +
116O GLY 3.0 6.4 + - - -
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Residues in contact with TYR 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O PHE* 3.9 13.2 - + - -
16O GLN* 3.3 33.2 - - + -
20O LEU* 3.6 25.5 - - + +
56O GLN* 3.1 16.3 + - - -
60O VAL* 4.7 2.5 - - + +
109O LEU* 2.9 26.4 + - + +
110O ARG* 3.7 6.1 - - - +
112O GLU* 1.3 75.0 - - - +
114O LYS* 1.3 60.5 + - - +
116O GLY* 2.8 17.5 + - - -
117O ILE* 2.8 22.3 + - + +
132O LEU* 4.0 20.6 - - + +
135O PHE* 3.6 32.6 - + + -
136O LYS* 4.3 12.3 - - + -
139O ILE* 3.6 29.6 - - + -
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Residues in contact with LYS 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O ARG 3.0 13.1 + - - +
111O ASP* 3.6 12.3 - - - +
112O GLU 3.3 0.2 - - - -
113O TYR* 1.3 77.2 - - - +
115O GLN* 1.3 63.9 + - - +
117O ILE* 3.2 14.6 + - - +
118O GLU* 3.0 48.8 + - + +
136O LYS* 4.8 18.7 - - - +
124V GLY* 3.7 15.5 + - - +
126V ASP* 2.8 33.1 + - - +
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Residues in contact with GLN 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 4.7 16.0 + - - +
12O PHE* 4.6 6.1 - - + -
111O ASP 3.3 9.2 + - - +
112O GLU* 3.3 13.3 + - - +
113O TYR 3.2 0.6 - - - -
114O LYS* 1.3 78.1 - - - +
116O GLY* 1.3 62.1 + - - +
118O GLU* 3.2 11.8 + - - +
119O LEU* 3.0 42.0 + - + +
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Residues in contact with GLY 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O PHE* 3.6 32.3 - - - -
112O GLU 3.0 7.9 + - - -
113O TYR 2.8 12.0 + - - -
115O GLN* 1.3 72.5 - - - +
117O ILE* 1.3 50.8 + - - +
119O LEU* 4.0 6.4 - - - +
120O THR* 2.7 40.1 + - - -
132O LEU* 3.9 6.9 - - - +
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Residues in contact with ILE 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O TYR 2.8 21.7 + - - +
114O LYS* 3.5 14.8 - - - +
116O GLY* 1.3 75.7 - - - +
118O GLU* 1.3 60.4 + - - +
120O THR* 3.2 5.6 - - - +
121O ASP* 2.9 15.5 + - + +
129O ASN* 2.9 31.4 + - - +
132O LEU* 3.6 24.2 - - + +
133O ILE* 3.8 36.1 - - + +
136O LYS* 4.1 19.1 - - + -
126V ASP* 3.2 29.8 - - + +
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Residues in contact with GLU 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O LYS* 3.0 43.3 + - + +
115O GLN* 3.5 15.7 - - - +
117O ILE* 1.3 78.0 - - - +
119O LEU* 1.3 58.7 + - - +
121O ASP* 3.4 7.1 - - - +
122O LYS* 3.0 25.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 3.6 24.2 - - + +
8O ASP 3.8 8.5 - - - +
9O THR* 3.9 5.2 - - - +
12O PHE* 3.9 28.0 - - + -
115O GLN* 3.0 42.3 + - - +
116O GLY* 4.0 9.6 - - - +
118O GLU* 1.3 78.1 - - - +
120O THR* 1.3 60.0 + - - +
122O LYS* 3.4 9.7 - - - +
123O GLU* 3.0 53.8 + - - +
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Residues in contact with THR 120 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O THR* 3.7 19.6 + - - +
116O GLY 2.7 22.7 + - - +
117O ILE* 3.2 4.5 - - - +
119O LEU* 1.3 79.6 - - - +
121O ASP* 1.3 62.1 + - - +
122O LYS 3.3 0.2 - - - -
123O GLU* 4.0 0.8 - - - +
124O GLY* 3.2 2.8 + - - -
125O ASP* 3.0 33.8 + - - +
128O THR* 3.8 22.9 - - - +
129O ASN* 3.0 43.7 - - + +
132O LEU* 4.3 4.5 - - + -
----------------------------------------------------------
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Residues in contact with ASP 121 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ILE* 2.9 14.4 + - + +
118O GLU* 3.4 12.3 - - - +
120O THR* 1.3 76.8 - - - +
122O LYS* 1.3 62.9 + - - +
124O GLY* 3.1 14.2 + - - -
129O ASN* 3.3 13.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O GLU 3.0 11.6 + - - +
119O LEU* 3.4 14.4 - - - +
120O THR 3.3 0.2 - - - -
121O ASP* 1.3 80.9 - - - +
123O GLU* 1.3 64.8 + - + +
124O GLY 3.6 0.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL 4.4 0.2 - - - +
8O ASP* 3.3 14.9 - - - +
9O THR* 3.1 33.3 + - - +
119O LEU* 3.0 41.3 + - - +
120O THR 3.6 3.1 + - - +
121O ASP 3.3 0.4 - - - -
122O LYS* 1.3 81.8 - - + +
124O GLY* 1.3 61.6 + - - +
125O ASP* 4.6 4.4 - - + +
----------------------------------------------------------
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Residues in contact with GLY 124 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120O THR 3.9 0.4 - - - -
121O ASP 3.1 15.6 + - - -
122O LYS 3.4 0.8 + - - -
123O GLU* 1.3 79.3 - - - +
125O ASP* 1.3 59.9 + - - +
126O ASP* 3.3 19.3 + - - +
114T LYS* 4.4 11.7 - - - -
----------------------------------------------------------
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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