Contacts of the helix formed by residues 125 - 151 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H THR* 3.8 18.6 - - - +
63H ARG* 3.0 26.6 + - - -
67H ILE* 4.2 8.5 - - - +
120H THR* 3.0 21.5 + - - +
123H GLU* 3.3 6.2 - - + +
124H GLY* 1.3 72.4 - - - +
126H ASP* 1.3 62.4 + - - +
127H VAL 3.5 2.1 + - - -
128H THR* 2.7 30.3 + - - -
129H ASN* 3.2 20.0 + - - +
136J LYS* 5.6 0.7 + - - -
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Residues in contact with ASP 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H GLY* 3.0 11.4 + - - +
125H ASP* 1.3 71.2 + - - +
127H VAL* 1.3 63.5 + - + +
129H ASN* 3.5 7.7 - - - +
130H ASP* 3.2 17.5 + - - +
114J LYS* 3.1 34.7 + - - +
117J ILE* 4.0 23.7 - - + +
129J ASN* 5.7 0.2 + - - -
133J ILE* 3.6 37.1 - - + +
136J LYS* 5.6 6.5 - - - +
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ARG* 3.2 42.4 - - - +
125H ASP* 3.4 1.6 + - - -
126H ASP* 1.3 78.1 - - + +
128H THR* 1.3 61.2 + - - +
130H ASP* 3.3 5.4 + - - +
131H MET* 3.2 21.9 + - + +
133J ILE* 3.5 30.5 - - + +
136J LYS* 4.0 22.5 - - + +
137J ALA* 3.5 31.4 - - + +
140J ASP* 4.2 2.5 - - - +
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Residues in contact with THR 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H THR* 3.8 14.8 - - + -
13H LEU* 3.9 25.7 - - + +
63H ARG* 2.8 27.0 + - - +
67H ILE* 4.6 0.5 - - - +
120H THR* 3.4 15.3 - - - +
125H ASP* 2.7 30.7 + - - -
127H VAL* 1.3 74.7 - - - +
129H ASN* 1.3 57.3 + - - +
131H MET* 3.3 12.4 + - + +
132H LEU* 3.1 35.1 + - + +
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Residues in contact with ASN 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ILE* 3.2 26.3 + - - +
120H THR* 3.0 36.2 - - + +
121H ASP* 3.8 18.2 + - - +
125H ASP 3.2 13.6 + - - +
126H ASP* 3.5 9.9 - - - +
128H THR* 1.3 73.5 - - - +
130H ASP* 1.3 64.8 + - - +
132H LEU* 3.5 4.4 + - - +
133H ILE* 3.1 49.0 + - - +
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Residues in contact with ASP 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP* 3.8 19.8 - - - +
126H ASP 3.2 15.2 + - - +
127H VAL* 3.3 5.0 + - - +
129H ASN* 1.3 77.7 - - - +
131H MET* 1.3 68.0 + - - +
133H ILE* 3.3 9.5 + - - +
134H ALA* 3.0 24.2 + - - +
130J ASP* 3.9 11.7 - - - +
133J ILE* 4.0 18.0 - - + +
134J ALA* 5.5 7.3 - - - +
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Residues in contact with MET 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LEU* 4.3 8.7 - - + -
59H GLU* 3.9 22.7 - - + +
60H VAL* 4.2 18.6 - - + -
63H ARG* 3.8 38.6 - - + -
127H VAL* 3.2 11.6 + - + +
128H THR* 3.5 9.2 - - + +
129H ASN 3.3 0.2 - - - -
130H ASP* 1.3 79.7 + - - +
132H LEU* 1.3 79.3 + - + +
134H ALA* 3.1 8.9 + - - +
135H PHE* 3.0 51.2 + - + -
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Residues in contact with LEU 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H PHE* 3.8 25.4 - - + -
13H LEU* 4.4 5.6 - - + -
16H GLN* 6.1 0.7 - - + -
