Contacts of the helix formed by residues 165 - 187 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C PRO* 4.3 2.0 - - - -
96D VAL 4.9 5.2 - - - +
97D ALA* 6.2 0.7 - - + -
157D ALA* 3.6 19.3 - - - +
160D GLU 4.5 0.5 - - - +
161D GLY* 3.7 0.7 - - - -
162D GLN* 2.9 58.0 + - + +
163D VAL 4.5 1.8 - - - +
164D GLY* 1.3 79.3 - - - +
166D ALA* 1.3 64.1 + - - +
167D ALA 3.4 2.9 + - - -
168D TYR* 3.4 32.8 + - + -
169D SER* 2.9 30.1 + - - +
259D MET* 5.9 0.9 - - - +
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 4.2 14.4 - - + -
178C MET* 3.8 5.7 - - + +
181C PRO* 4.1 14.9 - - + +
182C ILE* 3.8 28.7 - - + -
185C ASP* 4.4 5.8 - - - +
98D ILE 4.9 4.9 + - - +
100D THR* 4.0 11.9 - - - +
109D HIS* 5.3 1.6 - - + -
114D PHE* 4.1 2.1 - - - -
164D GLY 3.6 4.4 + - - +
165D GLN* 1.3 74.1 - - - +
167D ALA* 1.3 62.5 + - - +
170D ALA* 3.0 24.9 + - - +
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Residues in contact with ALA 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D VAL* 4.4 8.5 - - + -
98D ILE 5.7 0.2 + - - -
109D HIS* 4.2 16.2 + - - +
114D PHE* 3.7 34.4 - - + +
117D VAL* 3.8 27.1 - - + +
118D ILE* 4.1 3.4 - - + +
164D GLY 5.3 0.8 + - - -
165D GLN 3.4 0.8 - - - -
166D ALA* 1.3 77.3 - - - +
168D TYR* 1.3 63.4 + - - +
170D ALA* 3.4 3.1 + - - +
171D SER* 3.0 23.9 + - - -
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Residues in contact with TYR 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ILE 3.6 25.6 - - - -
95D ALA* 3.9 19.1 - - + -
96D VAL* 4.8 13.1 + - - +
117D VAL* 3.9 5.9 - - + +
121D ASN* 3.9 5.6 - - - -
155D SER* 3.6 23.3 - - - -
157D ALA* 3.9 9.9 - - + -
165D GLN* 3.4 34.2 + - + +
167D ALA* 1.3 76.5 - - - +
169D SER* 1.3 62.1 + - - +
171D SER* 2.8 22.2 + - - -
172D LYS* 3.0 26.2 + - + +
301D NAD 2.8 49.6 + + - -
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Residues in contact with SER 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C GLY* 3.5 21.7 - - - -
181C PRO* 3.7 9.3 - - - +
157D ALA* 2.8 35.3 + - - +
158D ALA* 4.3 1.9 - - - -
161D GLY* 3.3 16.5 - - - -
165D GLN* 2.9 24.9 + - - +
166D ALA 4.0 0.9 - - - -
168D TYR* 1.3 74.1 - - - +
170D ALA* 1.3 56.3 + - - +
172D LYS* 3.8 1.2 - - - +
173D GLY* 2.9 27.7 + - - -
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 4.2 7.6 - - + +
174C GLY* 3.4 29.1 - - - +
178C MET* 4.0 9.6 - - + +
114D PHE* 3.8 24.5 - - + -
118D ILE* 4.0 7.0 - - + -
122D LEU* 4.8 0.2 - - - +
166D ALA 3.0 19.5 + - - +
167D ALA 3.7 4.0 - - - +
169D SER* 1.3 74.5 - - - +
171D SER* 1.3 64.1 + - - +
174D GLY* 3.1 19.2 + - - -
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Residues in contact with SER 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D VAL* 4.1 6.9 - - - +
118D ILE* 3.8 19.0 - - - +
121D ASN* 3.1 40.5 + - - +
122D LEU* 3.9 12.0 - - - +
167D ALA 3.0 13.7 + - - -
168D TYR* 2.8 17.6 + - - -
170D ALA* 1.3 79.2 - - - +
172D LYS* 1.3 61.6 + - - +
174D GLY* 3.4 2.3 + - - -
175D ILE* 3.4 23.6 + - - +
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ALA 5.4 0.8 + - - -
121D ASN* 3.9 14.8 - - - +
153D THR 3.1 16.0 + - - -
154D ALA* 3.6 21.2 + - - +
155D SER* 3.8 26.7 - - - +
158D ALA* 3.9 11.9 - - + +
168D TYR* 3.0 40.2 + - + +
169D SER* 4.2 2.5 - - - +
171D SER* 1.3 76.2 + - - +
173D GLY* 1.3 64.4 + - - +
174D GLY 3.2 1.1 - - - -
175D ILE* 3.4 17.0 + - + +
176D VAL* 3.2 26.3 + - - +
301D NAD 3.0 42.4 + - - -
