Contacts of the helix formed by residues 165 - 187 (chain C) in PDB entry 1E3S
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 GLN 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL 5.0 5.2 - - - +
97C ALA* 6.1 1.1 - - + -
157C ALA* 3.7 13.6 - - - +
160C GLU 4.5 0.5 - - - +
161C GLY* 3.6 6.2 - - - -
162C GLN* 2.9 57.0 + - + +
163C VAL 4.5 1.8 - - - +
164C GLY* 1.3 79.6 - - - +
166C ALA* 1.3 63.6 + - - +
167C ALA 3.3 2.9 + - - -
168C TYR* 3.4 31.9 + - + -
169C SER* 2.8 31.8 + - - +
259C MET* 6.0 0.5 - - - +
181D PRO* 4.3 2.7 - - - -
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE 4.9 5.1 + - - +
100C THR* 3.9 12.6 - - - +
109C HIS* 5.4 1.8 - - + -
114C PHE* 4.0 2.8 - - - -
164C GLY 3.5 4.2 + - - +
165C GLN* 1.3 76.4 - - - +
167C ALA* 1.3 62.3 + - - +
170C ALA* 3.2 24.6 + - - +
126D PHE* 4.2 14.6 - - + -
178D MET* 3.8 5.9 - - + +
181D PRO* 4.2 14.7 - - + +
182D ILE* 3.8 28.7 - - + -
185D ASP* 4.4 5.4 + - - +
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL* 4.5 8.0 - - + +
109C HIS* 4.2 14.4 + - - +
114C PHE* 3.6 41.8 - - + +
117C VAL* 3.9 21.1 - - + +
118C ILE* 4.1 2.6 - - - +
164C GLY 5.2 1.0 + - - -
165C GLN 3.3 1.0 - - - -
166C ALA* 1.3 75.5 - - - +
168C TYR* 1.3 67.5 + - - +
170C ALA* 3.6 2.8 - - - +
171C SER* 3.1 22.3 + - - -
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Residues in contact with TYR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE 3.5 26.9 - - - -
95C ALA* 3.8 20.0 - - + -
96C VAL* 4.8 13.9 + - - +
117C VAL* 4.0 6.8 - - + +
121C ASN* 3.8 6.3 - - - -
155C SER* 3.7 22.9 - - - -
157C ALA* 3.9 10.1 - - + -
165C GLN* 3.4 33.9 + - + +
167C ALA* 1.3 77.9 - - - +
169C SER* 1.3 60.6 + - - +
171C SER* 2.8 23.0 + - - -
172C LYS* 3.0 26.3 + - + +
301C NAD 2.8 51.2 + + - -
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ALA* 2.7 36.6 + - - +
158C ALA* 4.4 1.4 - - - -
161C GLY* 3.3 16.5 - - - -
165C GLN* 2.8 24.9 + - - +
166C ALA 4.1 1.3 - - - -
168C TYR* 1.3 69.7 - - - +
170C ALA* 1.3 59.7 + - - +
172C LYS* 3.8 1.6 - - - +
173C GLY* 2.9 28.6 + - - -
177D GLY* 3.4 22.9 - - - -
181D PRO* 3.8 8.5 - - - -
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Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 3.9 23.1 - - + -
118C ILE* 4.0 7.6 - - + -
122C LEU* 4.8 0.2 - - - +
166C ALA 3.2 17.6 + - - +
167C ALA 3.6 4.3 - - - +
169C SER* 1.3 77.1 - - - +
171C SER* 1.3 63.7 + - - +
174C GLY* 3.0 19.6 + - - -
122D LEU* 4.3 7.5 - - + +
174D GLY* 3.4 28.6 - - - +
178D MET* 4.1 8.7 - - - +
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C VAL* 4.1 7.2 - - - -
118C ILE* 3.8 17.4 - - - +
121C ASN* 3.1 41.4 + - - +
122C LEU* 3.9 11.5 - - - +
167C ALA 3.1 13.5 + - - -
168C TYR* 2.8 18.4 + - - -
170C ALA* 1.3 78.6 - - - +
172C LYS* 1.3 62.6 + - - +
174C GLY* 3.4 2.3 + - - -
175C ILE* 3.3 23.8 + - - +
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Residues in contact with LYS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ALA 5.4 0.8 + - - -
93C GLY* 5.4 0.2 - - - -
121C ASN* 3.8 14.4 + - - +
153C THR 3.0 21.0 + - - -
154C ALA* 3.6 18.3 + - - +
155C SER* 3.8 27.6 - - - +
158C ALA* 3.9 11.9 - - + +
168C TYR* 3.0 38.8 + - + +
169C SER* 4.2 2.2 - - - +
171C SER* 1.3 81.9 + - - +
173C GLY* 1.3 60.3 + - - +
175C ILE* 3.3 17.5 + - + +
