Contacts of the helix formed by residues 185 - 212 (chain A) in PDB entry 4Y5U
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 GLU 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.7 25.8 + - - +
182A LEU* 2.9 47.6 - - - +
183A LEU* 3.8 1.8 - - - -
184A GLN* 1.3 58.3 + - - +
186A THR* 1.3 65.7 + - - +
187A THR* 3.0 5.4 + - - -
188A GLY* 3.2 6.5 + - - +
189A GLU* 3.0 26.9 + - - +
260A ARG* 4.9 3.4 - - - +
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.7 7.5 - - + +
140A ARG* 3.3 38.0 + - + +
141A VAL* 3.9 25.1 - - + +
144A ILE* 5.2 3.1 - - + -
183A LEU* 2.9 21.4 + - - +
184A GLN* 2.9 8.1 - - + +
185A GLU* 1.3 75.5 - - - +
187A THR* 1.3 56.8 + - + +
189A GLU* 3.1 8.5 - - - +
190A LEU* 2.9 24.8 + - - +
238A LEU* 3.8 24.5 - - + -
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLN* 2.9 33.9 - - + +
186A THR* 1.3 75.4 - - + +
188A GLY* 1.3 59.6 + - - +
189A GLU 3.2 0.9 - - - -
190A LEU* 3.5 10.0 + - - +
191A GLU* 3.1 28.4 + - - +
238A LEU* 3.9 20.9 - - + -
257A LEU* 4.6 10.1 - - + -
260A ARG* 2.3 36.3 + - - +
261A LEU* 4.2 19.2 - - + +
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU* 3.2 10.4 + - - +
187A THR* 1.3 80.8 + - - +
189A GLU* 1.3 57.4 + - - +
191A GLU* 3.2 17.7 + - - +
192A ALA* 3.0 27.9 + - - +
260A ARG* 4.0 8.2 - - - +
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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
----------------------------------------------------------
136A ARG* 4.8 14.9 + - - -
137A LEU* 4.1 22.6 + - + +
140A ARG* 3.4 44.5 + - - -
185A GLU* 3.0 13.2 + - + +
186A THR* 3.1 14.5 - - - +
188A GLY* 1.3 75.8 - - - +
190A LEU* 1.3 58.4 + - - +
192A ALA* 3.9 7.2 + - - +
193A ALA* 3.4 20.3 + - - +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 4.1 9.8 - - + +
186A THR 2.9 12.3 + - - +
187A THR* 3.5 8.5 - - - +
188A GLY 3.2 0.2 - - - -
189A GLU* 1.3 75.4 - - - +
191A GLU* 1.3 64.9 + - - +
192A ALA 3.1 0.4 - - - -
193A ALA* 3.3 3.8 + - - +
194A LYS* 3.1 19.4 + - - +
231A LEU* 3.7 40.6 - - + +
234A ILE* 4.1 10.8 - - + -
235A TYR* 4.2 13.7 - - - -
238A LEU* 4.1 13.0 - - + -
261A LEU* 3.6 29.6 - - + -
264A VAL* 3.9 21.3 - - + -
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A THR 3.1 20.0 + - - +
188A GLY* 3.2 9.8 + - - +
190A LEU* 1.3 75.9 - - - +
192A ALA* 1.3 57.4 + - - +
194A LYS* 3.2 12.8 + - - +
195A ALA* 3.1 23.4 + - - +
260A ARG* 3.3 51.0 + - - +
261A LEU* 6.1 0.7 - - + -
264A VAL* 3.7 24.9 - - + -
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLY 3.0 15.5 + - - +
189A GLU* 3.9 8.7 - - - +
191A GLU* 1.3 75.1 - - - +
193A ALA* 1.3 64.0 + - - +
195A ALA* 3.3 8.8 + - - +
196A LEU* 3.1 26.8 + - - +
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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
----------------------------------------------------------
133A GLY 6.3 0.9 - - - -
134A LEU* 6.0 2.0 - - + +
137A LEU* 4.3 9.0 - - + -
189A GLU 3.4 11.9 + - - +
190A LEU 3.3 9.5 + - - +
192A ALA* 1.3 79.7 - - - +
194A LYS* 1.3 61.1 + - - +
196A LEU* 3.3 12.3 + - - +
197A VAL* 3.2 26.5 + - - +
231A LEU* 4.0 24.7 - - + -
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU 3.1 12.1 + - - +
191A GLU* 3.2 20.1 + - - +
193A ALA* 1.3 75.7 - - - +
195A ALA* 1.3 73.5 + - - +
197A VAL* 3.4 3.1 + - - +
198A LEU* 3.2 42.8 + - + +
231A LEU* 4.0 11.6 - - + +
264A VAL* 4.2 31.9 - - + +
267A THR* 3.1 31.6 + - - +
268A LEU* 4.1 19.5 - - + +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU 3.1 12.9 + - - +
192A ALA* 3.5 11.9 - - - +
194A LYS* 1.3 85.0 - - - +
196A LEU* 1.3 66.3 + - + +
198A LEU* 3.5 7.3 + - - +
199A LYS* 3.2 24.1 + - - +
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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
