Contacts of the helix formed by residues 175 - 197 (chain A) in PDB entry 5F0L
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 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PRO* 3.2 17.9 - - - +
163A ASP 5.3 3.1 - - - +
174A GLY* 1.3 74.1 - - - +
176A ILE* 1.3 68.9 + - + +
177A SER* 3.2 29.2 + - - -
178A ASP* 2.9 23.1 + - - +
179A SER 3.2 3.1 + - - -
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PRO* 4.0 11.5 - - - +
163A ASP* 4.1 17.9 + - - +
164A GLU* 4.8 9.2 - - + +
175A ASP* 1.3 78.5 - - + +
177A SER* 1.3 64.8 + - - +
179A SER* 3.1 6.6 + - - -
180A MET* 2.9 38.6 + - + +
230A LEU* 3.9 30.7 - - + -
232A GLY* 3.6 36.1 - - - +
233A VAL* 4.3 1.1 - - + +
237A ARG* 3.7 34.3 - - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP* 3.1 18.9 + - - -
176A ILE* 1.3 83.7 - - - +
178A ASP* 1.3 60.5 + - - +
180A MET* 3.5 16.1 + - - +
181A ASP* 3.1 34.1 + - - +
237A ARG* 5.7 1.2 + - - -
241A ILE* 6.1 2.7 - - - -
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 3.7 34.8 + - + +
130A LEU* 6.4 1.3 - - + -
162A PRO* 4.8 4.3 - - + -
174A GLY* 3.2 13.4 - - - -
175A ASP* 2.9 34.6 + - - +
177A SER* 1.3 74.8 - - - +
179A SER* 1.3 61.6 + - - +
181A ASP* 3.9 9.9 - - - +
182A PHE* 2.9 30.2 + - - +
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.5 9.1 - - - +
162A PRO* 2.7 51.3 + - - +
175A ASP 3.2 4.0 + - - -
176A ILE* 3.1 12.4 + - - -
178A ASP* 1.3 77.4 - - - +
180A MET* 1.3 61.2 + - - +
182A PHE* 3.4 6.1 + - - +
183A VAL* 3.1 30.7 + - - +
230A LEU* 4.0 19.3 - - - -
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Residues in contact with MET 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE* 2.9 16.7 + - + +
177A SER* 3.8 24.0 - - - +
179A SER* 1.3 73.9 - - - +
181A ASP* 1.3 59.6 + - - +
183A VAL* 4.1 0.2 - - - -
184A LEU* 2.9 39.5 + - + +
227A LEU* 4.2 10.0 - - + +
230A LEU* 4.2 6.7 - - + -
233A VAL* 4.1 22.9 - - + -
237A ARG* 4.1 28.9 - - + +
241A ILE* 3.8 38.6 - - + -
242A VAL* 3.6 26.9 - - + -
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Residues in contact with ASP 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS* 5.6 8.7 - - + +
177A SER* 3.1 23.4 + - - +
178A ASP* 3.9 10.5 - - - +
180A MET* 1.3 75.5 - - - +
182A PHE* 1.3 62.5 + - - +
184A LEU* 4.6 8.2 - - - +
185A LEU* 2.9 29.4 + - - +
241A ILE* 5.8 2.4 - - - +
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Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.4 46.0 - - + -
131A LYS* 4.8 1.8 - - - +
134A VAL* 3.7 25.4 - - + +
153A LEU* 3.7 36.1 - - + -
154A LEU* 4.7 9.4 - - + -
157A THR* 3.7 24.7 - - + -
161A LEU* 3.7 20.9 - - + -
178A ASP 2.9 20.3 + - - +
179A SER* 3.5 7.0 - - - +
180A MET 3.3 0.2 - - - -
181A ASP* 1.3 76.0 - - - +
183A VAL* 1.3 71.5 + - + +
185A LEU* 3.8 4.4 - - - +
186A ASN* 3.1 25.5 + - + +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU* 4.3 4.9 - - + -
161A LEU* 3.9 17.0 - - + -
179A SER 3.1 16.7 + - - +
182A PHE* 1.3 87.2 - - + +
184A LEU* 1.3 57.3 + - - +
185A LEU 3.2 1.1 - - - -
186A ASN* 3.2 4.4 + - - +
187A PHE* 2.7 33.8 + - - +