60H VAL* 5.2 3.4 - - + -
113H TYR* 3.9 25.2 - - + +
116H GLY 3.6 32.5 - - - +
117H ILE* 3.7 17.5 - - + +
120H THR* 4.5 1.1 - - + -
128H THR* 3.1 28.6 + - + +
129H ASN 3.8 2.2 - - - +
130H ASP 3.3 0.2 - - - -
131H MET* 1.3 100.3 - - + +
133H ILE* 1.3 55.8 + - - +
135H PHE* 3.5 10.1 + - + +
136H LYS* 3.0 29.5 + - - +
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Residues in contact with ILE 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASP* 3.6 55.2 - - + +
127C VAL* 3.7 9.3 - - + +
130C ASP* 4.0 21.1 - - + +
117H ILE* 3.9 17.0 - - + -
129H ASN* 3.1 45.6 + - - +
130H ASP* 3.6 8.7 - - - +
131H MET 3.3 0.2 - - - -
132H LEU* 1.3 73.5 - - - +
134H ALA* 1.3 64.5 + - - +
136H LYS* 3.1 2.6 + - - +
137H ALA* 3.0 22.9 + - + +
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Residues in contact with ALA 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP* 5.3 7.6 - - - +
130H ASP* 3.0 16.0 + - - +
131H MET* 3.1 10.9 + - - +
133H ILE* 1.3 76.5 - - - +
135H PHE* 1.3 69.7 + - + +
137H ALA* 3.3 20.4 - - - +
138H SER* 3.6 7.6 + - - -
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Residues in contact with PHE 135 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H GLU* 4.1 10.8 - - - -
56H GLN* 3.5 44.8 + - + +
59H GLU* 3.9 25.6 - - + -
60H VAL* 3.9 23.6 - - + -
113H TYR* 3.4 28.5 - + + -
131H MET* 3.0 43.6 + - + -
132H LEU* 3.7 6.5 - - + +
133H ILE 3.3 0.2 - - - -
134H ALA* 1.3 81.8 - - + +
136H LYS* 1.3 63.4 + - - +
138H SER* 3.3 6.5 + - - -
139H ILE* 3.1 27.0 + - - +
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Residues in contact with LYS 136 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 4.4 6.1 - - - +
125C ASP* 5.4 1.4 + - - -
126C ASP* 5.9 5.8 - - - +
127C VAL* 3.9 15.2 - - + +
110H ARG* 4.3 29.4 - - + +
113H TYR* 4.4 7.6 - - + -
114H LYS* 4.5 23.6 - - + +
117H ILE* 4.3 20.2 - - + -
132H LEU 3.0 17.8 + - - +
133H ILE 3.1 4.4 + - - +
135H PHE* 1.3 76.7 - - - +
137H ALA* 1.3 57.9 + - - +
139H ILE* 3.6 10.0 - - - +
140H ASP* 2.8 63.6 + - - +
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Residues in contact with ALA 137 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 5.0 1.0 + - - -
127C VAL* 3.5 33.2 - - + +
133H ILE* 3.0 11.0 + - + +
134H ALA* 3.3 15.7 - - - +
136H LYS* 1.3 77.8 - - - +
138H SER* 1.3 60.4 + - - +
140H ASP* 3.5 5.9 + - - +
141H LYS* 3.2 24.7 + - - +
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Residues in contact with SER 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLU* 2.4 30.3 + - - -
53H PHE* 5.1 0.9 - - - -
56H GLN* 4.6 4.4 + - - -
134H ALA 3.6 6.2 + - - -
135H PHE* 3.3 10.2 + - - -
137H ALA* 1.3 76.8 - - - +
139H ILE* 1.3 60.8 + - - +
141H LYS* 3.3 11.1 + - - +
142H HIS* 3.0 42.3 + - - -
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Residues in contact with ILE 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H PHE* 4.0 28.7 - - + -
