Contacts of the helix formed by residues 170 - 194 (chain K) in PDB entry 5XVO
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 ASN 170 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K PHE* 3.9 17.0 - - - -
168K GLN* 3.1 23.7 + - - +
169K GLU* 1.3 77.2 - - - +
171K ASP* 1.3 63.1 + - - +
172K ILE* 2.9 12.9 + - - +
173K ASN* 2.6 40.5 + - - +
174K ALA* 3.1 21.7 + - - +
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Residues in contact with ASP 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170K ASN* 1.3 77.8 - - - +
172K ILE* 1.3 63.8 + - + +
174K ALA* 3.7 5.9 - - - +
175K GLY 3.0 17.0 + - - -
233K ARG 5.9 0.4 - - - +
235K GLU 4.1 3.7 - - - +
236K ALA* 4.0 8.1 - - - +
237K PHE* 3.6 30.6 + - - +
240K MET* 3.1 28.7 - - + +
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Residues in contact with ILE 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K PHE* 3.7 50.0 - - + -
164K PHE* 4.0 17.9 - - + -
170K ASN* 2.9 11.4 + - + +
171K ASP* 1.3 79.3 - - + +
173K ASN* 1.3 59.2 + - - +
176K LEU* 2.9 18.9 + - + +
229K ILE* 2.7 32.7 - - + +
233K ARG* 4.0 31.4 - - + +
240K MET* 4.0 5.2 - - + -
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Residues in contact with ASN 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K PHE* 3.2 21.3 - - - -
165K THR 3.1 21.8 + - - -
166K ARG* 2.7 40.9 + - - +
168K GLN 2.6 28.8 + - - +
169K GLU* 5.1 3.6 - - + -
170K ASN* 2.6 21.7 + - - +
172K ILE* 1.3 69.7 - - - +
174K ALA* 1.3 56.5 + - - +
176K LEU* 3.1 3.0 + - - +
177K ASN* 2.7 47.2 + - - +
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Residues in contact with ALA 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K GLU* 6.0 0.8 - - - +
170K ASN 3.1 17.5 + - - +
171K ASP* 3.7 9.0 - - - +
173K ASN* 1.3 76.8 - - - +
175K GLY* 1.3 56.6 + - - +
177K ASN* 3.7 8.9 - - - +
178K TYR* 2.9 30.3 + - - +
237K PHE* 3.6 24.0 - - + -
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Residues in contact with GLY 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K ASP 3.0 13.2 + - - -
174K ALA* 1.3 73.1 - - - +
176K LEU* 1.3 64.7 + - - +
178K TYR* 3.5 1.5 + - - -
179K GLY* 3.0 18.9 + - - -
225K VAL* 4.4 1.0 - - - +
229K ILE* 3.5 19.5 - - - -
237K PHE* 3.7 12.7 - - - -
240K MET* 4.1 9.9 - - - -
244K LEU* 3.4 14.7 - - - +
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Residues in contact with LEU 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156K PHE* 3.8 23.8 - - + -
160K PHE* 4.6 3.4 - - + -
164K PHE* 4.5 2.5 - - + -
166K ARG* 4.0 16.8 - - - +
172K ILE* 2.9 28.8 + - + +
173K ASN* 3.5 23.8 - - - +
175K GLY* 1.3 75.0 - - - +
177K ASN* 1.3 54.3 - - - +
179K GLY* 3.2 1.4 + - - -
180K TYR* 2.8 49.1 + - + +
225K VAL* 3.9 5.7 - - + +
226K ASP* 3.2 29.8 - - - +
229K ILE* 3.2 26.6 - - + +
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Residues in contact with ASN 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K ARG* 2.7 34.9 + - - +
169K GLU* 5.9 4.6 + - - +
173K ASN* 2.7 38.5 + - - +
174K ALA* 3.7 8.0 - - - +
176K LEU* 1.3 72.7 - - - +
178K TYR* 1.3 63.6 + - - +
180K TYR* 3.3 5.4 + - - +
181K THR* 2.9 31.6 + - + +
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Residues in contact with TYR 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K LYS* 6.0 1.8 - - - -
174K ALA 2.9 18.5 + - - +
175K GLY* 3.7 5.2 - - - +
177K ASN* 1.3 77.5 - - - +
179K GLY* 1.3 63.4 + - - +
181K THR* 2.7 21.7 + - - -
182K LEU* 3.1 40.4 + - + +
237K PHE* 4.3 11.7 - + + -
241K LYS* 3.4 44.7 + - + +
244K LEU* 3.7 13.0 - - + -
245K PHE* 3.3 24.3 - + - -
25O T 3.0 46.6 + + - -
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Residues in contact with GLY 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175K GLY 3.0 11.1 + - - -
