Contacts of the helix formed by residues 169 - 194 (chain A) in PDB entry 5E9W
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 ILE 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER 4.5 0.4 - - - +
168A ARG* 1.3 86.3 - - + +
170A PHE* 1.3 65.5 + - - +
171A TYR 3.2 3.1 - - - -
172A LEU* 3.0 17.3 + - + +
173A ARG* 2.9 50.0 + - + +
340A ILE* 4.1 27.6 - - + +
362A LEU* 4.3 22.0 - - + +
363A GLU* 4.0 27.4 - - + +
460A GLU* 5.6 0.9 - - - -
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER* 3.3 33.9 + - - +
169A ILE* 1.3 77.0 - - - +
171A TYR* 1.3 97.9 + + - +
173A ARG* 3.5 30.7 + - + +
174A ASN* 2.9 41.2 + - + +
415A MET 4.6 0.7 - - - -
416A GLN* 4.1 21.5 - - + -
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER 4.7 11.2 - - - -
168A ARG 5.5 0.6 + - - -
169A ILE 3.2 0.8 - - - -
170A PHE* 1.3 101.6 - + - +
172A LEU* 1.3 57.5 + - - +
174A ASN* 3.4 4.4 - - - +
175A PHE* 2.9 29.1 + - - +
416A GLN* 3.5 28.0 - - + -
455A THR 5.2 5.6 - - - +
456A LEU* 3.8 10.2 - - + +
460A GLU* 4.1 26.4 + - - +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 3.0 20.5 + - + +
171A TYR* 1.3 76.0 - - - +
173A ARG* 1.3 59.6 + - + +
175A PHE* 3.3 6.4 + - + +
176A ASN* 3.0 42.5 + - - +
340A ILE* 3.9 21.8 - - + -
362A LEU* 4.3 17.0 - - + -
456A LEU* 4.5 8.9 - - + +
460A GLU* 3.8 23.5 + - + +
463A ALA* 3.9 21.3 - - + -
464A THR* 3.8 32.1 - - - +
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER 5.0 6.7 - - - +
169A ILE* 2.9 42.7 + - + +
170A PHE* 3.8 35.0 - - - +
172A LEU* 1.3 74.2 - - + +
174A ASN* 1.3 65.9 + - - +
176A ASN* 3.2 12.1 + - - +
177A ASN* 3.0 31.2 + - - +
362A LEU* 6.2 0.9 - - + -
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PHE* 2.9 29.7 + - + +
171A TYR* 3.4 10.1 - - - +
172A LEU 3.2 0.2 - - - -
173A ARG* 1.3 77.2 - - - +
175A PHE* 1.3 58.2 - - - +
177A ASN* 3.2 10.2 + - - +
178A TRP* 2.9 25.5 + - - +
412A LEU* 4.7 4.3 - - - +
415A MET* 2.4 52.8 + - - +
416A GLN* 3.1 25.4 + - - +
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Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR 2.9 14.5 + - - +
172A LEU 3.4 5.6 - - - +
174A ASN* 1.3 79.4 - - - +
176A ASN* 1.3 64.0 + - - +
178A TRP* 3.0 17.5 + + - +
179A MET* 2.8 63.6 + - + +
395A PHE* 4.3 3.8 - + + -
399A TYR* 3.7 27.8 - + + -
412A LEU* 4.5 11.7 - - + -
455A THR* 4.7 6.1 - - + -
456A LEU* 3.8 24.0 - - + -
461A TRP* 3.8 27.4 - + - -
464A THR* 3.6 30.7 - - + -
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Residues in contact with ASN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 3.0 29.0 + - - +
173A ARG* 3.6 12.3 - - - +
175A PHE* 1.3 74.3 - - - +
177A ASN* 1.3 57.7 + - - +
179A MET* 3.2 8.3 + - - +
180A LYS* 2.9 36.6 + - - +
285A PHE* 4.0 32.3 - - + -
362A LEU* 6.2 2.6 - - - +
395A PHE* 3.9 7.3 - - - -
464A THR* 3.7 19.6 + - - -
467A TYR* 5.7 4.5 - - - -
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Residues in contact with ASN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 3.0 20.2 + - - +
174A ASN* 3.3 12.1 - - - +
176A ASN* 1.3 76.5 - - - +
178A TRP* 1.3 57.6 + - - +
180A LYS* 3.4 16.2 + - - +
181A SER* 2.8 34.0 + - - -
210A GLY* 4.1 5.0 - - - +
214A LYS* 2.9 29.7 + - - -
415A MET* 3.8 13.2 - - + -
