Contacts of the helix formed by residues 125 - 150 (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 ASP 125 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O THR* 3.6 19.8 - - - +
63O ARG* 2.8 28.0 + - - -
67O ILE* 4.2 10.3 - - - +
120O THR* 3.0 21.4 + - - +
123O GLU* 3.4 5.1 - - + +
124O GLY* 1.3 76.0 - - - +
126O ASP* 1.3 61.8 + - - +
127O VAL 3.6 1.0 + - - -
128O THR* 2.9 27.3 + - - -
129O ASN* 3.1 20.1 + - - +
136T LYS* 4.9 2.4 + - - -
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Residues in contact with ASP 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124O GLY* 3.3 14.6 + - - +
125O ASP* 1.3 73.2 + - - +
127O VAL* 1.3 58.7 + - + +
129O ASN* 3.4 8.7 - - - +
130O ASP* 3.0 28.6 + - - +
114T LYS* 4.1 14.2 + - - +
117T ILE* 3.8 29.0 - - + +
129T ASN* 5.3 0.9 + - - -
133T ILE* 3.6 30.9 - - + +
136T LYS* 5.8 3.9 - - + +
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Residues in contact with VAL 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63O ARG* 3.4 38.1 - - + +
125O ASP* 3.4 1.6 + - - -
126O ASP* 1.3 73.5 - - + +
128O THR* 1.3 66.5 + - - +
130O ASP* 3.2 4.7 + - - +
131O MET* 3.1 21.9 + - + +
133T ILE* 3.6 20.4 - - + +
136T LYS* 3.7 27.9 - - + +
137T ALA* 3.5 45.3 - - + +
140T ASP* 4.0 0.9 - - - +
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Residues in contact with THR 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O THR* 4.0 4.3 - - + -
13O LEU* 3.7 38.7 - - + +
63O ARG* 3.0 25.0 + - - +
67O ILE* 4.9 0.7 - - - +
120O THR* 3.8 11.9 - - - +
125O ASP* 2.9 31.1 + - - -
127O VAL* 1.3 77.0 - - - +
129O ASN* 1.3 62.0 + - - +
131O MET* 3.1 12.0 + - + +
132O LEU* 3.0 30.3 + - + +
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Residues in contact with ASN 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ILE* 2.9 37.9 + - - +
120O THR* 3.0 24.7 - - + +
121O ASP* 3.3 19.1 + - - +
125O ASP 3.1 16.9 + - - +
126O ASP* 3.4 10.5 - - - +
128O THR* 1.3 77.5 - - - +
130O ASP* 1.3 61.0 + - - +
132O LEU* 3.5 3.7 + - - +
133O ILE* 3.2 43.6 + - - +
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Residues in contact with ASP 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126O ASP 3.0 14.3 + - - +
127O VAL* 3.4 9.9 - - - +
129O ASN* 1.3 76.5 + - - +
131O MET* 1.3 65.9 + - - +
133O ILE* 3.2 11.1 + - - +
134O ALA* 3.1 23.1 + - - +
130T ASP* 3.8 12.6 - - - +
133T ILE* 4.2 17.3 - - + +
134T ALA* 5.2 9.6 - - - +
130V ASP* 3.8 19.8 - - - +
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Residues in contact with MET 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O LEU* 3.9 28.7 - - + -
59O GLU* 3.8 20.2 - - + +
60O VAL* 4.4 8.1 - - + -
63O ARG* 3.7 34.5 - - + -
127O VAL* 3.1 13.8 + - + +
128O THR* 3.4 10.3 - - + +
130O ASP* 1.3 77.2 - - - +
132O LEU* 1.3 74.9 + - + +
134O ALA* 3.4 7.3 + - - +
135O PHE* 3.2 48.2 + - + -
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Residues in contact with LEU 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O PHE* 4.1 23.6 - - + -
13O LEU* 4.2 9.4 - - + -
16O GLN* 5.8 0.7 - - + -
60O VAL* 5.5 2.5 - - + -
113O TYR* 4.0 20.0 - - + +
116O GLY 3.9 26.7 - - - +
117O ILE* 3.6 19.0 - - + +
120O THR* 4.3 3.4 - - + +
128O THR* 3.0 35.5 + - + +
129O ASN 3.8 1.6 - - - +
130O ASP 3.2 0.2 - - - -
131O MET* 1.3 94.4 - - + +
133O ILE* 1.3 63.1 + - - +
135O PHE* 3.5 13.8 + - + +
136O LYS* 3.0 23.4 + - - +
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Residues in contact with ILE 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ILE* 3.8 24.2 - - + -
129O ASN* 3.2 34.7 + - - +
130O ASP* 3.2 13.1 + - - +
132O LEU* 1.3 78.9 - - - +
134O ALA* 1.3 57.8 + - - +
136O LYS* 3.2 4.5 + - - +
137O ALA* 2.9 26.5 + - + +
126V ASP* 3.8 44.6 - - + +
127V VAL* 3.7 8.6 - - + +
130V ASP* 4.1 21.8 - - + -