223A ASN* 3.2 42.6 - - + +
226A ARG* 4.1 14.8 - - + -
227A LEU* 3.7 20.2 - - + +
230A LEU* 5.3 2.9 - - + -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A MET* 2.9 27.7 + - + +
181A ASP* 4.2 8.3 - - - +
183A VAL* 1.3 76.8 - - - +
185A LEU* 1.3 56.5 + - - +
187A PHE* 3.6 11.0 - - + +
188A ALA* 3.0 27.9 + - - +
227A LEU* 3.8 24.9 - - + -
241A ILE* 3.9 36.8 - - + +
242A VAL* 3.7 22.0 - - - +
245A GLY* 4.2 9.2 - - - -
246A ILE* 4.1 16.6 - - + +
249A GLN* 5.6 0.2 - - - +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS* 3.6 17.7 - - - +
134A VAL* 3.8 23.3 - - + +
135A GLU* 3.3 27.1 - - - +
181A ASP 2.9 19.0 + - - +
182A PHE 3.8 3.4 - - - +
184A LEU* 1.3 74.7 - - - +
186A ASN* 1.3 64.7 + - - +
188A ALA* 3.2 7.9 + - + +
189A GLU* 3.0 53.6 + - + +
510A EDO 5.7 2.2 - - - +
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Residues in contact with ASN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.0 5.5 - - + +
150A ARG* 3.1 61.8 + - - +
153A LEU* 3.6 14.0 - - + +
154A LEU* 3.8 15.2 - - + +
182A PHE* 3.1 18.1 + - + +
183A VAL* 3.2 4.5 + - - +
185A LEU* 1.3 77.9 - - - +
187A PHE* 1.3 56.4 + - - +
189A GLU* 3.5 1.0 + - - +
190A MET* 2.9 42.0 + - - +
223A ASN* 2.9 22.5 + - - +
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL* 2.7 21.7 + - + +
184A LEU* 3.6 14.4 - - + +
186A ASN* 1.3 73.2 - - - +
188A ALA* 1.3 59.2 + - - +
190A MET* 3.2 1.9 + - - +
191A ASN* 2.8 31.9 + - + +
220A VAL* 3.8 15.3 - - + -
223A ASN* 3.5 23.9 + - + +
224A LEU* 3.6 30.3 - - + -
227A LEU* 5.7 0.7 - - + -
245A GLY 5.3 0.4 - - - -
246A ILE* 3.9 31.2 - - + -
249A GLN* 3.9 30.5 - - + -
250A VAL* 4.9 0.2 - - + -
262A LEU* 3.6 36.1 - - + -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU 3.0 16.2 + - - +
185A LEU* 3.2 9.4 + - + +
187A PHE* 1.3 79.7 - - - +
189A GLU* 1.3 58.7 + - - +
191A ASN* 4.7 0.2 - - - -
192A LYS* 3.3 18.5 + - - +
249A GLN* 3.4 41.7 - - + +
510A EDO 3.0 25.7 + - - +
22C TYR* 3.9 1.2 + - - -
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ARG* 5.0 14.0 - - + +
150A ARG* 3.4 44.9 + - - +
185A LEU* 3.0 40.9 + - + +
186A ASN 3.8 0.7 - - - +
188A ALA* 1.3 78.2 - - - +
190A MET* 1.3 59.9 + - - +
192A LYS* 2.7 37.9 + - - +
193A LEU* 3.1 31.4 + - + +
510A EDO 4.0 15.7 + - - -
244B GLU* 4.6 0.4 - - - +
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Residues in contact with MET 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.2 50.3 - - + +
150A ARG* 3.4 33.2 - - + +
151A ASN* 3.8 7.2 - - + +
154A LEU* 5.2 0.9 - - - -
186A ASN* 2.9 27.8 + - - +
187A PHE 3.8 2.5 - - - +
189A GLU* 1.3 76.3 - - - +
191A ASN* 1.3 57.9 + - - +
193A LEU* 3.5 2.1 + - - -
194A TRP* 2.9 30.5 + - - +
219A LEU* 3.6 29.4 - - + +
220A VAL* 4.1 6.5 - - + -
223A ASN* 3.3 25.6 - - - +
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Residues in contact with ASN 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 2.8 23.9 + - + +
188A ALA* 4.3 0.9 - - - +
190A MET* 1.3 74.1 - - - +
192A LYS* 1.3 60.1 + - - +
194A TRP* 3.4 25.0 - - - -
195A VAL* 3.0 37.8 + - - +
