Contacts of the helix formed by residues 158 - 184 (chain B) in PDB entry 3KDH
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 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 5.3 1.5 + - - +
92A PRO* 5.9 0.8 - - - +
153B ILE* 4.2 2.7 - - - -
156B GLY 5.1 2.7 - - - +
157B ASN* 1.3 78.4 - - - +
159B GLU* 1.3 60.8 + - - +
160B GLU* 3.7 6.5 + - - +
161B ASP* 3.0 41.0 + - - +
162B THR* 2.7 33.9 + - - -
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP 5.2 0.9 - - - +
32B PRO* 5.1 5.7 - - - +
34B THR 3.6 13.9 - - - +
35B CYS* 4.3 12.3 - - + -
36B THR 5.4 0.3 + - - -
153B ILE* 3.6 33.7 - - + +
158B THR* 1.3 73.2 - - - +
160B GLU* 1.3 66.1 + - + +
162B THR* 3.8 1.4 - - - -
163B LYS* 3.0 26.6 + - + +
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B THR* 3.3 6.4 - - - +
159B GLU* 1.3 80.8 - - + +
161B ASP* 1.3 64.9 + - - +
163B LYS* 3.4 8.8 + - - +
164B MET* 3.0 27.7 + - - +
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 2.8 39.9 + - - +
88A ILE* 3.3 41.0 - - + +
89A SER 5.3 1.3 - - - -
92A PRO* 6.2 1.3 - - + -
93A ALA* 3.8 17.8 + - + +
157B ASN* 5.7 1.3 - - - +
158B THR* 3.0 29.5 + - - +
160B GLU* 1.3 79.5 - - - +
162B THR* 1.3 60.3 + - - +
164B MET 3.4 0.2 + - - -
165B PHE* 3.0 23.2 + - - +
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER 5.3 1.1 - - - -
35B CYS* 4.5 7.2 - - + -
121B LEU* 4.2 24.7 - - + -
151B VAL* 4.3 20.0 - - + -
152B ASP 4.8 0.9 - - - +
153B ILE* 4.0 6.8 - - - +
154B PRO* 4.4 5.6 - - + -
157B ASN* 3.1 28.3 + - - +
158B THR 2.7 22.8 + - - -
159B GLU* 3.8 5.2 - - - -
161B ASP* 1.3 76.5 - - - +
163B LYS* 1.3 62.8 + - - +
165B PHE* 3.3 6.9 + - + +
166B VAL* 3.0 27.1 + - + +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B CYS* 3.2 26.5 - - - -
36B THR 2.7 29.7 + - - -
37B SER* 3.3 16.0 + - - +
149B TYR* 3.3 5.3 + - - +
159B GLU* 3.0 18.4 + - + +
160B GLU* 3.5 8.7 - - - +
162B THR* 1.3 76.9 - - - +
164B MET* 1.3 57.5 + - - +
167B ASP* 2.8 48.8 + - - +
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Residues in contact with MET 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 6.0 5.2 - - + -
67A VAL 6.1 1.3 - - - +
88A ILE* 3.6 24.9 - - + -
160B GLU 3.0 17.4 + - - +
161B ASP* 3.7 5.2 - - - +
162B THR 3.3 0.2 - - - -
163B LYS* 1.3 75.3 - - - +
165B PHE* 1.3 60.8 + - - +
167B ASP* 4.4 9.0 - - - +
168B THR* 2.7 45.4 + - - +
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.7 27.1 - + - -
88A ILE* 3.6 7.4 - - + +
89A SER* 3.4 37.9 - - - +
90A GLY* 3.7 24.2 - - - -
121B LEU* 3.9 16.4 - - + -
161B ASP 3.0 14.4 + - - +
162B THR* 3.6 4.5 - - + +
163B LYS 3.3 0.2 - - - -
164B MET* 1.3 78.8 - - - +
166B VAL* 1.3 74.4 + - + +
168B THR* 3.2 4.3 + - - -
169B VAL* 3.1 39.2 + - + +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 4.1 17.7 - - + -
124B TYR* 3.9 16.4 - - + -
149B TYR* 3.5 40.6 - - + +
151B VAL* 4.4 16.2 - - + -
162B THR* 3.0 15.6 + - + +
