Contacts of the helix formed by residues 181 - 206 (chain B) in PDB entry 4JDA
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 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 4.4 1.8 - - - -
180B ASN* 1.3 78.0 + - - +
182B GLU* 1.3 64.4 + - - +
183B GLU* 3.7 5.5 + - - +
184B ASP* 3.0 38.3 + - - +
185B THR* 3.0 26.3 + - - -
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR 4.1 6.1 - - - +
50B CYS* 3.9 18.6 - - + -
51B THR 5.8 0.7 - - - -
176B ILE* 3.6 32.6 - - + +
181B THR* 1.3 72.8 - - - +
183B GLU* 1.3 60.8 + - - +
185B THR* 3.1 3.6 + - - -
186B ARG* 2.4 59.8 + - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR* 3.5 6.1 + - - +
182B GLU* 1.3 78.4 + - - +
184B ASP* 1.3 63.9 + - - +
186B ARG* 3.4 24.2 + - - +
187B MET* 3.0 31.9 + - - +
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASN* 5.1 8.5 - - - +
181B THR* 3.0 34.0 + - - +
182B GLU 3.2 1.2 - - - -
183B GLU* 1.3 81.7 - - - +
185B THR* 1.3 59.7 + - - +
187B MET* 3.4 31.2 - - - +
188B PHE* 3.7 11.3 + - - +
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B CYS* 4.3 8.5 - - + -
141B LEU* 4.4 8.5 - - + -
174B VAL* 4.2 24.5 - - + -
175B ASP 4.9 0.2 - - - +
176B ILE* 4.4 4.0 - - - +
177B PRO* 3.5 30.8 - - + +
180B ASN* 4.1 5.9 - - - +
181B THR 3.0 14.0 + - - -
182B GLU* 3.1 9.0 + - - -
184B ASP* 1.3 75.6 - - - +
186B ARG* 1.3 64.3 + - - +
188B PHE* 3.2 5.8 + - + +
189B VAL* 3.0 31.4 + - + +
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Residues in contact with ARG 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B CYS* 3.6 11.6 - - - -
51B THR 4.0 9.2 - - - -
52B SER* 3.9 19.7 - - - +
172B TYR* 3.5 17.7 - - - +
182B GLU* 2.4 48.6 + - - +
183B GLU* 3.8 21.6 + - - +
185B THR* 1.3 76.5 - - - +
187B MET* 1.3 62.4 + - - +
190B ASP* 2.8 41.2 + - - +
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Residues in contact with MET 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 3.2 45.5 - - + +
205A THR* 5.5 4.3 - - + +
183B GLU 3.0 14.4 + - - +
184B ASP* 3.4 35.9 - - - +
186B ARG* 1.3 77.2 - - - +
188B PHE* 1.3 61.0 + - + +
190B ASP* 3.5 6.6 + - - +
191B THR* 2.6 34.2 + - - +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL* 4.6 17.0 - - + -
205A THR* 4.6 12.1 - - + -
206A ALA 3.7 19.1 - - - +
207A SER* 3.5 31.6 - - - -
111B LEU* 5.3 5.4 - - + -
141B LEU* 4.3 17.7 - - + -
184B ASP 3.7 11.6 + - - +
185B THR* 3.2 9.9 + - + +
187B MET* 1.3 83.6 - - + +
189B VAL* 1.3 72.0 + - + +
191B THR* 3.3 8.7 + - - -
192B VAL* 3.2 41.7 + - + +
301B A9S 4.1 25.6 - - + -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.8 32.8 - - + -
144B TYR* 3.9 6.5 - - + -
172B TYR* 3.4 45.1 - - + +
174B VAL* 4.8 1.8 - - + -
185B THR* 3.0 18.0 + - + +
188B PHE* 1.3 80.8 - - + +
190B ASP* 1.3 59.4 + - - +
191B THR 3.1 1.8 - - - -
192B VAL* 2.9 7.2 + - - +
193B VAL* 2.8 29.0 + - + +
301B A9S 3.6 20.4 - - + -
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B SER* 2.8 19.5 + - - -
54B ILE* 4.3 20.2 - - + +
172B TYR* 2.7 30.1 + - - -
186B ARG* 2.8 24.6 + - - +
187B MET* 3.7 6.8 - - - +
189B VAL* 1.3 75.5 - - - +
191B THR* 1.3 57.1 - - - +
193B VAL* 3.8 1.5 - - - +
