Contacts of the helix formed by residues 125 - 151 (chain X) 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 X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P LYS* 4.9 4.1 + - - +
9X THR* 3.5 22.3 - - - +
63X ARG* 3.0 26.4 + - - -
67X ILE* 4.2 9.8 - - - +
120X THR* 2.9 37.5 + - + +
123X GLU* 3.3 5.2 - - + +
124X GLY* 1.3 73.1 - - - +
126X ASP* 1.3 59.4 + - - +
127X VAL* 3.8 1.9 + - - +
128X THR* 2.5 29.9 + - - -
129X ASN* 2.9 9.6 + - - +
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Residues in contact with ASP 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P LYS* 3.5 25.8 + - - +
117P ILE* 3.6 22.9 - - + +
129P ASN* 5.5 0.3 - - - +
133P ILE* 3.7 31.3 - - + +
136P LYS* 5.9 3.8 - - + +
124X GLY* 3.3 12.8 + - - +
125X ASP* 1.3 72.0 + - - +
127X VAL* 1.3 59.2 + - + +
129X ASN* 3.5 8.7 - - - +
130X ASP* 2.9 29.5 + - - +
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Residues in contact with VAL 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P ILE* 3.4 31.4 - - + +
136P LYS* 3.9 25.5 - - + +
137P ALA* 3.5 33.9 - - + +
140P ASP* 4.1 2.7 - - - +
63X ARG* 3.2 41.7 - - - +
125X ASP* 3.3 1.4 + - - -
126X ASP* 1.3 71.8 - - - +
128X THR* 1.3 66.5 + - - +
130X ASP* 3.1 3.7 + - - +
131X MET* 2.9 24.5 + - + +
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Residues in contact with THR 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X THR* 3.8 8.4 - - + +
13X LEU* 3.7 33.1 - - + +
63X ARG* 3.1 21.0 + - - +
67X ILE* 4.6 0.7 - - - +
120X THR* 3.6 17.0 - - - +
125X ASP* 2.5 32.9 + - - -
127X VAL* 1.3 77.2 - - - +
129X ASN* 1.3 63.4 + - - +
130X ASP 3.3 0.2 + - - -
131X MET* 3.3 10.5 + - + +
132X LEU* 3.1 27.6 + - + +
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Residues in contact with ASN 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R ASP* 5.5 0.2 + - - -
117X ILE* 3.1 43.2 + - - +
120X THR* 3.0 23.0 - - + +
121X ASP* 3.9 15.1 - - - +
125X ASP 2.9 12.4 + - - +
126X ASP* 3.5 10.1 - - - +
128X THR* 1.3 75.1 - - - +
130X ASP* 1.3 64.8 + - - +
132X LEU* 3.4 5.3 + - - +
133X ILE* 3.2 38.2 + - - +
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Residues in contact with ASP 130 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P ASP* 3.5 19.2 - - - +
133P ILE* 4.2 16.4 - - + +
134P ALA* 5.7 5.7 - - - +
130R ASP* 3.3 25.9 - - - +
126X ASP 2.9 18.2 + - - +
127X VAL* 3.1 4.7 + - - +
129X ASN* 1.3 77.5 - - - +
131X MET* 1.3 66.0 + - - +
133X ILE* 3.1 18.4 + - - +
134X ALA* 3.1 13.6 + - - +
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Residues in contact with MET 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13X LEU* 4.1 9.4 - - + -
59X GLU* 3.8 16.8 - - + +
60X VAL* 4.1 10.3 - - + -
63X ARG* 3.6 39.5 - - + -
127X VAL* 2.9 17.3 + - + +
128X THR* 3.7 5.2 - - + +
130X ASP* 1.3 76.7 - - - +
132X LEU* 1.3 88.4 + - + +
134X ALA* 3.3 5.9 + - - +
135X PHE* 3.2 56.7 + - + -
