Contacts of the helix formed by residues 154 - 178 (chain B) in PDB entry 1XV9
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 VAL 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.4 4.9 - - + -
152B ALA 4.3 2.9 - - - +
153B PRO* 1.3 68.6 - - - +
155B LEU* 1.3 68.6 + - - +
156B PRO* 3.1 4.2 - - - +
157B LEU* 2.8 28.1 + - + +
158B VAL* 3.4 21.8 + - + -
231B ARG* 3.8 57.2 - - + +
232B VAL 4.6 0.4 - - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO* 5.4 2.2 - - + -
154B VAL* 1.3 76.5 - - - +
156B PRO* 1.3 68.5 - - + +
158B VAL* 3.8 8.9 - - + +
159B THR* 2.7 46.9 + - - +
339B MET* 3.9 23.1 - - + -
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Residues in contact with PRO 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG 4.5 4.2 - - - +
138B PRO* 3.8 18.4 - - + +
153B PRO* 3.3 33.4 - - + +
154B VAL 3.1 7.0 - - - +
155B LEU* 1.3 95.9 - - + +
157B LEU* 1.3 59.5 + - - +
159B THR* 3.8 5.4 + - - +
160B HIS* 3.6 12.0 + - - +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO* 3.4 20.3 - - + +
140B HIS* 3.8 19.7 - - + +
141B LEU* 4.5 10.1 - - + -
148B LEU* 3.9 26.2 - - + -
154B VAL* 2.8 18.1 + - + +
156B PRO* 1.3 71.9 - - - +
158B VAL* 1.3 56.4 + - - +
160B HIS* 2.7 26.4 + - + +
161B PHE* 2.8 11.3 + - - +
228B ASP* 3.6 28.5 - - + +
231B ARG* 4.4 7.6 - - + -
232B VAL* 4.2 23.3 - - + -
1001D CI2 4.5 13.5 - - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 3.6 31.0 - - + +
155B LEU* 3.4 12.5 + - + +
157B LEU* 1.3 75.2 - - - +
159B THR* 1.3 63.2 + - - +
161B PHE* 3.0 7.5 + - - +
162B ALA* 3.0 24.8 + - - +
232B VAL* 3.8 30.5 - - + +
336B LEU* 4.3 15.0 - - + -
339B MET* 3.9 22.9 - - + -
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 5.6 6.7 - - - -
155B LEU* 2.7 40.5 + - - +
156B PRO* 4.0 6.6 - - - +
158B VAL* 1.3 76.7 - - - +
160B HIS* 1.3 50.6 + - - +
162B ALA* 4.8 0.3 - - - +
163B ASP* 2.7 52.4 + - - +
339B MET* 4.2 13.9 - - - -
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE 3.2 26.9 - - - -
135B PHE* 2.9 29.5 + - + +
136B ARG 4.1 1.6 - - - +
137B PRO* 3.7 12.4 - - + +
138B PRO* 3.9 15.0 - - + -
141B LEU* 3.8 22.5 - - + +
156B PRO 3.6 4.3 + - - +
157B LEU* 2.7 17.0 + - + +
159B THR* 1.3 78.5 - - - +
161B PHE* 1.3 62.6 + - - -
163B ASP* 2.9 6.0 + - - +
164B ILE* 2.9 37.2 + - + +
224B TYR* 3.1 22.1 + + - -
1001D CI2 3.7 16.6 - - - -
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 2.8 10.1 + - - +
158B VAL* 3.3 11.2 - - - +
160B HIS* 1.3 77.8 - - - +
162B ALA* 1.3 64.2 + - - +
163B ASP 2.9 5.9 + - - -
164B ILE* 3.0 6.0 + - + +
165B ASN* 3.0 45.7 + - - +
232B VAL* 3.7 23.8 - - + -
234B PHE* 3.5 34.3 - + - -
326B TYR* 4.2 2.5 - - - -
336B LEU* 4.2 13.2 - - + -
340B MET* 4.0 18.4 - - + -
1001D CI2 3.3 67.3 + - + +
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL 3.0 11.4 + - - +
159B THR 4.8 1.3 - - - +
161B PHE* 1.3 79.8 - - - +
163B ASP* 1.3 59.7 + - - +
165B ASN* 4.0 2.0 - - - -
166B THR* 3.1 32.2 + - - -
336B LEU* 4.5 5.8 - - + -
339B MET* 3.7 36.8 - - + +
340B MET* 3.9 25.9 - - + +
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 4.0 19.8 - - + +