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Residues in contact with ALA 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130O ASP* 3.1 14.6 + - - +
131O MET* 3.7 10.8 - - - +
132O LEU 3.3 0.2 - - - -
133O ILE* 1.3 78.4 - - - +
135O PHE* 1.3 66.7 + - + +
137O ALA* 3.2 22.1 + - - +
138O SER* 3.4 6.6 + - - -
130V ASP* 5.6 6.3 - - - +
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Residues in contact with PHE 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O GLU* 6.5 0.2 - - + -
56O GLN* 3.5 44.3 + - + +
59O GLU* 3.7 26.7 - - + -
60O VAL* 3.9 21.8 - - + -
113O TYR* 3.6 25.8 - + + -
131O MET* 3.2 41.4 + - + -
132O LEU* 3.8 7.0 - - + +
134O ALA* 1.3 81.2 - - + +
136O LYS* 1.3 59.1 + - - +
138O SER* 3.3 5.9 + - - +
139O ILE* 3.0 32.4 + - - +
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Residues in contact with LYS 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O ARG* 4.3 27.0 - - + +
113O TYR* 4.3 8.3 - - + -
114O LYS* 4.8 19.5 - - + +
117O ILE* 4.1 19.7 - - + -
132O LEU 3.0 18.2 + - - +
133O ILE* 3.2 5.4 + - - +
135O PHE* 1.3 74.3 - - - +
137O ALA* 1.3 66.1 + - - +
139O ILE* 3.7 10.5 - - - +
140O ASP* 2.7 59.9 + - - +
63V ARG* 4.1 7.1 - - - +
125V ASP* 5.3 1.0 + - - -
126V ASP* 5.9 3.5 - - + +
127V VAL* 3.6 18.1 - - + +
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Residues in contact with ALA 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133O ILE* 2.9 11.6 + - + +
134O ALA* 3.2 14.8 - - - +
136O LYS* 1.3 78.1 - - - +
138O SER* 1.3 61.6 + - - +
140O ASP* 3.6 5.0 + - - +
141O LYS* 3.4 21.0 + - - +
63V ARG* 5.0 1.2 + - - -
127V VAL* 3.4 31.8 - - + +
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Residues in contact with SER 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O GLU* 2.5 29.4 + - - -
53O PHE* 5.0 0.7 - - - -
56O GLN* 4.6 5.3 + - - -
134O ALA 3.4 7.0 + - - -
135O PHE* 3.3 12.4 + - - -
136O LYS 3.2 0.4 - - - -
137O ALA* 1.3 76.2 - - - +
139O ILE* 1.3 67.3 + - - +
141O LYS* 3.1 24.7 + - - +
142O HIS* 3.1 30.6 + - - -
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Residues in contact with ILE 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53O PHE* 4.0 24.2 - - + -
56O GLN* 4.3 6.5 - - - +
106O LEU* 3.3 34.8 - - + +
109O LEU* 4.3 13.5 - - + -
110O ARG* 3.9 11.4 - - + +
113O TYR* 3.6 35.9 - - + -
135O PHE 3.0 21.3 + - - +
136O LYS* 3.1 6.9 + - - +
138O SER* 1.3 76.2 - - - +
140O ASP* 1.3 63.5 + - - +
142O HIS* 3.4 8.0 + - - +
143O ILE* 3.1 31.7 + - + +
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Residues in contact with ASP 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O ARG* 3.3 29.5 - - - +
136O LYS* 2.7 51.3 + - - +
137O ALA 3.8 3.1 - - - +
139O ILE* 1.3 72.2 - - - +
141O LYS* 1.3 57.5 + - - +
143O ILE* 3.3 9.1 + - - +
144O TRP* 3.1 27.0 + - - +
63V ARG* 2.8 33.4 + - - +
66V ALA* 3.9 14.5 - - + +
67V ILE* 6.1 0.2 - - - -
127V VAL* 4.1 1.2 - - - +
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Residues in contact with LYS 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137O ALA 3.4 10.2 + - - +
138O SER* 3.1 15.9 + - - +
140O ASP* 1.3 76.4 - - - +
142O HIS* 1.3 78.0 + - - +
144O TRP* 3.4 21.7 + - + -
145O MET* 3.0 56.9 + - + +
62V GLU* 4.0 20.9 - - + +
66V ALA* 4.6 7.2 - - + -
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Residues in contact with HIS 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48O ASP* 6.4 0.2 - - + -
49O LEU* 3.3 33.4 - - + +
52O GLU* 2.8 24.9 + - - -
53O PHE* 4.4 12.5 - + - -
106O LEU* 4.2 16.6 - - + -
138O SER* 3.1 32.5 + - - -
139O ILE* 3.6 9.6 - - - +
141O LYS* 1.3 92.2 + - - +
143O ILE* 1.3 57.4 + - - +
145O MET* 4.1 15.8 - - + +
146O PHE* 2.9 45.8 + - + -
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Residues in contact with ILE 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O VAL* 4.9 7.4 - - + +