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Residues in contact with TRP 178 (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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174A ASN 2.9 12.9 + - - +
175A PHE* 3.0 15.2 + + - +
177A ASN* 1.3 75.0 - - - +
179A MET* 1.3 89.2 + - + +
181A SER* 3.2 2.6 + - - -
182A VAL* 3.1 36.8 + - + +
398A PHE* 5.8 0.4 - + - -
399A TYR* 3.8 26.2 - + - -
402A LYS* 4.0 18.6 - - + -
403A ILE* 3.9 24.7 - - + -
408A ASN* 2.8 44.5 + - + -
411A LEU* 3.9 9.5 - - + +
412A LEU* 3.3 41.6 - - + +
415A MET* 3.7 19.3 - - - +
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Residues in contact with MET 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PHE* 2.8 52.0 + - + +
176A ASN* 3.4 8.1 - - - +
178A TRP* 1.3 93.8 - - + +
180A LYS* 1.3 64.4 + - + +
182A VAL* 3.4 1.1 + - - -
183A LEU* 3.0 24.3 + - - +
317A THR* 6.0 1.6 - - + -
395A PHE* 3.4 63.3 - - + +
398A PHE* 3.5 36.7 - - + -
399A TYR* 4.5 2.0 - - - -
469A VAL* 4.1 2.5 - - + -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASN* 2.9 20.5 + - - +
177A ASN* 3.7 23.0 + - - +
179A MET* 1.3 76.7 - - + +
181A SER* 1.3 56.8 + - - +
183A LEU* 3.3 7.0 + - - +
184A ILE* 2.8 42.0 + - + +
210A GLY* 4.7 2.2 - - - -
211A ASP* 2.7 31.9 + - - +
214A LYS* 4.0 8.5 - - + -
284A GLN* 3.6 33.9 - - + +
285A PHE* 3.9 18.6 - - + -
317A THR* 5.1 3.1 - - + +
500A SAH 2.6 32.1 + - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASN 2.8 22.5 + - - -
178A TRP* 3.2 9.5 + - - -
180A LYS* 1.3 76.1 - - - +
182A VAL* 1.3 56.9 + - - +
184A ILE* 3.8 3.0 - - - +
185A GLY* 2.8 26.5 + - - -
214A LYS* 3.2 27.0 - - - +
411A LEU* 4.5 18.2 - - - -
415A MET* 4.7 7.3 - - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TRP* 3.1 41.1 + - + +
179A MET* 4.0 2.9 - - - +
181A SER* 1.3 73.4 - - - +
183A LEU* 1.3 61.8 + - - +
185A GLY* 3.7 1.3 - - - -
186A GLU* 2.9 28.1 + - - +
398A PHE* 4.4 4.5 - - + -
402A LYS* 3.5 33.0 - - + +
408A ASN* 3.4 43.5 - - - +
411A LEU* 4.6 5.2 - - + -
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A MET 3.0 17.3 + - - +
180A LYS* 3.6 5.2 - - - +
182A VAL* 1.3 74.2 - - - +
184A ILE* 1.3 66.0 + - - +
186A GLU* 3.2 10.9 + - - +
187A PHE* 3.3 52.2 + - + +
284A GLN* 3.9 31.6 - - - +
315A ILE* 4.2 11.7 - - + -
316A GLY 4.1 21.3 - - - +
317A THR* 4.6 7.2 - - + -
391A TYR* 3.8 13.0 - - + +
398A PHE* 4.1 17.8 - - + -
469A VAL* 4.7 7.6 - - + -
470A PHE 4.6 5.8 - - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 2.8 26.1 + - + +
181A SER* 3.9 3.8 - - - +
183A LEU* 1.3 73.5 - - - +
185A GLY* 1.3 63.0 + - - +
187A PHE* 3.4 0.9 + - - +
188A LEU* 3.0 34.5 + - + +
211A ASP* 4.3 11.9 - - - +
214A LYS* 4.1 32.1 - - + +
215A TRP* 3.4 56.5 - - + +
280A ILE* 5.2 0.5 - - - +
282A SER* 4.4 5.2 - - - +
284A GLN* 4.8 5.2 - - - +
315A ILE* 4.4 16.4 - - + -
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Residues in contact with GLY 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A SER 2.8 19.7 + - - -
182A VAL* 3.7 2.7 - - - -
183A LEU 3.1 0.2 - - - -
184A ILE* 1.3 79.6 - - - +
186A GLU* 1.3 61.3 + - - +
188A LEU* 3.6 6.4 + - - +
189A GLU* 3.4 21.0 + - - +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL 2.9 17.1 + - - +
183A LEU* 3.2 5.3 + - - +
185A GLY* 1.3 76.9 - - - +
187A PHE* 1.3 63.1 + - + +
189A GLU* 3.4 9.6 + - - +
190A LYS* 2.3 60.3 + - + +