194B LYS* 2.9 31.9 + - - +
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Residues in contact with THR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLN* 4.4 10.1 - - - +
201A ALA* 4.3 15.3 - - + +
202A VAL* 3.3 31.1 - - + +
205A THR* 5.1 5.5 - - + +
187B MET* 2.6 23.3 + - - +
188B PHE* 3.4 10.0 - - + -
189B VAL 3.1 0.6 - - - -
190B ASP* 1.3 77.0 - - - +
192B VAL* 1.3 57.8 + - - +
194B LYS* 4.1 4.1 - - - +
195B SER* 3.1 26.9 + - - -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 4.3 15.0 - - + -
81B PHE* 5.0 5.6 - - + -
188B PHE* 3.2 41.7 + - + +
189B VAL* 2.9 7.9 + - - +
191B THR* 1.3 77.8 - - - +
193B VAL* 1.3 61.3 + - - +
195B SER* 3.1 5.4 + - - -
196B ASN* 2.9 37.9 + - - +
301B A9S 3.7 52.9 - - + -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.3 19.5 - - + -
144B TYR* 4.0 20.9 - - - +
170B GLU* 3.4 44.0 - - + +
172B TYR* 4.4 8.5 - - + -
189B VAL* 2.8 28.8 + - + +
190B ASP 4.2 1.8 - - - +
192B VAL* 1.3 76.1 - - - +
194B LYS* 1.3 57.5 + - - +
196B ASN* 3.2 8.0 + - - +
197B LEU* 2.9 36.4 + - + +
301B A9S 4.2 10.1 - - + -
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLN* 3.1 33.7 - - - +
54B ILE* 4.5 19.2 - - + +
56B HIS* 5.4 10.8 - - + -
190B ASP 2.9 20.4 + - - +
191B THR* 4.3 1.3 - - - +
193B VAL* 1.3 77.7 - - - +
195B SER* 1.3 60.7 + - - +
197B LEU* 3.6 4.1 + - - +
198B GLN* 3.3 23.2 + - + +
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Residues in contact with SER 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A SER* 6.0 0.2 - - - -
198A GLN* 3.7 25.0 + - - +
199A ASN* 2.5 31.9 + - - -
202A VAL* 4.2 4.3 - - - -
80B HIS* 5.3 0.2 - - - +
81B PHE* 4.1 7.8 - - - -
191B THR 3.1 20.4 + - - -
192B VAL* 3.1 8.0 + - - -
193B VAL 3.1 0.2 - - - -
194B LYS* 1.3 75.1 - - - +
196B ASN* 1.3 66.7 + - - +
198B GLN* 3.4 3.2 + - - +
199B ASN* 3.1 28.8 + - - -
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Residues in contact with ASN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 3.6 23.7 - - + -
79B LYS* 3.5 35.2 - - - +
80B HIS 4.3 3.5 + - - -
81B PHE* 5.1 4.9 - - - -
82B ILE* 5.9 0.4 - - - +
170B GLU* 4.8 3.4 + - - +
192B VAL* 2.9 25.0 + - - +
193B VAL* 3.5 10.5 - - - +
195B SER* 1.3 78.5 + - - +
197B LEU* 1.3 67.0 + - + +
198B GLN 3.3 0.2 + - - -
199B ASN* 3.3 3.1 + - - +
200B LEU* 3.0 22.5 + - - +
301B A9S 3.4 34.2 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 4.1 22.0 - - + +
56B HIS* 3.3 41.9 + - + +
58B VAL* 4.9 0.9 - - - +
78B TYR* 5.2 3.4 - - + -
148B THR* 5.1 1.1 - - + -
168B VAL* 3.9 35.4 - - + +
170B GLU* 4.0 30.3 - - + +
193B VAL* 2.9 21.7 + - + +
194B LYS* 3.6 5.1 + - - +
195B SER 3.3 0.2 - - - -
196B ASN* 1.3 79.7 - - + +
198B GLN* 1.3 57.8 + - - +
200B LEU* 3.4 16.2 - - + +
201B ALA* 3.0 21.5 + - - +
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Residues in contact with GLN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A THR* 3.7 29.3 + - - +
194A LYS* 3.9 20.4 - - + +
195A SER* 3.5 30.7 - - - +
198A GLN* 4.7 11.2 - - + +
56B HIS* 3.2 29.4 + - - +
194B LYS* 3.3 18.7 + - + +
195B SER* 3.9 5.6 - - - +
196B ASN 3.3 0.2 - - - -