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Residues in contact with LEU 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X PHE* 4.0 20.4 - - + -
13X LEU* 4.1 10.3 - - + -
16X GLN* 6.3 0.7 - - + -
60X VAL* 5.2 2.2 - - + -
113X TYR* 4.1 17.5 - - + +
116X GLY 3.6 30.3 - - - +
117X ILE* 3.7 18.7 - - + +
120X THR* 4.1 2.7 - - - +
128X THR* 3.1 32.8 + - + +
129X ASN* 3.8 1.1 - - - +
131X MET* 1.3 97.2 - - + +
133X ILE* 1.3 61.2 + - - +
135X PHE* 3.6 15.6 + - + +
136X LYS* 2.9 29.3 + - - +
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Residues in contact with ILE 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R ASP* 3.5 47.3 - - + +
127R VAL* 4.0 7.8 - - + +
130R ASP* 4.1 21.8 - - + +
117X ILE* 3.5 22.7 - - + -
129X ASN* 3.2 36.3 + - - +
130X ASP* 3.1 13.8 + - - +
132X LEU* 1.3 74.9 - - - +
134X ALA* 1.3 58.0 + - - +
136X LYS* 3.2 3.8 + - - +
137X ALA* 2.9 28.0 + - + +
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Residues in contact with ALA 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130R ASP* 6.1 2.0 - - - +
130X ASP* 3.1 13.2 + - - +
131X MET* 3.6 10.8 - - - +
133X ILE* 1.3 74.2 - - - +
135X PHE* 1.3 71.4 + - + +
137X ALA* 3.0 22.2 + - - +
138X SER* 3.2 8.1 + - - -
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Residues in contact with PHE 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X GLN* 3.2 42.6 + - + +
59X GLU* 3.5 32.1 - - + -
60X VAL* 3.7 23.1 - - + -
113X TYR* 3.5 27.8 - + + -
131X MET* 3.2 37.6 + - + -
132X LEU* 3.7 9.9 - - + +
134X ALA* 1.3 77.1 - - + +
136X LYS* 1.3 64.6 + - - +
138X SER* 3.1 7.1 + - - -
139X ILE* 3.0 25.9 + - - +
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Residues in contact with LYS 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R ARG* 4.9 3.2 - - - +
125R ASP* 5.8 0.6 + - - -
126R ASP* 5.3 5.8 - - - +
127R VAL* 4.0 16.3 - - + +
110X ARG* 4.0 34.4 - - + +
113X TYR* 4.2 7.8 - - + -
114X LYS* 4.2 23.1 - - - +
117X ILE* 4.2 19.3 - - + -
132X LEU 2.9 21.3 + - - +
133X ILE 3.2 5.6 + - - +
135X PHE* 1.3 73.4 - - - +
137X ALA* 1.3 56.7 + - - +
139X ILE* 3.3 9.9 + - - +
140X ASP* 3.0 54.7 + - - +
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Residues in contact with ALA 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R ARG* 5.1 0.7 + - - -
127R VAL* 3.6 29.0 - - + +
133X ILE* 2.9 14.0 + - + +
134X ALA* 3.0 14.6 + - - +
136X LYS* 1.3 78.2 - - - +
138X SER* 1.3 61.2 + - - +
140X ASP* 3.6 3.8 + - - +
141X LYS* 3.4 21.7 + - - +
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Residues in contact with SER 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X GLU* 2.4 35.7 + - - -
56X GLN* 5.1 1.6 - - - -
134X ALA 3.2 7.3 + - - -
135X PHE* 3.1 10.8 + - - -
137X ALA* 1.3 76.3 - - - +
139X ILE* 1.3 65.7 + - - +
141X LYS* 3.3 9.4 + - - +
142X HIS* 2.9 33.1 + - - -
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Residues in contact with ILE 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X PHE* 3.9 31.0 - - + -