136B ARG* 3.1 37.4 + - - -
159B THR* 2.7 27.4 + - - +
160B HIS* 2.9 15.4 + - - +
161B PHE 2.9 1.0 + - - -
162B ALA* 1.3 81.5 - - - +
164B ILE* 1.3 55.2 + - - +
166B THR* 4.0 3.7 - - - +
167B PHE* 3.0 26.3 + - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 4.1 23.8 - - + -
135B PHE* 3.7 24.0 - - + -
160B HIS* 2.9 40.4 + - + +
161B PHE* 3.2 12.3 - - + +
163B ASP* 1.3 73.5 - - - +
165B ASN* 1.3 62.5 + - - +
167B PHE* 3.6 9.8 - - + +
168B MET* 2.7 58.7 + - + +
1001D CI2 3.1 42.2 - - + -
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Residues in contact with ASN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 3.0 36.0 + - + +
162B ALA* 4.0 4.0 - - - +
164B ILE* 1.3 77.2 - - + +
166B THR* 1.3 68.8 + - - +
167B PHE 3.0 1.1 - - - -
168B MET* 3.0 13.8 + - - +
169B VAL* 2.9 31.4 + - - +
202B CYS* 5.6 2.8 - - - -
326B TYR* 2.6 26.8 + - - -
340B MET* 3.8 10.4 - - - +
343B LEU* 4.0 15.3 - - - +
1001D CI2 3.3 21.6 - - - +
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ALA 3.1 12.5 + - - -
163B ASP* 4.0 4.0 - - - +
165B ASN* 1.3 78.2 - - - +
167B PHE* 1.3 52.7 + - - +
170B LEU* 2.6 47.4 + - + +
339B MET 4.6 0.9 + - - -
340B MET* 2.8 38.0 - - - +
341B PRO* 4.7 3.3 - - + +
342B LEU* 3.4 19.2 - - + +
343B LEU* 3.8 11.2 - - - +
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Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 3.7 20.9 - - + -
131B GLN* 4.1 22.2 - - + -
132B PHE* 3.5 32.3 - + - -
135B PHE* 3.6 34.8 - + + -
163B ASP 3.0 20.1 + - - +
164B ILE* 3.6 11.0 - - - +
166B THR* 1.3 76.0 - - - +
168B MET* 1.3 67.4 + - - +
170B LEU* 3.1 28.7 + - + +
171B GLN* 3.2 40.7 + - + +
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 3.7 35.5 - - + +
132B PHE* 3.9 20.9 - - + -
164B ILE* 2.7 49.5 + - + +
165B ASN* 3.0 17.2 + - - +
167B PHE* 1.3 73.0 - - - +
169B VAL* 1.3 60.3 + - - +
171B GLN* 2.8 21.0 + - - +
172B VAL* 3.0 15.8 + - - +
202B CYS* 4.2 27.1 - - + +
206B LEU* 5.1 12.3 - - + -
1001D CI2 3.7 22.4 - - + -
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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
----------------------------------------------------------
165B ASN* 2.9 12.7 + - - +
168B MET* 1.3 76.1 - - - +
170B LEU* 1.3 60.2 + - - +
172B VAL* 3.6 10.4 + - + +
173B ILE* 3.2 25.0 + - + +
198B ALA* 4.5 16.2 - - + +
199B VAL* 5.8 0.7 - - + -
202B CYS* 4.5 10.8 - - - -
342B LEU* 3.6 29.4 - - + -
343B LEU* 3.1 37.2 - - + -
346B ILE* 4.0 21.1 - - + -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 2.6 32.8 - - + +
167B PHE* 3.1 26.5 - - + +
168B MET 2.9 0.2 + - - -
169B VAL* 1.3 77.3 - - - +
171B GLN* 1.3 61.3 + - - +
173B ILE* 3.3 7.9 + - - +
174B LYS* 2.9 31.5 + - + +
342B LEU* 3.3 22.0 - - + -
689F ILE* 5.6 4.3 - - + -
693F LEU* 4.4 21.1 - - + -
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Residues in contact with GLN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG 5.1 0.4 + - - -
124B HIS* 3.1 41.1 + - - +
125B MET* 4.4 3.6 - - + -
128B MET* 4.1 14.4 - - - -
131B GLN* 5.4 3.3 + - - +
167B PHE* 3.2 44.3 - - + +
168B MET 2.8 7.2 + - - +
