Contacts of the helix formed by residues 187 - 218 (chain A) in PDB entry 1UPX
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 SER 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 5.5 0.7 - - - -
185A SER 3.5 3.5 + - - -
186A LEU* 1.3 75.9 - - - +
188A VAL* 1.3 64.2 - - - +
189A ALA* 3.4 10.2 + - - +
190A ASP* 3.0 33.9 + - - -
191A LEU* 3.0 24.9 + - - +
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP* 4.8 2.2 - - - +
138A ASP* 4.1 28.7 - - + +
139A VAL* 4.2 17.6 - - + +
142A LEU* 3.9 19.5 - - + -
187A SER* 1.3 73.1 - - - +
189A ALA* 1.3 56.7 + - - +
191A LEU* 3.0 6.0 + - - +
192A VAL* 2.8 36.4 + - + +
519A VAL* 6.0 0.4 - - + -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 3.2 9.9 + - - +
188A VAL* 1.3 79.1 - - - +
190A ASP* 1.3 62.6 + - - +
192A VAL* 3.4 8.1 + - - +
193A ALA* 3.0 23.9 + - - +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER 4.5 1.7 - - - +
186A LEU* 3.6 31.8 - - + +
187A SER* 3.0 40.2 + - - +
189A ALA* 1.3 77.7 - - - +
191A LEU* 1.3 58.2 + - - +
193A ALA* 3.4 8.1 + - - +
194A LEU* 2.9 26.2 + - - +
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.9 46.2 - - + +
142A LEU* 3.8 18.8 - - + -
143A ARG* 4.5 15.0 - - + +
146A ILE* 3.5 21.0 - - + +
180A LYS 4.8 5.2 - - - +
181A THR* 5.2 1.8 - - - -
183A ASP 6.1 0.2 - - - +
186A LEU* 4.1 30.1 - - + +
187A SER 3.0 17.1 + - - +
188A VAL* 3.0 6.3 + - - +
190A ASP* 1.3 74.6 - - - +
192A VAL* 1.3 59.9 + - - +
194A LEU* 3.2 8.5 + - + -
195A THR* 2.9 32.7 + - - -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.9 22.0 - - + -
188A VAL* 2.8 27.8 + - + +
189A ALA* 3.8 7.0 - - - +
191A LEU* 1.3 71.5 - - - +
193A ALA* 1.3 66.2 + - - +
195A THR* 3.2 9.7 + - - -
196A LEU* 3.1 34.9 + - + +
519A VAL* 6.0 0.9 - - + -
522A VAL* 4.7 27.1 - - + -
527A PHE* 6.5 1.1 - - + -
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA 3.0 14.3 + - - +
190A ASP* 3.4 12.1 - - - +
192A VAL* 1.3 77.4 - - - +
194A LEU* 1.3 55.4 + - - +
196A LEU* 3.2 10.1 + - - +
197A GLU* 2.9 27.6 + - - +
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.9 23.1 - - + -
173A PHE* 4.0 19.7 - - + -
177A ALA* 4.1 15.7 - - + +
180A LYS* 3.7 44.4 - - + +
181A THR* 4.9 2.2 - - + -
186A LEU* 4.8 2.0 - - + -
190A ASP 2.9 17.8 + - - +
191A LEU* 3.7 13.9 - - + +
192A VAL 3.2 0.4 - - - -
193A ALA* 1.3 73.6 - - - +
195A THR* 1.3 57.0 + - - +
197A GLU* 3.8 21.3 - - - +
198A THR* 2.7 41.2 + - - +
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Residues in contact with THR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.6 15.3 - - + +
145A LEU* 3.7 27.7 - - + +
146A ILE* 3.4 20.5 - - + +
191A LEU 2.9 19.5 + - - -
192A VAL* 3.2 13.4 + - - -
194A LEU* 1.3 76.7 - - - +
196A LEU* 1.3 64.8 + - + +
198A THR* 3.3 6.3 + - - -
199A GLY* 3.1 17.5 + - - -
495A LEU* 3.7 24.3 - - + +
498A LEU* 6.3 0.4 - - + -
523A LEU* 6.1 3.8 - - + -
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 3.1 25.5 + - + +
193A ALA* 3.2 8.9 + - - +
195A THR* 1.3 78.6 - - + +
197A GLU* 1.3 64.9 + - - +
199A GLY* 3.2 4.3 + - - +
200A LYS* 3.0 18.9 + - - +
495A LEU* 5.3 2.2 - - + +
498A LEU* 4.4 24.7 - - + +
499A SER* 3.7 13.6 - - - +
527A PHE* 3.7 35.0 - - + -
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Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 3.5 26.2 - - + -
176A GLU* 5.5 2.2 - - - +
180A LYS* 4.9 7.8 + - - -
193A ALA 2.9 17.0 + - - +
194A LEU* 3.7 16.5 - - - +
195A THR 3.3 0.2 - - - -
196A LEU* 1.3 72.7 - - - +
198A THR* 1.3 66.5 + - - +
200A LYS* 3.1 20.9 + - - +
201A PHE* 3.0 41.3 + - + -
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.8 20.6 - - + +
149A GLY 4.3 7.0 - - - -
150A LEU* 4.1 12.9 - - + +