176K LEU 3.7 2.7 - - - -
178K TYR* 1.3 78.9 - - - +
180K TYR* 1.3 62.7 + - - +
182K LEU* 3.1 19.4 + - - +
183K LEU* 3.1 10.0 + - - +
225K VAL* 3.7 26.6 - - - +
244K LEU* 3.7 20.4 - - - -
247K LEU* 5.2 0.4 - - - -
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Residues in contact with TYR 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156K PHE* 3.7 14.1 - + - -
166K ARG* 3.4 35.0 - - - -
176K LEU* 2.8 26.4 + - + +
177K ASN* 3.6 6.1 - - - +
179K GLY* 1.3 76.6 - - - +
181K THR* 1.3 58.1 + - + +
183K LEU* 3.3 4.7 + - + +
184K LEU* 2.8 28.5 + - - +
218K MET* 3.5 13.7 - - + +
222K ARG* 3.5 64.7 + - + +
225K VAL* 4.0 11.9 - - + -
226K ASP* 2.5 33.2 + - - -
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Residues in contact with THR 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K LYS* 5.0 8.7 + - - +
72K LEU* 5.2 0.9 - - - +
177K ASN* 2.9 17.9 + - + +
178K TYR* 2.7 24.9 + - - -
180K TYR* 1.3 74.1 - - + +
182K LEU* 1.3 65.4 + - - +
184K LEU* 3.2 17.4 + - + +
185K SER* 3.0 23.7 + - - -
25O T 3.6 22.6 + - - +
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Residues in contact with LEU 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178K TYR* 3.1 58.3 + - + +
179K GLY* 3.1 6.9 + - - +
181K THR* 1.3 74.6 - - - +
183K LEU* 1.3 61.5 + - - +
185K SER* 2.8 21.0 + - - -
186K ILE* 3.2 13.3 + - + +
244K LEU* 4.2 12.6 - - + +
245K PHE* 4.2 12.1 - - + -
247K LEU* 4.1 20.4 - - + -
248K PHE* 3.5 36.9 - - + -
25O T 3.6 26.5 - - + -
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Residues in contact with LEU 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K GLY 3.1 10.6 + - - +
180K TYR* 3.5 8.1 - - + +
182K LEU* 1.3 75.6 - - - +
184K LEU* 1.3 68.7 + - - +
186K ILE* 3.0 18.9 + - + +
187K PHE* 3.2 25.4 + - + -
218K MET* 3.8 20.0 - - + -
221K PHE* 3.7 40.2 - - + +
222K ARG* 4.1 7.0 - - - +
224K LEU* 5.5 0.9 - - + -
225K VAL* 3.6 23.3 - - + -
247K LEU* 4.8 10.5 - - + -
261K LEU* 3.9 28.0 - - + -
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Residues in contact with LEU 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K LEU* 4.7 11.7 - - + -
180K TYR 2.8 15.1 + - - +
181K THR* 3.2 22.4 + - + +
183K LEU* 1.3 76.3 - - - +
185K SER* 1.3 57.4 + - - +
187K PHE* 3.2 1.0 + - - -
188K ALA* 2.8 30.0 + - - +
209K ASN* 5.2 4.9 - - - +
211K PHE* 4.1 29.8 - - + +
214K ALA* 3.6 26.7 - - + +
215K SER* 3.7 25.1 - - - +
218K MET* 3.8 14.5 - - - -
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Residues in contact with SER 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K ARG 4.0 7.4 - - - +
72K LEU* 3.4 26.5 - - - -
181K THR 3.0 6.9 + - - -
182K LEU 2.8 13.7 + - - -
183K LEU 3.1 0.2 - - - -
184K LEU* 1.3 74.1 - - - +
186K ILE* 1.3 66.1 + - - +
188K ALA* 3.7 0.9 - - - +
189K ARG* 3.1 44.1 + - - +
248K PHE* 5.9 0.2 - - - -
25O T 2.9 31.6 - - - +
26O T 5.4 0.9 + - - +
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Residues in contact with ILE 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182K LEU* 3.5 13.7 - - + +
183K LEU* 3.0 16.9 + - + +
185K SER* 1.3 84.6 + - - +
187K PHE* 1.3 60.1 + - + +
189K ARG* 3.6 27.5 + - - +
190K GLU* 3.2 30.0 + - + +
247K LEU* 6.2 0.7 - - + -
248K PHE* 3.7 29.4 - - + -
261K LEU* 4.1 25.8 - - + -
262K THR* 4.5 14.6 - - + +
265K ALA* 3.5 31.0 - - + -
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Residues in contact with PHE 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K LEU* 3.2 31.5 + - + +
184K LEU 4.0 3.8 - - - +
186K ILE* 1.3 80.5 - - + +
188K ALA* 1.3 67.6 + - - +
189K ARG 3.2 0.4 - - - -
190K GLU* 3.8 3.2 - - - +