56H GLN* 4.4 2.0 - - - +
106H LEU* 3.4 32.3 - - + +
109H LEU* 4.2 19.7 - - + -
110H ARG* 3.9 13.5 - - + +
113H TYR* 4.1 28.7 - - + -
135H PHE 3.1 15.0 + - - +
136H LYS* 3.6 10.1 - - - +
138H SER* 1.3 73.3 - - - +
140H ASP* 1.3 64.5 + - - +
142H HIS* 3.2 8.1 + - - +
143H ILE* 2.9 31.9 + - + +
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Residues in contact with ASP 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 2.9 34.0 + - - +
66C ALA* 4.0 14.4 - - + +
127C VAL* 4.0 2.6 - - - +
110H ARG* 3.3 29.3 + - - +
136H LYS* 2.8 50.6 + - - +
137H ALA 3.6 4.3 - - - +
138H SER 3.4 0.2 - - - -
139H ILE* 1.3 70.7 - - - +
141H LYS* 1.3 55.5 + - - +
143H ILE* 3.5 9.2 + - - +
144H TRP* 3.1 26.2 + - - +
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Residues in contact with LYS 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU* 3.8 29.2 + - + +
63C ARG* 6.4 0.7 - - - -
66C ALA* 4.6 7.4 - - + -
137H ALA 3.2 12.9 + - - +
138H SER* 3.4 14.1 - - - +
139H ILE 3.2 0.4 - - - -
140H ASP* 1.3 75.3 - - - +
142H HIS* 1.3 63.5 + - + +
144H TRP* 3.3 25.8 + - + +
145H MET* 2.9 51.8 + - + +
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Residues in contact with HIS 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H LYS* 4.5 8.0 + - - -
48H ASP* 6.3 2.5 - - + -
49H LEU* 3.3 27.2 - - + +
52H GLU* 2.6 29.4 + - - -
53H PHE* 4.2 8.5 - + - -
106H LEU* 4.1 17.5 - - + -
138H SER* 3.0 34.7 + - - +
139H ILE* 3.7 5.6 - - - +
141H LYS* 1.3 73.7 - - + +
143H ILE* 1.3 60.6 + - - +
145H MET* 4.2 20.8 - - + +
146H PHE* 3.0 49.9 + - + -
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Residues in contact with ILE 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H VAL* 4.8 6.2 - - + +
106H LEU* 3.8 33.4 - - + +
107H GLU* 4.1 18.4 - - + +
110H ARG* 3.8 39.3 - - + +
139H ILE* 2.9 39.4 + - + +
140H ASP* 3.6 6.3 - - - +
142H HIS* 1.3 75.6 - - - +
144H TRP* 1.3 57.3 + - - +
146H PHE* 5.3 0.9 - - - -
147H LYS* 3.0 40.0 + - + +
154H PRO* 4.1 19.3 - - + +
155H LEU* 5.8 0.2 - - + -
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Residues in contact with TRP 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 5.7 8.1 - + - -
32A TRP* 5.0 7.7 + + - -
34A MET 5.8 0.4 + - - -
39A PHE* 3.9 25.3 - + - -
62C GLU* 4.1 42.0 - - + -
65C LEU* 3.9 35.1 - - + +
66C ALA* 3.9 17.5 - - + +
140H ASP 3.1 13.6 + - - +
141H LYS* 3.6 22.4 - - + +
143H ILE* 1.3 78.6 - - - +
145H MET* 1.3 79.5 + - + +
147H LYS* 3.5 2.2 + - - +
148H ALA* 2.8 36.9 + - + +
152H LYS 5.0 0.6 - - - +
154H PRO* 4.1 31.2 - - + -
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Residues in contact with MET 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.7 32.0 - - + -
40A PHE* 4.0 16.2 - - + -
45H LYS* 4.2 15.7 - - - +
141H LYS* 2.9 45.4 + - + +
142H HIS* 4.1 25.4 - - + +
144H TRP* 1.3 98.3 - - + +
146H PHE* 1.3 59.2 + - + +
148H ALA* 3.3 3.3 + - - +
149H PHE* 3.0 25.6 + - - +