153A MET* 3.2 25.1 - - + +
173A PHE* 3.7 18.5 - - - -
194A LEU* 2.7 24.7 + - - +
195A THR* 3.3 9.4 - - - -
197A GLU* 1.3 77.2 - - - +
199A GLY* 1.3 55.1 + - - +
201A PHE 3.3 0.7 + - - -
202A GLY 2.8 23.7 + - - -
492A ILE* 3.6 13.6 - - + +
495A LEU* 4.1 11.4 - - + -
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR 3.1 12.1 + - - -
196A LEU 3.2 4.6 + - - -
198A THR* 1.3 75.5 - - - +
200A LYS* 1.3 61.2 + - - +
202A GLY* 3.0 3.0 + - - -
203A VAL 3.0 18.2 + - - -
492A ILE* 4.5 1.3 - - - -
495A LEU* 3.3 36.2 - - - +
496A ALA* 3.4 10.3 - - - -
499A SER* 3.4 7.4 + - - -
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU 3.0 12.2 + - - +
197A GLU* 3.1 23.4 + - - +
199A GLY* 1.3 75.8 - - - +
201A PHE* 1.3 84.0 + - + +
203A VAL* 3.2 10.1 + - + +
204A SER* 3.1 22.7 + - - +
499A SER* 3.5 13.1 + - - +
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Residues in contact with PHE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A MET* 3.7 15.4 - - + +
169A SER* 3.7 30.7 - - - -
170A LEU* 4.3 12.2 - - + +
173A PHE* 3.4 52.9 - + + -
197A GLU* 3.0 42.0 + - + +
200A LYS* 1.3 88.9 - - + +
202A GLY* 1.3 59.5 + - - +
203A VAL 3.3 0.2 - - - -
204A SER* 3.4 16.1 - - - -
205A ALA* 2.8 29.6 + - - +
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Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A MET* 3.6 2.4 - - - +
156A TYR* 5.2 0.3 - - - -
198A THR 2.8 10.5 + - - -
199A GLY 3.0 6.4 + - - -
201A PHE* 1.3 74.7 - - - +
203A VAL* 1.3 64.1 + - - +
205A ALA* 3.3 5.6 + - - +
206A MET* 2.9 35.1 + - - +
492A ILE* 3.6 30.0 - - - +
496A ALA* 4.7 0.9 - - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLY 3.0 13.6 + - - +
200A LYS* 3.2 8.7 + - + +
202A GLY* 1.3 74.8 - - - +
204A SER* 1.3 59.5 + - - +
206A MET* 3.2 9.4 + - + +
207A ALA* 2.8 29.1 + - + +
456A TYR* 4.1 19.8 - - + -
496A ALA* 3.7 20.3 - - + +
499A SER* 3.8 12.1 - - - +
500A LEU* 4.0 27.1 - - + -
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 4.6 13.9 - - - +
170A LEU* 4.7 5.6 - - - -
200A LYS* 3.1 15.7 + - - +
201A PHE* 3.4 25.8 - - - -
203A VAL* 1.3 77.2 - - - +
205A ALA* 1.3 57.2 + - - +
207A ALA* 3.3 6.9 + - - +
208A LEU* 2.9 29.7 + - - +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A MET* 3.8 33.2 - - + +
156A TYR* 4.3 13.6 - - + +
157A ALA* 4.5 2.4 - - - +
170A LEU* 3.7 20.6 - - + +
201A PHE 2.8 16.3 + - - +
202A GLY* 3.7 4.5 - - - +
204A SER* 1.3 76.0 - - - +
206A MET* 1.3 58.8 + - - +
208A LEU* 3.3 3.4 + - - +
209A LEU* 3.0 28.9 + - - +
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Residues in contact with MET 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 3.5 32.8 - - + -
202A GLY* 2.9 23.6 + - - +
203A VAL* 3.7 5.4 - - + +
205A ALA* 1.3 76.7 - - - +
207A ALA* 1.3 57.9 + - - +
209A LEU* 3.8 5.4 - - - +
210A ASP* 2.8 30.5 + - - +
453A ASN* 3.5 24.4 - - - +
455A SER* 4.6 2.0 - - - -
456A TYR* 3.8 29.2 - - + +
492A ILE* 4.6 2.0 - - + +
493A VAL* 4.1 23.1 - - + +
496A ALA* 3.7 27.6 - - + -
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 2.8 22.5 + - + +
204A SER* 3.6 8.1 - - - +
206A MET* 1.3 73.2 - - - +
208A LEU* 1.3 58.2 + - - +
210A ASP* 3.4 2.4 + - - +
211A ALA* 3.0 29.1 + - - +
456A TYR* 3.5 34.4 - - + +
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ALA* 5.4 3.1 - - + +
160A ALA* 3.9 20.6 - - + -
165A LYS* 3.9 33.5 - - + +
166A HIS* 4.0 11.9 - - - +
167A GLU* 3.8 33.9 - - + +
170A LEU* 4.1 21.3 - - + -
204A SER 2.9 16.6 + - - +
205A ALA 3.6 5.2 - - - +
207A ALA* 1.3 78.9 - - - +
209A LEU* 1.3 56.9 + - - +
211A ALA* 3.3 6.7 + - + +
212A ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 3.8 31.2 - - + +
159A HIS* 3.6 32.3 - - + +