176C VAL* 3.1 29.6 + - - +
301C NAD 3.0 39.0 + - - -
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Residues in contact with GLY 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ALA* 3.9 14.3 - - - +
169C SER 2.9 17.4 + - - -
170C ALA 4.0 0.4 - - - -
172C LYS* 1.3 76.0 - - - +
174C GLY* 1.3 58.7 + - - +
176C VAL* 3.7 4.6 - - - +
177C GLY 3.0 22.9 + - - -
173D GLY* 3.3 26.4 - - - +
177D GLY* 4.4 5.2 - - - -
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Residues in contact with GLY 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 3.6 15.7 - - - -
170C ALA 3.0 14.8 + - - -
171C SER 3.4 4.7 + - - -
172C LYS 3.2 0.2 - - - -
173C GLY* 1.3 75.5 - - - +
175C ILE* 1.3 64.2 + - - +
177C GLY 3.5 0.5 + - - -
178C MET* 3.1 24.9 + - - +
170D ALA* 3.4 29.9 - - - -
174D GLY 3.7 1.2 - - - +
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Residues in contact with ILE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ASN 3.6 22.7 - - - +
122C LEU* 4.1 11.2 - - + -
125C THR* 4.5 8.7 - - + +
152C ASN* 3.9 30.3 - - + +
153C THR 3.8 20.2 - - - +
154C ALA* 4.4 4.0 - - + -
171C SER 3.3 15.7 + - - +
172C LYS* 3.3 23.1 + - + +
174C GLY* 1.3 75.5 - - - +
176C VAL* 1.3 62.2 + - - +
178C MET* 3.3 20.2 + - + +
179C THR* 3.0 23.8 + - - +
195C THR* 4.2 13.5 - - + +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ALA* 4.1 14.1 - - + -
158C ALA* 3.9 17.9 - - + -
159C PHE* 4.1 26.5 - - + -
172C LYS 3.1 14.6 + - - +
173C GLY* 3.7 9.6 - - - +
174C GLY 3.4 0.2 - - - -
175C ILE* 1.3 76.8 - - - +
177C GLY* 1.3 64.0 + - - +
179C THR* 3.2 23.4 + - - -
180C LEU 4.6 1.0 + - - -
195C THR* 5.1 0.4 - - - -
250C VAL* 4.3 24.3 - - + +
158D ALA 5.4 3.4 - - - +
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Residues in contact with GLY 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLY 3.0 16.5 + - - -
174C GLY 3.9 1.6 - - - -
175C ILE 3.4 0.2 - - - -
176C VAL* 1.3 77.0 - - - +
178C MET* 1.3 58.7 + - - +
180C LEU* 4.5 0.7 + - - +
181C PRO* 3.5 9.9 - - - +
157D ALA 4.1 3.8 - - - +
158D ALA 3.6 21.7 - - - +
159D PHE 6.0 0.3 - - - -
161D GLY 5.2 0.2 + - - -
169D SER* 3.5 29.5 - - - -
173D GLY* 4.4 3.4 - - - -
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Residues in contact with MET 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 4.0 17.7 - - + -
125C THR* 4.0 27.1 - - + -
126C PHE* 4.2 15.3 - - + +
129C ILE* 4.4 10.3 - - + -
152C ASN* 5.8 2.0 - - - +
174C GLY 3.1 14.4 + - - +
175C ILE* 3.6 15.0 - - + +
176C VAL 3.3 0.4 - - - -
177C GLY* 1.3 75.8 - - - +
179C THR* 1.3 64.5 + - - +
180C LEU 3.4 0.9 - - - -
181C PRO* 3.4 7.7 - - + +
182C ILE* 3.2 45.2 + - + +
114D PHE* 4.0 26.2 - - - -
166D ALA 3.8 17.9 - - - +
169D SER* 4.4 1.1 - - - -
170D ALA* 4.0 8.0 - - + +
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASN* 4.4 3.3 + - - +
175C ILE 3.0 17.4 + - - -
176C VAL* 3.2 13.7 + - - -
178C MET* 1.3 77.1 - - - +
180C LEU* 1.3 58.9 + - - +
182C ILE* 4.0 2.0 - - - +
183C ALA* 3.1 26.9 + - - +
193C VAL* 4.1 19.3 - - + +
194C VAL* 4.7 0.2 - - - -
195C THR* 2.7 32.0 + - - +
248C GLY* 3.9 18.6 - - - +
249C GLU 3.9 21.1 - - - +
250C VAL* 4.5 4.0 - - + -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ALA* 3.8 36.1 - - + +
258A ARG* 3.8 38.6 - - + +
176C VAL 4.6 1.2 + - - -
177C GLY 4.5 1.2 + - - +