165B PHE* 1.3 87.3 - - + +
167B ASP* 1.3 66.2 + - - +
168B THR 3.2 0.3 + - - -
169B VAL* 3.3 6.3 + - + +
170B VAL* 2.9 27.9 + - + +
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 2.8 26.5 + - - -
39B ILE* 3.5 21.7 - - + +
149B TYR* 2.7 26.7 + - - -
163B LYS* 2.8 38.9 + - - +
164B MET* 3.8 10.3 - - - +
166B VAL* 1.3 72.7 - - - +
168B THR* 1.3 57.8 + - - +
170B VAL* 4.0 0.7 - - - +
171B LYS* 3.0 31.5 + - - +
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 4.0 20.6 - - + +
66A PHE* 3.6 33.5 + - + +
164B MET* 2.7 37.0 + - - +
165B PHE 3.6 4.5 - - - -
166B VAL 3.2 0.2 - - - -
167B ASP* 1.3 76.0 - - - +
169B VAL* 1.3 65.7 + - - +
171B LYS* 3.8 4.4 - - - +
172B LEU* 3.0 40.3 + - + +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 4.2 12.8 - - + -
66B PHE* 5.4 18.2 - - + -
165B PHE* 3.1 42.1 + - + +
166B VAL* 3.8 9.2 - - + +
168B THR* 1.3 76.5 - - - +
170B VAL* 1.3 66.8 + - + +
172B LEU* 3.2 8.8 + - - +
173B ASN* 3.0 38.5 + - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.7 27.8 - - + -
124B TYR* 3.6 24.2 - - - +
147B GLU* 3.7 34.1 - - + +
149B TYR* 4.3 7.2 - - + -
166B VAL* 2.9 30.2 + - + +
167B ASP 4.0 2.7 - - - +
169B VAL* 1.3 80.1 - - + +
171B LYS* 1.3 64.2 + - - +
173B ASN* 3.2 9.2 + - - +
174B LEU* 3.0 23.0 + - + +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 6.1 2.2 - - - -
39B ILE* 3.9 16.3 - - + +
40B THR* 2.8 29.1 + - - +
41B GLN* 2.9 25.9 + - - +
42B ARG 5.2 0.6 - - - +
167B ASP 3.0 18.8 + - - +
168B THR* 3.8 5.6 - - - +
170B VAL* 1.3 79.0 - - - +
172B LEU* 1.3 58.0 + - + +
174B LEU* 3.1 4.0 + - + +
175B GLN* 2.9 49.5 + - - +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 3.4 37.7 - - + +
66A PHE* 4.4 8.5 - - + -
172A LEU* 3.9 31.9 - - + +
65B HIS* 3.7 23.8 + - + -
66B PHE* 6.0 1.3 - - + -
168B THR* 3.0 38.0 + - + +
169B VAL* 3.2 6.5 + - - +
171B LYS* 1.3 77.9 - - + +
173B ASN* 1.3 63.4 + - - +
175B GLN* 3.3 26.9 + - - +
176B LYS 3.0 17.5 + - - -
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Residues in contact with ASN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 2.9 23.6 - - + +
64B LYS* 3.7 34.0 - - + +
65B HIS* 2.9 34.0 + - - +
66B PHE* 5.6 0.2 - - - -
147B GLU* 6.0 0.9 - - - +
169B VAL* 3.0 32.0 + - - +
170B VAL* 3.6 10.4 - - - +
172B LEU* 1.3 78.7 - - - +
174B LEU* 1.3 58.2 + - + +
176B LYS* 3.1 1.5 + - - -
177B LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 4.0 32.1 - - + +
40B THR 4.3 1.1 - - - -
41B GLN* 3.6 38.2 - - + +
63B TYR* 4.6 7.0 - - + -
128B THR* 5.4 1.1 - - + -
145B VAL* 4.0 23.3 - - + +
147B GLU* 3.4 36.8 - - + +
170B VAL* 3.0 16.2 + - + +
171B LYS 3.1 6.5 + - - +
173B ASN* 1.3 77.4 - - + +
175B GLN* 1.3 57.4 + - - +
177B LEU* 3.3 17.7 + - + +
178B GLY 2.9 22.9 + - - -
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Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 5.5 2.5 - - - -
179A VAL* 6.0 3.7 - - - +
41B GLN* 3.3 24.7 - - - +