56X GLN* 4.2 1.3 - - - +
106X LEU* 3.4 33.9 - - + +
109X LEU* 4.2 15.5 - - + -
110X ARG* 4.0 11.9 - - + +
113X TYR* 3.8 31.0 - - + -
135X PHE 3.0 16.5 + - - +
136X LYS* 3.8 6.3 - - - +
138X SER* 1.3 73.9 - - - +
140X ASP* 1.3 63.8 + - - +
142X HIS* 3.1 9.8 + - - +
143X ILE* 2.9 32.0 + - + +
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Residues in contact with ASP 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R ARG* 2.8 35.9 + - - +
66R ALA* 4.2 13.0 - - + +
127R VAL* 3.7 4.2 - - - +
110X ARG* 3.4 30.0 + - - +
136X LYS* 3.0 42.4 + - - +
137X ALA 3.9 3.6 - - - +
139X ILE* 1.3 73.8 - - - +
141X LYS* 1.3 58.2 + - - +
143X ILE* 3.1 11.6 + - - +
144X TRP* 3.0 27.5 + - - +
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Residues in contact with LYS 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R GLU* 6.1 2.6 - - - +
62R GLU* 2.8 32.4 + - + +
66R ALA* 4.6 6.0 - - + +
137X ALA 3.4 10.2 + - - +
138X SER* 3.3 10.7 + - - +
139X ILE 3.3 0.2 - - - -
140X ASP* 1.3 75.4 - - - +
142X HIS* 1.3 68.4 + - + +
144X TRP* 3.4 18.4 + - + +
145X MET* 3.2 47.6 + - + +
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Residues in contact with HIS 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X LYS* 4.8 5.6 - - - -
48X ASP* 6.4 0.9 - - + -
49X LEU* 3.3 30.4 - - + +
52X GLU* 2.7 27.4 + - - -
53X PHE* 4.5 9.2 - + - -
106X LEU* 4.1 17.3 - - + -
138X SER* 2.9 34.3 + - - -
139X ILE* 3.1 10.0 + - - +
141X LYS* 1.3 77.8 - - + +
143X ILE* 1.3 56.6 + - - +
145X MET* 3.4 23.2 + - + +
146X PHE* 2.9 44.3 + - + -
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Residues in contact with ILE 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R ALA 5.9 0.7 - - - +
103X VAL* 4.7 5.6 - - + +
106X LEU* 3.9 18.8 - - + -
107X GLU* 3.8 33.2 - - + +
110X ARG* 3.8 33.4 - - - +
139X ILE* 2.9 30.4 + - + +
140X ASP* 3.1 10.9 + - - +
142X HIS* 1.3 75.5 - - - +
144X TRP* 1.3 59.7 + - - +
146X PHE* 4.5 1.9 - - - +
147X LYS* 3.0 40.1 + - + +
154X PRO* 3.8 25.6 - - + +
155X LEU* 5.1 1.6 - - + -
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Residues in contact with TRP 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R GLU* 3.7 47.8 - - + -
65R LEU* 4.1 33.4 - - + +
66R ALA* 4.1 15.9 - - + -
31T HIS* 4.8 11.9 - - - -
32T TRP* 4.4 12.3 + + - -
34T MET 5.7 0.4 + - - -
39T PHE* 3.7 27.2 - + - -
140X ASP 3.0 12.5 + - - +
141X LYS* 3.8 17.3 - - + +
143X ILE* 1.3 78.5 - - - +
145X MET* 1.3 75.0 + - + +
147X LYS* 3.7 2.1 - - - +
148X ALA* 2.8 41.5 + - + +
152X LYS 5.0 0.4 - - - +
154X PRO* 4.1 27.8 - - + +
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Residues in contact with MET 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T PHE* 3.6 33.9 - - + -
40T PHE* 4.0 11.9 - - + -
45X LYS* 3.8 26.0 - - - +
141X LYS* 3.2 32.6 + - + +
142X HIS* 3.8 25.6 - - + +
144X TRP* 1.3 95.5 - - + +
146X PHE* 1.3 61.0 + - + +