170B LEU* 1.3 77.5 - - - +
172B VAL* 1.3 55.5 + - - +
174B LYS* 3.0 37.1 + - - +
175B PHE* 2.7 36.1 + - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 4.1 15.2 - - + -
128B MET* 6.1 2.9 - - + -
168B MET* 3.0 8.6 + - + +
169B VAL* 3.6 9.9 - - - +
170B LEU 3.3 0.2 - - - -
171B GLN* 1.3 74.6 - - + +
173B ILE* 1.3 60.2 + - + +
175B PHE* 3.0 20.8 - - + +
176B THR* 3.1 17.1 + - + +
194B LEU* 5.2 3.8 - - + -
198B ALA* 4.2 13.9 - - + +
201B ILE* 4.0 40.8 - - + -
202B CYS* 3.4 34.8 - - - +
205B VAL* 6.0 0.2 - - + -
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 3.2 18.9 + - + +
170B LEU* 3.5 9.9 - - - +
171B GLN 3.1 0.4 - - - -
172B VAL* 1.3 76.9 - - + +
174B LYS* 1.3 67.5 + - + +
175B PHE 3.0 1.8 - - - -
176B THR* 2.9 22.3 + - - -
177B LYS* 3.2 22.1 + - - +
194B LEU* 4.0 22.0 - - + -
198B ALA* 6.3 0.4 - - + -
342B LEU* 4.4 5.4 - - + -
346B ILE* 5.3 0.7 - - + -
690F LEU* 3.9 18.6 - - + -
693F LEU* 3.5 41.1 - - + -
694F LEU* 4.2 20.2 - - + -
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Residues in contact with LYS 174 (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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124B HIS* 3.2 45.3 + - + +
170B LEU* 2.9 18.4 + - + +
171B GLN* 3.4 31.9 + - - +
173B ILE* 1.3 78.9 - - + +
175B PHE* 1.3 62.9 + - - +
177B LYS* 3.5 20.5 + - - +
178B ASP* 3.6 5.2 + - - -
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.5 42.8 - - + -
120B ALA* 3.5 27.0 - - + +
121B HIS* 3.7 11.4 - - + -
124B HIS* 3.9 10.0 + - + -
125B MET* 3.9 31.4 - - + -
171B GLN 2.7 12.9 + - - +
172B VAL* 3.0 18.2 - - + +
174B LYS* 1.3 78.3 - - - +
176B THR* 1.3 71.4 + - + +
178B ASP 3.3 10.4 + - - -
179B LEU* 3.5 20.5 - - + +
201B ILE* 5.3 6.1 - - + -
260B VAL* 4.8 4.5 - - + -
263B ALA* 5.1 12.1 - - + -
264B ALA* 5.8 3.1 - - - -
267B LEU* 5.3 5.8 - - + -
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Residues in contact with THR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 3.1 15.1 + - + +
173B ILE* 2.9 21.3 + - - +
175B PHE* 1.3 84.7 - - + +
177B LYS* 1.3 57.0 + - - +
178B ASP 3.3 0.2 - - - -
179B LEU* 3.2 28.3 - - - +
182B PHE* 3.3 35.3 - - + +
183B ARG* 4.2 0.5 - - - -
194B LEU* 3.9 26.1 - - + +
201B ILE* 5.4 0.9 - - + -
267B LEU* 4.0 24.5 - - + -
694F LEU* 4.5 2.4 - - - +
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ILE* 3.2 23.0 + - - +
174B LYS* 3.8 16.8 - - - +
175B PHE 3.2 1.4 - - - -
176B THR* 1.3 74.5 - - - +
178B ASP* 1.3 58.0 + - - +
179B LEU 3.0 10.2 + - - -
183B ARG* 3.2 54.1 + - - +
693F LEU* 2.8 29.0 + - - +
694F LEU* 4.1 15.3 - - + -
696F GLU 2.8 26.4 + - - +
697F GLY* 3.9 11.4 + - - +
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Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B THR* 4.3 8.8 - - - +
120B ALA* 3.1 23.7 - - + +
123B ARG* 3.7 30.8 + - - +
124B HIS* 2.9 30.2 + - + -
174B LYS 3.6 1.8 + - - -
175B PHE 3.3 3.8 + - - +
177B LYS* 1.3 76.4 - - - +
179B LEU* 1.3 70.8 + - - +
180B PRO* 4.3 4.1 - - - +
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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