171B LYS* 2.9 41.9 + - - +
172B LEU* 3.5 29.1 - - - +
173B ASN 3.2 0.2 - - - -
174B LEU* 1.3 77.1 - - - +
176B LYS* 1.3 61.3 + - - +
178B GLY* 3.2 2.9 + - - -
179B VAL* 3.0 26.6 + - - +
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU 2.9 29.4 + - - -
62B ARG* 3.5 12.3 - - - +
63B TYR* 3.4 23.3 - - - +
64B LYS 3.1 14.7 + - - +
65B HIS* 3.7 39.6 + - + +
172B LEU 3.0 6.2 + - - +
173B ASN 3.1 1.8 + - - +
175B GLN* 1.3 73.5 - - - +
177B LEU* 1.3 66.8 + - - +
179B VAL* 3.2 9.9 + - + +
180B ALA* 3.0 22.5 + - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.9 18.8 - - + -
50B VAL* 4.1 9.2 - - + +
53B LEU* 3.6 36.3 - - + -
54B ILE* 3.8 28.0 - - + -
63B TYR* 3.5 27.2 - - + +
145B VAL* 4.0 10.3 - - + -
173B ASN 2.9 12.9 + - - +
174B LEU* 3.3 24.7 - - + +
176B LYS* 1.3 76.3 - - - +
178B GLY* 1.3 61.2 + - - +
180B ALA* 3.3 3.4 + - - +
181B ALA* 3.0 23.2 + - - +
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Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 5.4 2.0 - - - -
43B ILE* 3.6 28.5 - - - -
174B LEU 2.9 13.4 + - - -
175B GLN* 3.2 5.5 + - - -
177B LEU* 1.3 76.4 - - - +
179B VAL* 1.3 61.1 + - - +
181B ALA* 3.4 0.5 + - - -
182B THR* 2.9 32.2 + - - +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLN 3.0 15.8 + - - +
176B LYS* 3.2 10.9 + - + +
178B GLY* 1.3 74.0 - - - +
180B ALA* 1.3 65.2 + - - +
182B THR* 3.3 6.2 + - - -
183B SER* 2.8 42.3 + - - +
184B ALA* 6.2 0.4 - - + -
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 5.4 0.3 - - - +
53B LEU* 4.1 19.7 - - + -
62B ARG* 4.1 22.1 + - - +
63B TYR* 5.4 0.2 - - + -
176B LYS* 3.0 15.7 + - + +
177B LEU* 3.7 5.6 - - - +
178B GLY 3.2 0.4 - - - -
179B VAL* 1.3 78.6 - - - +
181B ALA* 1.3 59.8 + - - +
184B ALA* 3.0 45.5 + - + +
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 4.1 6.1 - - + -
45B ALA* 3.7 8.0 - - + +
49B VAL* 3.5 27.7 - - + +
50B VAL* 3.7 30.3 - - + -
53B LEU* 3.8 16.3 - - + +
177B LEU 3.0 16.6 + - - +
178B GLY 4.0 2.9 - - - +
180B ALA* 1.3 78.6 - - - +
182B THR* 1.3 59.3 + - - +
184B ALA 5.2 1.6 + - - +
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Residues in contact with THR 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.8 17.9 - - + -
44B HIS* 3.6 30.5 - - + +
45B ALA* 4.6 2.7 - - - -
178B GLY 2.9 26.3 + - - +
179B VAL* 3.3 9.2 + - - +
181B ALA* 1.3 78.5 - - - +
183B SER* 1.3 65.5 + - - +
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 2.8 33.1 + - - +
181B ALA 3.5 0.6 - - - -
182B THR* 1.3 84.9 - - - +
184B ALA* 1.3 64.0 + - - +
185B PRO* 4.1 3.3 - - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 6.1 0.9 - - - +
62B ARG* 4.5 7.5 + - - +
179B VAL* 4.8 0.7 - - + +
180B ALA* 3.0 32.6 + - + +
181B ALA 5.3 1.4 - - - +
183B SER* 1.3 81.3 + - - +
185B PRO* 1.3 80.5 - - + +
186B MET* 3.5 5.4 + - - +
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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