148X ALA* 3.1 2.8 + - - +
149X PHE* 2.9 28.1 + - - +
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Residues in contact with PHE 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40T PHE* 3.4 32.1 - + - -
42X LEU* 4.3 4.7 - - + -
45X LYS* 4.1 14.8 - - + -
46X MET* 3.9 21.3 - - + -
49X LEU* 4.1 14.1 - - + -
99X MET* 3.9 30.7 - - + +
102X LEU* 4.0 15.7 - - + -
103X VAL* 3.6 20.6 - - + -
106X LEU* 4.3 5.8 - - + -
142X HIS* 2.9 46.0 + - + +
145X MET* 1.3 77.0 - - + +
147X LYS* 1.3 61.7 + - - +
149X PHE* 3.3 6.8 - - + +
150X LEU* 3.1 30.9 + - + +
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Residues in contact with LYS 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100X GLU* 5.7 4.4 + - + +
103X VAL* 3.8 22.8 - - + +
107X GLU* 3.4 25.9 + - - -
143X ILE* 3.0 28.9 + - + +
144X TRP 3.8 2.7 - - - +
146X PHE* 1.3 78.1 - - - +
148X ALA* 1.3 59.9 - - - +
150X LEU* 3.1 17.4 + - + +
151X GLY 3.1 0.2 + - - -
152X LYS* 2.9 47.4 + - + +
153X ALA 3.9 9.9 - - - +
154X PRO* 3.7 21.1 - - + +
156X GLU* 3.4 28.5 - - - +
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Residues in contact with ALA 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T MET 4.1 7.4 - - - +
35T ARG* 3.4 13.1 - - + +
36T GLY 2.9 24.9 + - - -
39T PHE* 3.7 28.7 - - + -
144X TRP* 2.8 27.9 + - + +
145X MET 3.6 4.3 - - - +
147X LYS* 1.3 77.6 - - - +
149X PHE* 1.3 59.0 + - - +
151X GLY 3.3 6.1 + - - -
152X LYS 3.6 9.1 + - - +
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Residues in contact with PHE 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36T GLY* 3.2 29.7 - - - -
37T HIS* 3.0 45.7 + + - -
39T PHE* 4.1 5.2 - - + +
40T PHE* 3.8 28.7 - + + -
38X ASN* 3.7 20.9 - - - -
41X THR* 5.4 1.6 - - - -
42X LEU* 3.4 38.6 - - + -
95X MET* 4.7 4.3 - - + -
96X ASP* 4.5 13.5 - - - -
99X MET* 4.1 16.2 - - + -
145X MET 2.9 13.1 + - - +
146X PHE* 3.3 10.8 - + - +
148X ALA* 1.3 75.1 - - - +
150X LEU* 1.3 70.5 + - + +
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Residues in contact with LEU 150 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36T GLY* 5.5 0.2 - - - -
37T HIS* 5.4 1.3 - - - -
96X ASP* 3.6 38.5 - - + +
99X MET* 3.8 26.7 - - + +
100X GLU* 3.9 31.0 - - + +
103X VAL* 4.2 19.5 - - + -
146X PHE 3.1 15.7 + - - +
147X LYS* 3.1 15.7 + - + +
149X PHE* 1.3 80.9 - - + +
151X GLY* 1.3 58.0 + - - +
152X LYS* 3.4 17.1 + - + +
----------------------------------------------------------
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Residues in contact with GLY 151 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35T ARG* 4.0 24.2 + - - -
36T GLY* 4.7 5.6 - - - -
147X LYS 3.1 1.8 + - - -
148X ALA 3.3 11.2 + - - -
149X PHE 3.4 1.8 + - - -
150X LEU* 1.3 77.3 - - - +
152X LYS* 1.3 73.2 + - - +
----------------------------------------------------------
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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