179C THR* 1.3 77.4 - - - +
181C PRO* 1.3 71.2 - - + +
183C ALA* 3.2 4.9 + - + +
184C ARG* 2.9 55.2 + - + +
248C GLY* 4.3 10.1 - - - +
159D PHE 4.1 7.0 - - - +
160D GLU* 4.0 19.5 - - - -
161D GLY 4.3 2.0 - - - +
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Residues in contact with PRO 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C GLY 3.5 14.8 - - - +
178C MET* 3.4 14.1 - - - +
180C LEU* 1.3 95.2 - - + +
182C ILE* 1.3 54.5 + - - +
184C ARG* 3.7 4.0 - - + +
185C ASP* 2.8 36.8 + - - +
161D GLY* 3.6 21.5 - - - +
162D GLN 3.5 21.2 - - - +
165D GLN 4.3 0.9 - - - +
166D ALA* 4.1 17.0 - - - +
169D SER* 3.7 22.4 - - - +
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Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 4.0 18.4 - - + -
129C ILE* 4.0 26.0 - - + -
178C MET* 3.2 48.2 + - + +
179C THR* 4.1 2.5 - - - +
181C PRO* 1.3 73.4 - - - +
183C ALA* 1.3 64.3 + - - +
185C ASP* 3.2 4.6 + - - +
186C LEU* 3.0 36.4 + - + +
193C VAL* 4.0 22.2 - - + -
100D THR* 3.6 19.3 - - - +
166D ALA* 3.8 11.7 - - + -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PRO* 5.3 0.7 - - - +
256A ALA* 4.5 7.2 - - + -
179C THR 3.1 15.8 + - - +
180C LEU 3.2 7.2 + - - +
182C ILE* 1.3 77.2 - - - +
184C ARG* 1.3 58.5 + - - +
186C LEU 3.5 1.0 + - - -
187C ALA* 3.2 23.7 + - - +
191C ILE 4.7 4.1 - - - +
193C VAL* 4.0 15.1 - - + +
247C ASN* 3.6 30.2 + - - +
248C GLY* 3.9 16.4 - - - -
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Residues in contact with ARG 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PRO* 4.8 12.8 - - + -
256A ALA* 4.9 3.0 + - + -
258A ARG* 3.8 27.3 + - - +
180C LEU* 2.9 37.2 + - + +
181C PRO* 3.8 4.5 - - + +
183C ALA* 1.3 72.8 - - - +
185C ASP* 1.3 67.0 + - - +
186C LEU 3.4 0.2 + - - -
187C ALA* 3.5 17.3 + - - +
188C PRO* 3.8 4.3 - - - +
160D GLU* 3.3 17.2 + - - +
161D GLY 2.9 36.7 + - - -
162D GLN* 4.5 2.2 - - - +
163D VAL* 3.9 22.1 - - + +
259D MET 3.0 24.0 + - - -
260D GLN* 3.8 9.9 + - - +
261D PRO* 3.3 41.2 - - + +
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Residues in contact with ASP 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C PRO* 2.8 20.1 + - - +
182C ILE* 3.2 6.4 + - - +
184C ARG* 1.3 77.7 - - - +
186C LEU* 1.3 63.3 + - + +
188C PRO* 3.4 15.9 - - - +
98D ILE 4.7 0.2 - - - +
99D LYS* 3.7 14.6 - - + +
100D THR* 2.8 46.9 + - - +
101D TYR 4.5 7.4 - - - +
163D VAL* 3.4 17.7 - - - +
164D GLY 2.9 29.9 + - - -
166D ALA* 4.4 7.6 - - - +
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ILE* 5.0 0.9 - - + -
133C ALA* 4.3 20.0 - - + -
150C ILE* 4.3 6.5 - - + -
182C ILE* 3.0 32.8 + - + +
183C ALA 3.8 1.1 - - - +
185C ASP* 1.3 78.8 - - + +
187C ALA* 1.3 64.5 + - - +
188C PRO* 3.4 2.2 - - - -
189C ILE* 3.2 25.6 + - + +
190C GLY 3.3 8.7 + - - -
191C ILE* 3.5 43.8 + - + +
193C VAL* 4.1 7.4 - - + -
100D THR* 4.3 14.4 - - + -
101D TYR* 4.2 28.3 - - + +
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PRO* 3.5 37.2 - - + +
223A PHE* 3.9 20.7 - - + -
183C ALA 3.2 12.3 + - - +
184C ARG 3.7 9.9 - - - +
185C ASP 3.3 0.4 - - - -
186C LEU* 1.3 75.2 - - - +
188C PRO* 1.3 71.4 - - + +
190C GLY* 3.0 14.8 + - - +
191C ILE 5.0 2.0 - - - -
247C ASN* 5.8 0.7 - - - +
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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