197B LEU* 1.3 73.2 - - - +
199B ASN* 1.3 66.1 + - - +
201B ALA* 3.2 11.3 + - - +
202B VAL* 3.2 16.0 + - - +
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Residues in contact with ASN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A HIS* 3.7 21.2 + - - +
81A PHE* 3.5 11.5 - - - -
195A SER* 2.6 30.8 + - - -
199A ASN* 3.2 24.9 + - - -
78B TYR* 3.2 27.3 + - - +
80B HIS* 3.8 15.6 - - - +
195B SER* 3.1 19.0 + - - -
196B ASN* 3.6 1.8 - - - +
198B GLN* 1.3 74.7 - - - +
200B LEU* 1.3 64.0 + - - +
202B VAL 3.2 1.6 + - - -
203B ILE* 3.1 24.5 + - - +
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 5.7 1.1 - - + -
65B ILE* 3.8 25.8 - - + -
68B PHE* 3.8 25.8 - - + -
69B VAL* 3.9 15.7 - - + -
78B TYR* 3.7 21.5 - - + -
148B THR* 6.0 0.2 - - + -
168B VAL* 4.4 12.1 - - + -
196B ASN 3.0 16.7 + - - +
197B LEU* 3.4 25.8 - - + +
198B GLN 3.1 0.2 - - - -
199B ASN* 1.3 77.7 - - - +
201B ALA* 1.3 57.7 + - - +
203B ILE* 3.1 10.8 - - + +
204B SER* 2.8 50.4 + - - +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A THR* 5.2 3.1 - - + +
56B HIS* 3.6 12.3 - - + -
57B ARG 4.8 0.2 - - - +
58B VAL* 3.6 40.4 - - + -
197B LEU 3.0 14.0 + - - +
198B GLN* 3.2 12.5 + - - +
200B LEU* 1.3 78.0 - - - +
202B VAL* 1.3 55.5 + - - +
204B SER* 4.2 0.2 - - - -
205B THR* 2.7 35.3 + - - -
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.3 41.5 - - + -
111A LEU* 4.8 11.2 - - + -
188A PHE* 4.8 8.9 - - + -
191A THR* 3.0 43.7 - - + +
192A VAL* 4.5 13.0 - - + +
195A SER* 4.3 3.6 - - - -
198B GLN 3.2 12.5 + - - +
199B ASN 3.2 1.3 + - - +
200B LEU 3.1 0.6 - - - -
201B ALA* 1.3 76.0 - - - +
203B ILE* 1.3 63.8 + - - +
205B THR* 3.4 3.3 + - - -
206B ALA* 3.1 24.3 + - - +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.6 22.9 - - + -
108A VAL* 5.8 1.3 - - + -
110A GLY* 4.4 23.1 - - - +
111A LEU* 5.5 0.7 - - + -
68B PHE* 3.4 57.8 - - + -
77B LYS* 4.0 13.0 - - + +
78B TYR* 3.5 26.5 - - + -
199B ASN 3.1 16.1 + - - +
200B LEU* 3.1 14.6 - - + +
202B VAL* 1.3 77.5 - - - +
204B SER* 1.3 60.4 + - - +
205B THR 3.5 0.2 + - - -
206B ALA* 3.5 18.2 + - - +
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Residues in contact with SER 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 4.4 0.2 - - - -
60B ALA* 3.8 12.6 - - - +
61B PRO* 5.4 0.5 - - - +
64B ALA* 3.9 15.5 - - - +
65B ILE* 3.3 42.5 - - - +
68B PHE* 3.7 11.1 - - - -
200B LEU* 2.8 34.9 + - - +
201B ALA* 4.0 6.1 - - - -
203B ILE* 1.3 77.7 - - - +
205B THR* 1.3 60.6 + - - +
206B ALA 4.9 1.2 - - - -
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A MET* 6.4 2.0 - - - -
188A PHE* 5.7 9.6 - - + -
58B VAL* 4.0 4.3 - - - +
59B ASP* 3.3 25.6 + - + +
60B ALA* 3.9 9.0 - - - +
201B ALA* 2.7 21.9 + - - +
202B VAL* 4.0 3.8 - - - -
204B SER* 1.3 76.6 - - - +
206B ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLY 4.7 6.3 - - - +
111A LEU* 3.6 29.2 - - + -
112A PRO* 4.7 13.8 - - + +
188A PHE* 5.1 10.9 - - + -
202B VAL 3.1 18.5 + - - +
203B ILE* 3.5 12.3 + - - +
204B SER 3.5 1.7 - - - -
205B THR* 1.3 82.1 - - - +
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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