220A VAL* 3.9 11.4 - - + +
249A GLN* 4.1 7.1 + - - +
253A CYS* 3.8 14.3 - - - +
258A ALA* 3.9 3.5 - - - +
262A LEU* 3.4 27.8 - - - +
22C TYR* 2.9 34.4 + - - +
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ARG* 5.9 0.2 - - - +
141A GLN* 4.7 3.5 - - - +
188A ALA 3.3 16.0 + - - +
189A GLU* 2.7 31.4 + - - +
191A ASN* 1.3 78.6 - - - +
193A LEU* 1.3 61.2 + - - +
195A VAL* 3.8 1.4 - - - +
196A ARG* 2.9 49.2 + - - +
510A EDO 4.0 9.8 + - - +
244B GLU* 2.9 38.5 + - - -
16C GLN* 3.3 21.6 + - - +
21C ALA* 3.2 32.8 - - + +
22C TYR* 3.7 13.2 - - + -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL 4.4 5.6 - - - +
141A GLN* 3.6 34.8 - - - +
143A PRO* 3.5 28.6 - - + +
146A GLY* 3.5 38.4 - - - +
147A LEU* 3.5 11.0 - - + +
150A ARG* 4.3 13.0 - - - +
189A GLU* 3.1 21.2 + - + +
190A MET 3.7 4.3 - - - +
191A ASN 3.4 0.2 - - - -
192A LYS* 1.3 79.3 - - - +
194A TRP* 1.3 62.9 + - - +
196A ARG* 3.3 17.4 + - - +
197A MET* 3.1 18.5 + - - +
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Residues in contact with TRP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.1 20.4 - - + +
190A MET 2.9 18.9 + - - +
191A ASN* 3.4 20.4 - - - +
193A LEU* 1.3 78.1 - - - +
195A VAL* 1.3 58.6 + - - +
197A MET* 3.4 12.4 - - - +
213A ARG* 2.9 76.4 + - + +
216A LEU* 4.4 5.8 - - + -
217A ARG* 3.5 25.0 - - + +
220A VAL* 3.6 25.1 - - + -
257A LEU* 4.4 13.5 - - + -
258A ALA* 3.7 32.3 - - + -
261A TYR* 3.9 32.5 - + + -
262A LEU* 4.6 1.3 - - + -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASN* 3.0 26.6 + - - +
192A LYS 4.0 0.4 - - - +
194A TRP* 1.3 73.5 - - - +
196A ARG* 1.3 65.0 + - - +
197A MET 3.2 0.4 - - - -
198A GLN* 3.1 21.1 + - - +
199A HIS* 4.1 7.0 + - + -
213A ARG* 3.8 9.4 - - - +
253A CYS* 4.2 4.7 - - + +
255A ASP* 4.0 24.0 - - + +
258A ALA* 3.9 27.8 - - + -
22C TYR* 3.9 41.3 - - + +
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Residues in contact with ARG 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLN* 3.1 33.8 + - - -
143A PRO* 4.4 17.0 - - + -
192A LYS* 2.9 42.7 + - - +
193A LEU* 3.3 14.2 + - - +
195A VAL* 1.3 77.4 - - - +
197A MET* 1.3 56.0 + - - +
199A HIS* 2.9 29.8 + - - +
200A GLN* 3.6 8.9 + - + +
239B ALA* 3.9 17.3 + - - -
241B VAL* 3.5 37.9 - - - +
244B GLU* 3.8 2.8 + - - -
21C ALA 3.5 23.6 + - - +
22C TYR 5.7 2.2 - - - -
25C PRO* 4.7 15.5 - - + -
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Residues in contact with MET 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PRO* 5.3 5.4 - - + -
143A PRO* 3.4 19.4 - - + +
144A LEU* 3.9 33.2 - - + +
147A LEU* 4.6 2.2 - - + -
193A LEU 3.1 12.5 + - - +
194A TRP* 3.4 19.5 - - - +
196A ARG* 1.3 72.1 - - - +
198A GLN* 1.3 61.3 + - - +
199A HIS 3.2 0.6 + - - -
200A GLN* 3.7 30.4 + - - +
209A ARG* 3.0 22.2 - - - +
212A GLU* 5.2 4.9 - - + +
213A ARG* 3.9 23.8 - - + -
216A LEU* 3.3 35.4 - - + -
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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
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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