391A TYR* 2.7 35.9 + - - -
398A PHE* 4.3 1.7 - - - -
401A GLU* 5.2 0.8 - - - +
402A LYS* 3.0 31.0 + - - +
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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
----------------------------------------------------------
183A LEU* 3.3 35.4 + - + +
184A ILE 4.4 0.9 - - - +
186A GLU* 1.3 80.2 - - + +
188A LEU* 1.3 60.8 + - - +
189A GLU 3.2 1.1 - - - -
190A LYS* 3.7 22.7 - - + +
191A VAL* 2.9 33.4 + - - +
280A ILE* 3.9 14.8 - - + -
313A TYR* 3.7 37.6 - + + -
315A ILE* 3.9 16.8 - - + -
390A VAL* 4.2 6.5 - - + -
391A TYR* 3.1 38.6 - + - -
471A ALA* 3.3 29.2 - - + -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 3.0 28.0 + - + +
185A GLY* 3.9 7.0 - - - +
187A PHE* 1.3 77.5 - - - +
189A GLU* 1.3 58.7 + - - +
191A VAL* 3.5 3.3 + - + +
192A ARG* 3.0 46.9 + - - +
199A ILE* 3.9 19.5 - - + -
214A LYS 4.9 0.7 - - - +
215A TRP* 3.8 25.6 - - + -
218A GLY* 3.6 30.7 - - - +
220A ILE* 3.7 21.3 - - + -
280A ILE* 4.0 11.8 - - + +
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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
----------------------------------------------------------
185A GLY 3.4 10.4 + - - +
186A GLU* 3.6 11.8 - - - +
187A PHE 3.2 0.6 - - - -
188A LEU* 1.3 78.4 - - - +
190A LYS* 1.3 60.6 + - + +
192A ARG* 3.2 7.8 + - + +
193A GLN* 2.8 53.9 + - - +
231C VAL* 5.2 10.8 - - + +
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Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU* 2.3 49.3 + - + +
187A PHE* 3.7 31.6 - - + +
189A GLU* 1.3 77.5 - - + +
191A VAL* 1.3 64.6 + - - +
193A GLN* 3.3 16.3 + - - +
194A LYS* 3.3 20.2 + - - +
313A TYR* 3.9 27.6 - - + +
390A VAL* 4.8 6.3 - - + +
391A TYR* 4.4 4.2 - - - -
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE 2.9 21.3 + - - +
188A LEU* 3.7 6.1 - - - +
190A LYS* 1.3 75.2 - - - +
192A ARG* 1.3 63.4 + - - +
194A LYS* 3.3 17.2 + - - +
196A LYS* 3.4 24.2 + - + +
199A ILE* 3.5 29.4 - - + -
279A ASP* 3.9 20.9 - - + +
280A ILE* 3.7 25.6 - - + -
311A GLY 5.3 2.0 - - - +
312A GLY* 5.4 0.4 - - - -
313A TYR* 3.8 18.8 - - + -
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.0 36.3 + - - +
189A GLU* 3.2 8.2 + - - +
191A VAL* 1.3 77.9 - - - +
193A GLN* 1.3 56.1 + - - +
195A LYS* 3.0 19.8 + - - -
196A LYS 3.7 18.9 + - - +
197A ARG 4.6 7.1 + - - -
199A ILE* 4.0 22.6 - - + +
218A GLY* 2.5 32.1 + - - -
219A ARG* 3.0 52.1 + - - +
230C ASP* 3.7 8.3 - - - +
231C VAL* 4.1 18.8 - - + +
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 2.8 45.2 + - - +
190A LYS* 3.3 8.5 + - - +
192A ARG* 1.3 68.6 - - - +
194A LYS* 1.3 58.7 + - + +
195A LYS 3.0 4.9 - - - -
208C LYS* 6.2 0.4 - - - +
228C ILE 3.3 12.0 - - - +
229C ALA* 3.4 34.2 - - + +
230C ASP* 2.9 31.5 + - - +
231C VAL* 3.4 29.1 - - + +
232C SER* 4.0 9.3 + - - -
259C THR* 4.6 0.3 - - - +
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LYS 3.3 12.9 + - - +
191A VAL* 3.6 9.9 - - - +
192A ARG 3.2 0.6 - - - -
193A GLN* 1.3 77.6 - - - +
195A LYS* 1.3 67.7 + - - +
196A LYS* 3.4 6.9 + - + +
311A GLY* 2.8 30.9 + - - +
313A TYR* 3.0 21.4 + - + -
473A GLU* 2.3 32.5 + - - -
228C ILE 5.2 1.1 - - - -
259C THR* 5.5 1.8 - - - -
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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