191K LEU* 3.0 29.0 + - + +
214K ALA* 4.2 19.1 - - + +
217K LEU* 4.1 15.7 - - + -
218K MET* 3.7 22.9 - - + -
221K PHE* 3.5 44.9 - + + -
261K LEU* 5.8 1.3 - - + -
265K ALA* 3.6 31.6 - - + -
268K TYR* 4.1 9.6 - + - -
269K THR* 3.4 21.1 - - - -
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Residues in contact with ALA 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K LEU* 4.0 6.7 - - + -
73K PRO* 3.8 18.6 - - + -
184K LEU 2.8 18.3 + - - +
185K SER 3.7 4.9 - - - +
187K PHE* 1.3 77.7 - - - +
189K ARG* 1.3 62.0 + - - +
191K LEU* 3.4 1.7 + - - +
192K VAL* 3.2 28.9 + - - +
198K THR* 3.9 5.6 - - + +
211K PHE* 3.8 24.2 - - + -
214K ALA* 3.8 11.3 - - + +
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Residues in contact with ARG 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K LEU* 3.9 26.8 - - + +
43K GLU* 2.7 41.9 + - - -
65K LEU* 5.0 2.1 - - - +
67K CYS* 4.0 8.7 - - - -
71K ARG* 3.1 42.5 + - - +
73K PRO* 4.0 9.6 - - + +
185K SER* 3.1 32.6 + - - +
186K ILE* 3.6 28.7 + - - +
188K ALA* 1.3 83.2 - - - +
190K GLU* 1.3 66.2 + - + +
192K VAL* 3.4 3.2 + - - +
193K GLN* 3.1 27.6 + - - +
262K THR* 4.5 10.9 - - - +
26O T 4.2 10.1 + - - -
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Residues in contact with GLU 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K LEU* 5.7 0.3 - - - +
186K ILE* 3.2 20.9 + - + +
187K PHE* 3.8 3.1 - - - +
188K ALA 3.3 0.4 - - - -
189K ARG* 1.3 81.3 + - - +
191K LEU* 1.3 63.5 + - - +
193K GLN* 3.3 28.0 + - - +
194K THR* 3.1 25.6 + - - +
262K THR* 4.3 5.5 - - - +
265K ALA* 4.0 18.6 - - + +
266K THR* 3.1 41.9 + - - +
269K THR* 3.7 22.4 - - - +
270K LYS* 5.8 0.7 - - - +
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Residues in contact with LEU 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K PHE 3.0 21.0 + - - +
188K ALA 3.8 4.3 - - - +
190K GLU* 1.3 75.3 - - - +
192K VAL* 1.3 65.4 + - - +
194K THR* 2.7 23.5 + - - -
196K CYS* 3.2 19.0 + - + +
198K THR* 4.0 11.2 - - + -
213K LEU* 3.7 32.1 - - + +
214K ALA* 3.6 36.1 - - + +
217K LEU* 3.8 14.6 - - + -
269K THR* 3.8 20.9 - - + -
273K VAL* 4.2 15.7 - - + -
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Residues in contact with VAL 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K LEU* 4.6 6.9 - - - +
65K LEU* 3.4 34.1 - - + -
73K PRO* 3.6 22.7 - - + -
188K ALA 3.2 17.4 + - - +
189K ARG 3.7 3.6 - - - +
191K LEU* 1.3 76.2 - - - +
193K GLN* 1.3 63.3 + - - +
195K GLY* 3.0 13.7 + - - -
196K CYS 3.8 12.6 - - - +
197K PHE* 5.9 0.2 - - - -
198K THR* 4.0 14.8 - - + -
80L PHE* 3.5 25.1 - - + -
81L TYR* 4.5 4.9 - - - +
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Residues in contact with GLN 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K THR* 3.2 31.6 + - - +
7K VAL* 5.5 1.4 - - - +
39K VAL* 4.2 17.1 - - + +
41K LEU* 3.5 26.1 - - + +
63K LEU* 3.9 15.4 - - - +
65K LEU* 3.9 22.2 - - + -
84K HIS* 5.4 1.4 - - - -
86K SER* 4.4 3.1 - - - -
189K ARG* 3.1 13.1 + - - +
190K GLU* 3.3 41.1 + - - +
191K LEU 3.1 0.4 - - - -
192K VAL* 1.3 78.5 - - - +
194K THR* 1.3 60.7 + - + +
195K GLY 3.5 0.2 + - - -
266K THR* 5.4 3.8 - - - +
270K LYS* 6.0 1.4 - - - -
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Residues in contact with THR 194 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K SER* 4.3 7.8 - - - +
89K GLN* 3.4 19.1 - - - +
190K GLU 3.1 17.5 - - - +
191K LEU* 2.7 15.9 + - - -
193K GLN* 1.3 77.7 - - + +
195K GLY* 1.3 56.4 + - - +
196K CYS* 3.4 19.9 - - - -
269K THR* 4.3 15.0 - - + -
270K LYS* 4.4 22.7 - - + -
273K VAL* 4.1 14.5 - - + +
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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