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Residues in contact with PHE 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.7 27.8 - + - -
42H LEU* 4.5 5.6 - - + -
45H LYS* 3.9 20.0 - - + -
46H MET* 4.0 27.6 - - + -
49H LEU* 4.0 21.3 - - + -
99H MET* 4.4 16.1 - - + +
102H LEU* 4.1 12.6 - - + -
103H VAL* 3.8 19.7 - - + -
106H LEU* 4.1 7.2 - - + -
142H HIS* 3.0 48.1 + - + +
145H MET* 1.3 74.2 - - + +
147H LYS* 1.3 65.7 + - - +
149H PHE* 3.4 8.1 + - + +
150H LEU* 3.2 26.8 + - + +
----------------------------------------------------------
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Residues in contact with LYS 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H VAL* 4.0 22.0 - - + -
107H GLU* 3.4 24.8 + - - -
143H ILE* 3.0 26.8 + - - +
144H TRP 3.9 3.1 - - - +
146H PHE* 1.3 74.7 - - - +
148H ALA* 1.3 62.2 + - - +
150H LEU* 3.1 9.1 + - + +
151H GLY 2.9 5.0 + - - -
152H LYS* 2.8 53.8 + - + +
153H ALA 3.6 12.6 + - - +
154H PRO* 3.4 24.3 + - + +
155H LEU 4.4 1.0 - - - -
156H GLU 2.6 35.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 148 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A MET 4.2 7.2 - - - +
35A ARG* 3.8 8.1 - - + +
36A GLY 3.0 20.6 + - - -
39A PHE* 3.8 27.8 - - + -
144H TRP* 2.8 28.7 + - + +
145H MET 3.6 5.6 - - - +
147H LYS* 1.3 77.4 - - - +
149H PHE* 1.3 61.3 + - - +
151H GLY* 3.0 9.8 + - - +
152H LYS 3.5 7.5 + - - +
----------------------------------------------------------
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Residues in contact with PHE 149 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY* 3.3 26.2 - - - -
37A HIS* 3.1 36.4 + - + +
39A PHE* 4.2 4.9 - - + +
40A PHE* 4.0 28.3 - + + -
38H ASN* 3.5 27.1 - - + -
41H THR* 4.6 4.0 - - + -
42H LEU* 3.4 40.2 - - + -
95H MET* 5.1 3.1 - - + -
96H ASP* 5.8 1.8 - - - -
99H MET* 4.6 7.9 - - + -
145H MET 3.0 13.6 + - - +
146H PHE* 3.5 10.3 - + - +
147H LYS 3.3 0.2 - - - -
148H ALA* 1.3 76.2 - - - +
150H LEU* 1.3 78.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU 150 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY* 5.5 0.2 - - - -
96H ASP* 4.1 25.8 - - - +
99H MET* 3.7 28.0 - - + -
100H GLU* 4.2 26.2 - - + +
103H VAL* 4.3 19.5 - - + -
146H PHE 3.2 15.7 + - - +
147H LYS* 3.1 9.0 + - + +
149H PHE* 1.3 88.0 - - + +
151H GLY* 1.3 60.5 + - - +
152H LYS* 3.4 23.6 + - + +
----------------------------------------------------------
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Residues in contact with GLY 151 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 4.8 21.0 + - - -
36A GLY* 4.6 8.5 - - - -
147H LYS 2.9 2.4 + - - -
148H ALA* 3.0 13.8 + - - -
149H PHE 3.3 1.0 + - - -
150H LEU* 1.3 79.7 - - - +
152H LYS* 1.3 61.9 + - - +
156H GLU* 4.6 2.4 - - - +
----------------------------------------------------------
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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