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Residues in contact with GLY 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C GLY* 3.3 26.7 - - - +
177C GLY* 4.4 5.8 - - - -
158D ALA* 3.9 14.1 - - - +
169D SER 2.9 18.3 + - - -
170D ALA 4.0 0.2 - - - -
172D LYS* 1.3 77.4 - - - +
174D GLY* 1.3 56.4 + - - +
175D ILE 3.3 0.2 - - - -
176D VAL* 3.7 5.1 - - - +
177D GLY 3.0 22.7 + - - -
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Residues in contact with GLY 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ALA* 3.4 29.4 - - - -
173C GLY 4.2 0.2 - - - -
174C GLY 3.7 2.6 - - - +
122D LEU* 3.6 17.3 - - - -
170D ALA 3.1 12.8 + - - -
171D SER 3.4 4.9 + - - -
172D LYS 3.2 0.6 - - - -
173D GLY* 1.3 73.5 - - - +
175D ILE* 1.3 61.8 + - - +
177D GLY 3.4 0.7 + - - -
178D MET* 3.1 24.3 + - - +
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Residues in contact with ILE 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ASN 3.7 22.9 - - - +
122D LEU* 4.0 11.7 - - + -
125D THR* 4.6 10.5 - - + +
152D ASN* 3.9 30.7 - - + +
153D THR 3.8 19.5 - - - +
154D ALA* 4.3 4.0 - - + -
171D SER 3.4 15.3 + - - +
172D LYS* 3.4 23.2 + - + +
173D GLY 3.3 0.8 - - - -
174D GLY* 1.3 73.7 - - - +
176D VAL* 1.3 63.4 + - - +
178D MET* 3.4 18.1 + - + +
179D THR* 2.9 26.0 + - - +
195D THR* 4.1 13.9 - - + +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ALA 5.1 3.3 - - - +
154D ALA* 4.0 15.0 - - + -
158D ALA* 4.0 17.5 - - + -
159D PHE* 4.2 26.5 - - + -
172D LYS 3.2 14.7 + - - +
173D GLY* 3.7 9.9 - - - +
175D ILE* 1.3 77.8 - - - +
177D GLY* 1.3 63.6 + - - +
179D THR* 3.3 18.6 + - - -
180D LEU 4.6 1.4 + - - -
195D THR* 4.9 0.9 - - + -
250D VAL* 4.2 23.5 - - + +
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Residues in contact with GLY 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ALA 4.3 3.8 - - - +
158C ALA 3.7 21.0 - - - +
159C PHE 6.0 0.3 - - - -
161C GLY 5.2 0.5 + - - -
169C SER* 3.4 30.4 - - - -
173C GLY* 4.4 3.4 - - - -
173D GLY 3.0 15.3 + - - -
174D GLY 3.8 3.8 - - - -
176D VAL* 1.3 79.2 - - - +
178D MET* 1.3 58.7 + - - +
179D THR 3.7 0.2 + - - -
180D LEU* 4.5 0.7 + - - +
181D PRO* 3.5 9.7 - - - +
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Residues in contact with MET 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 4.0 25.1 - - - -
166C ALA 3.8 17.7 - - - +
169C SER* 4.4 0.9 - - - -
170C ALA* 4.1 8.5 - - + +
122D LEU* 4.2 16.4 - - + -
125D THR* 4.0 26.5 - - + -
126D PHE* 4.2 16.2 - - + +
129D ILE* 4.2 15.3 - - + -
152D ASN* 5.7 1.8 - - - +
174D GLY 3.1 14.9 + - - +
175D ILE* 3.7 13.9 - - + +
176D VAL 3.3 0.2 - - - -
177D GLY* 1.3 75.8 - - - +
179D THR* 1.3 64.4 + - - +
180D LEU 3.5 1.1 - - - -
181D PRO* 3.4 8.5 - - + +
182D ILE* 3.2 42.2 + - + +
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Residues in contact with THR 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ASN* 4.4 3.4 + - - +
175D ILE 2.9 18.4 + - - -
176D VAL* 3.3 12.9 + - - -
178D MET* 1.3 77.1 - - - +
180D LEU* 1.3 63.9 + - - +
182D ILE* 3.9 2.1 - - - +
183D ALA* 3.1 22.4 + - - +
193D VAL* 4.0 26.8 - - + +
195D THR* 2.8 33.0 + - - +
248D GLY 4.0 10.3 - - - +
249D GLU 4.0 21.1 - - - +
250D VAL* 4.7 3.4 - - + -
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ALA* 3.9 31.6 - - + +
258B ARG* 3.7 45.8 - - + +
159C PHE 4.0 19.1 - - - +
160C GLU* 4.1 7.4 - - - -