160A ALA* 3.7 14.8 - - - +
163A LEU* 4.8 0.2 - - + -
205A ALA 3.0 16.3 + - - +
206A MET* 3.9 4.7 - - - +
208A LEU* 1.3 73.4 - - - +
210A ASP* 1.3 60.6 + - - +
212A ALA* 3.1 3.0 + - + -
213A ASN* 2.8 53.4 + - - +
453A ASN* 3.7 36.3 - - + +
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Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A MET 2.8 18.3 + - - +
207A ALA 3.6 5.1 - - - +
208A LEU 3.3 0.2 - - - -
209A LEU* 1.3 75.9 - - - +
211A ALA* 1.3 59.7 + - - +
213A ASN* 3.5 4.7 + - - +
214A THR* 2.9 48.0 + - - +
370A ALA* 5.7 1.0 - - - +
371A HIS* 2.8 40.4 + - - -
453A ASN* 5.9 0.7 - - - +
454A ASP* 4.4 12.8 - - - +
456A TYR* 3.7 22.7 - - + +
457A SER* 4.0 5.0 + - - -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 3.8 19.8 - - + +
207A ALA 3.0 17.2 + - - +
208A LEU* 3.6 7.9 - - + +
209A LEU 3.2 0.2 - - - -
210A ASP* 1.3 78.4 + - - +
212A ALA* 1.3 57.0 + - - +
214A THR* 3.9 5.6 - - - -
215A GLY* 2.8 28.9 + - - -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ALA* 4.0 13.5 - - - -
163A LEU* 3.9 28.6 - - + +
165A LYS* 3.7 23.0 - - + +
208A LEU 2.9 17.9 + - - +
209A LEU* 3.1 4.2 + - - +
211A ALA* 1.3 77.6 - - - +
213A ASN* 1.3 60.5 + - - +
216A THR* 2.7 32.9 + - - -
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Residues in contact with ASN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.2 21.3 - - - +
209A LEU* 2.8 44.6 + - - +
210A ASP* 4.0 5.2 - - - +
212A ALA* 1.3 73.9 - - - +
214A THR* 1.3 58.8 + - + +
217A TYR* 2.9 36.1 + - - +
242A LEU* 3.4 21.5 + - + +
271A TYR* 3.4 25.5 + - + +
451A GLN* 4.2 6.3 + - - -
453A ASN* 3.8 15.2 - - - +
454A ASP* 5.3 1.6 + - - -
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Residues in contact with THR 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 2.9 37.8 + - - +
211A ALA* 3.7 5.5 + - - -
213A ASN* 1.3 75.8 - - + +
215A GLY* 1.3 63.3 + - - +
218A GLY* 2.9 34.9 + - - -
219A HIS* 3.6 42.1 + - + -
220A PRO* 3.8 19.7 - - + -
271A TYR* 4.4 3.8 - - + +
371A HIS* 5.1 0.4 - - + +
----------------------------------------------------------
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Residues in contact with GLY 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 5.7 2.9 - - - -
211A ALA 2.8 20.2 + - - -
212A ALA 4.0 0.2 - - - -
214A THR* 1.3 79.8 + - - +
216A THR* 1.3 59.9 + - - +
218A GLY 4.9 0.3 + - - -
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Residues in contact with THR 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.0 21.8 + - + +
212A ALA* 2.7 22.7 + - - -
215A GLY* 1.3 80.1 - - - +
217A TYR* 1.3 99.3 + - + +
218A GLY 3.7 0.6 + - - -
246A GLU* 4.8 2.9 - - - +
273A ALA* 4.7 3.1 - - - +
----------------------------------------------------------
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Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.7 19.6 - - + +
213A ASN 2.9 17.7 + - - +
216A THR* 1.3 97.2 - - + +
218A GLY* 1.3 59.9 + - - +
242A LEU* 3.7 30.5 - - + -
243A ARG* 3.3 19.9 - - - -
246A GLU* 2.7 38.8 + - + +
271A TYR* 3.6 18.9 - - + +
272A PRO* 3.4 8.3 - - - +
273A ALA* 3.1 41.7 + - + -
274A PHE* 3.5 29.8 - + + -
----------------------------------------------------------
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Residues in contact with GLY 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A THR* 2.9 26.0 + - - -
215A GLY 4.7 0.4 + - - -
216A THR 3.7 1.2 - - - -
217A TYR* 1.3 78.0 - - - +
219A HIS* 1.3 61.6 + - - -
271A TYR* 3.0 24.3 - - - -
272A PRO* 3.9 10.1 - - - -
----------------------------------------------------------
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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