106O LEU* 3.8 26.2 - - + -
107O GLU* 4.1 18.6 - - + +
110O ARG* 3.8 35.4 - - - +
139O ILE* 3.1 34.7 + - + +
140O ASP* 3.5 8.5 - - - +
141O LYS 3.2 0.2 - - - -
142O HIS* 1.3 72.7 - - - +
144O TRP* 1.3 70.4 + - - +
146O PHE* 5.1 2.0 - - - -
147O LYS* 3.1 29.3 + - + +
154O PRO* 3.9 24.0 - - + +
155O LEU* 5.6 0.9 - - + -
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Residues in contact with TRP 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O ASP 3.1 12.8 + - - +
141O LYS* 3.5 17.5 - - + +
143O ILE* 1.3 80.8 - - - +
145O MET* 1.3 91.9 + - + +
147O LYS* 3.7 1.7 - - - +
148O ALA* 2.9 33.4 + - + +
152O LYS 5.1 0.2 - - - +
154O PRO* 4.1 24.7 - - + +
62V GLU* 3.9 47.3 - - + -
65V LEU* 3.7 45.7 - - + +
66V ALA* 4.0 16.4 - - + -
31Y HIS* 4.9 14.4 - + - -
32Y TRP* 4.6 7.4 + + - -
34Y MET 5.8 0.4 + - - -
39Y PHE* 3.9 23.2 - + - -
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Residues in contact with MET 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O LYS* 5.0 8.3 - - - +
141O LYS* 3.0 48.7 + - + +
142O HIS* 3.9 22.0 - - + +
143O ILE 3.3 0.2 - - - -
144O TRP* 1.3 102.3 - - + +
146O PHE* 1.3 58.6 + - + +
148O ALA* 3.3 6.2 - - - +
149O PHE* 3.0 25.3 + - - +
62V GLU* 5.9 0.9 - - - +
39Y PHE* 3.7 28.7 - - + -
40Y PHE* 3.8 24.5 - - + -
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Residues in contact with PHE 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O LEU* 4.0 16.2 - - + -
45O LYS* 4.5 7.2 - - + -
46O MET* 4.0 20.4 - - + -
49O LEU* 4.2 14.4 - - + -
99O MET* 4.2 15.0 - - + -
102O LEU* 3.8 19.5 - - + -
103O VAL* 3.7 19.3 - - + -
106O LEU* 4.2 8.1 - - + -
142O HIS* 2.9 48.0 + - + +
143O ILE* 4.4 0.9 - - - +
145O MET* 1.3 73.3 - - + +
147O LYS* 1.3 61.4 + - - +
149O PHE* 3.1 7.4 + + + +
150O LEU* 2.9 33.9 + - + +
40Y PHE* 3.3 33.7 - + - -
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Residues in contact with LYS 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O VAL* 4.3 20.9 - - + -
107O GLU* 4.0 20.1 + - - -
143O ILE* 3.1 22.2 + - + +
144O TRP 3.7 2.5 - - - +
146O PHE* 1.3 74.8 - - - +
148O ALA* 1.3 59.0 + - - +
150O LEU* 2.8 26.2 + - + +
151O GLY 3.0 0.2 + - - -
152O LYS* 2.9 46.4 + - + +
153O ALA 2.8 27.1 + - - +
154O PRO* 3.6 16.5 + - + +
155O LEU* 4.5 0.4 - - - +
156O GLU* 3.1 37.4 + - - +
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Residues in contact with ALA 148 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O TRP* 2.9 22.3 + - + +
145O MET* 3.3 12.1 - - - +
147O LYS* 1.3 77.7 - - - +
149O PHE* 1.3 60.1 + - - +
151O GLY 3.1 7.4 + - - -
152O LYS 3.4 10.7 + - - +
34Y MET 4.4 0.4 - - - +
35Y ARG* 3.5 17.3 - - + +
36Y GLY 2.9 23.8 + - - -
39Y PHE* 3.9 25.6 - - + -
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Residues in contact with PHE 149 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O ASN* 3.9 18.6 - - + -
42O LEU* 3.7 30.1 - - + -
95O MET* 4.9 5.6 - - + -
96O ASP* 4.7 3.8 - - - -
99O MET* 4.2 17.7 - - + -
145O MET 3.0 14.1 + - - +
146O PHE* 3.1 10.3 + + - +
148O ALA* 1.3 76.8 - - - +
150O LEU* 1.3 82.5 + - + +
151O GLY 3.4 2.4 + - - -
36Y GLY 3.3 26.3 - - - -
37Y HIS* 3.1 56.3 - + - -
39Y PHE* 4.2 5.1 - - + +
40Y PHE* 4.0 27.4 - + + -
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Residues in contact with LEU 150 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O ASP* 3.9 28.5 - - + +
99O MET* 3.7 25.1 - - + -
100O GLU* 3.8 26.7 - - + -
103O VAL* 4.3 18.6 - - + -
146O PHE 2.9 16.3 + - - +
147O LYS* 2.8 14.1 + - + +
149O PHE* 1.3 97.7 - - + +
151O GLY* 1.3 57.5 + - - -
152O LYS* 3.4 21.4 + - + +
37Y HIS* 5.3 3.8 - - - -
----------------------------------------------------------
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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