161C GLY 4.3 2.0 - - - +
176D VAL 4.6 1.2 + - - -
177D GLY 4.5 1.2 + - - +
179D THR* 1.3 79.4 - - - +
181D PRO* 1.3 70.9 - - + +
183D ALA* 3.2 4.6 + - - +
184D ARG* 2.9 49.4 + - + +
248D GLY* 4.1 13.4 + - - +
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Residues in contact with PRO 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLY* 3.6 22.0 - - - +
162C GLN 3.5 21.9 - - - +
165C GLN 4.3 0.9 - - - -
166C ALA* 4.2 16.4 - - - +
169C SER* 3.8 16.6 - - - +
177D GLY 3.5 19.5 - - - +
178D MET* 3.4 17.3 - - - +
180D LEU* 1.3 94.2 - - + +
182D ILE* 1.3 55.7 + - - +
184D ARG* 3.5 4.4 + - + +
185D ASP* 2.9 34.1 + - - +
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C THR* 3.7 16.8 - - - +
166C ALA* 3.8 10.3 - - + -
126D PHE* 4.0 20.2 - - + -
129D ILE* 4.1 27.6 - - + -
152D ASN* 6.3 0.2 - - - +
178D MET* 3.2 47.8 + - + +
179D THR* 4.0 2.9 - - - +
181D PRO* 1.3 73.3 - - - +
183D ALA* 1.3 63.4 + - - +
185D ASP* 3.2 6.0 + - - +
186D LEU* 3.0 36.2 + - + +
193D VAL* 3.9 22.4 - - + -
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Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PRO* 5.3 1.0 - - - +
256B ALA* 4.6 7.0 - - + -
179D THR 3.1 14.8 + - - +
180D LEU* 3.6 7.4 - - + +
182D ILE* 1.3 75.7 - - - +
184D ARG* 1.3 60.9 + - - +
186D LEU* 3.4 2.1 + - - +
187D ALA* 3.1 24.8 + - - +
191D ILE 4.7 3.8 - - - +
193D VAL* 4.0 15.6 - - + +
247D ASN* 3.5 30.3 + - - +
248D GLY* 3.9 15.9 - - - -
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Residues in contact with ARG 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B PRO* 4.8 13.4 - - + +
256B ALA* 4.9 3.2 + - + -
258B ARG* 3.9 26.5 + - - +
160C GLU* 3.4 16.4 + - - +
161C GLY 2.8 37.8 + - - -
162C GLN* 3.9 2.0 - - - +
163C VAL* 3.8 23.7 - - + +
259C MET 3.0 24.0 + - - -
260C GLN* 3.8 10.1 + - - +
261C PRO* 3.4 40.1 - - + +
180D LEU* 2.9 39.3 + - + +
181D PRO* 3.8 4.5 - - + +
183D ALA* 1.3 75.4 - - + +
185D ASP* 1.3 62.6 + - - +
187D ALA* 3.5 15.9 + - - +
188D PRO* 3.8 4.5 - - - +
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Residues in contact with ASP 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ILE 4.7 0.2 - - - +
99C LYS* 3.8 13.1 - - + +
100C THR* 2.7 48.1 + - - +
101C TYR 4.6 7.9 - - - +
163C VAL* 3.4 13.1 - - - +
164C GLY* 2.9 28.3 + - - -
166C ALA* 4.4 8.0 + - - +
181D PRO 2.9 21.0 + - - +
182D ILE* 3.5 8.4 - - - +
184D ARG* 1.3 75.8 - - - +
186D LEU* 1.3 63.0 + - + +
188D PRO* 3.4 16.1 - - - +
189D ILE* 5.6 0.5 - - - +
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Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C THR* 4.4 13.5 - - + -
101C TYR* 4.3 18.6 - - + +
129D ILE* 5.0 0.7 - - + -
133D ALA* 4.2 23.1 - - + -
150D ILE* 4.3 10.5 - - + -
182D ILE* 3.0 34.4 + - + +
183D ALA 3.4 1.5 + - - +
185D ASP* 1.3 79.9 - - + +
187D ALA* 1.3 64.4 + - - +
188D PRO* 3.4 1.8 - - - -
189D ILE* 3.1 27.9 + - + +
190D GLY 3.4 7.8 + - - -
191D ILE* 3.5 45.7 + - + +
193D VAL* 4.1 6.5 - - + -
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Residues in contact with ALA 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PRO* 3.5 37.7 - - + +
223B PHE* 3.9 20.2 - - + +
183D ALA 3.1 15.2 + - - +
184D ARG 3.7 7.0 - - - +
185D ASP 3.4 0.2 - - - -
186D LEU* 1.3 76.5 - - - +
188D PRO* 1.3 69.0 - - + +
190D GLY* 3.1 13.9 + - - +
191D ILE 5.0 2.0 - - - -
247D 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