----------------------------------------------------------
130A PHE* 4.7 22.4 - - - +
192A ALA 3.1 15.7 + - - +
193A ALA* 3.4 14.6 - - - +
194A LYS 3.2 0.2 - - - -
195A ALA* 1.3 82.3 - - + +
197A VAL* 1.3 58.4 + - + +
199A LYS* 3.3 24.2 - - + +
200A ARG* 3.1 26.0 + - - +
227A ARG* 4.8 3.9 + - - +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA 3.2 16.3 + - - +
194A LYS* 3.4 6.5 + - - +
196A LEU* 1.3 73.5 - - + +
198A LEU* 1.3 59.6 + - - +
199A LYS 3.2 0.2 - - - -
200A ARG* 3.1 7.0 + - - +
201A ILE* 2.9 36.3 + - + +
224A LEU* 4.4 11.0 - - + +
227A ARG* 4.3 31.6 - - + +
228A CYS* 3.8 28.5 - - - -
231A LEU* 4.3 15.0 - - + -
268A LEU* 4.4 7.2 - - + -
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 3.2 48.2 + - + +
195A ALA* 3.7 7.2 - - - +
197A VAL* 1.3 77.3 - - - +
199A LYS* 1.3 56.8 + - - +
201A ILE* 3.8 9.1 + - + +
202A GLN* 3.2 28.2 + - - +
267A THR* 4.5 8.1 - - - +
268A LEU* 4.4 13.0 - - + -
271A SER* 3.5 35.4 - - - +
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Residues in contact with LYS 199 (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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195A ALA 3.2 12.0 + - - +
196A LEU* 3.3 29.7 - - + +
198A LEU* 1.3 79.8 - - - +
200A ARG* 1.3 58.2 + - - +
202A GLN* 3.4 6.3 - - + +
203A ILE* 2.9 46.8 + - + +
435A MET* 5.5 6.5 - - + -
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Residues in contact with ARG 200 (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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196A LEU 3.1 9.2 + - - +
197A VAL 3.1 9.3 + - - +
199A LYS* 1.3 77.9 - - - +
201A ILE* 1.3 64.6 + - - +
202A GLN 3.2 1.1 - - - -
203A ILE* 3.0 39.6 + - - +
204A TRP* 3.1 37.5 + - - +
207A GLN* 4.0 6.3 + - - +
219A GLU* 3.8 18.6 + - - -
220A SER 5.8 0.4 + - - -
224A LEU* 3.7 33.0 - - + +
227A ARG* 3.3 35.4 - - - +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 2.9 41.2 + - + +
198A LEU* 4.0 10.5 - - + +
200A ARG* 1.3 71.2 - - - +
202A GLN* 1.3 62.3 + - - +
204A TRP* 3.2 7.8 + - - +
205A LYS* 3.1 34.8 + - + +
221A LEU* 6.0 0.4 - - + -
224A LEU* 4.3 16.2 - - + -
228A CYS* 4.8 9.9 - - - -
268A LEU* 5.7 1.1 - - + +
271A SER* 3.9 27.8 - - - +
272A CYS* 5.1 0.9 - - - +
274A LEU* 3.7 39.0 - - + -
296A LEU* 4.8 5.8 - - + -
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Residues in contact with GLN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU 3.2 17.6 + - - +
199A LYS* 3.4 10.3 - - + +
201A ILE* 1.3 77.5 - - - +
203A ILE* 1.3 64.8 + - - +
205A LYS* 3.2 29.2 + - - +
206A ARG* 3.3 20.4 + - - +
435A MET* 3.6 49.6 + - + +
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Residues in contact with ILE 203 (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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199A LYS* 2.9 33.6 + - + +
200A ARG* 3.0 30.7 - - - +
201A ILE 3.3 0.2 - - - -
202A GLN* 1.3 77.2 - - - +
204A TRP* 1.3 60.2 + - - +
206A ARG* 3.5 6.4 + - - +
207A GLN* 3.3 32.0 + - + +
435A MET* 3.9 24.7 - - + -
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Residues in contact with TRP 204 (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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200A ARG* 3.1 33.5 + - - +
201A ILE* 3.6 7.2 - - - +
202A GLN 3.2 0.2 - - - -
203A ILE* 1.3 74.5 - - - +
205A LYS* 1.3 73.2 + - + +
207A GLN* 3.3 11.5 + - - +
208A GLN* 3.1 53.0 + - - +
217A PHE* 3.8 17.0 - + - -
219A GLU* 3.5 40.9 + - + +
220A SER 4.2 5.5 + - - -
221A LEU* 3.5 46.1 - - + +
224A LEU* 4.5 10.5 - - + -
274A LEU* 4.6 11.4 - - + -
275A VAL 4.5 7.9 - - - -
276A GLU* 4.5 6.5 - - + -
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 3.1 28.1 + - + +
202A GLN* 3.2 32.7 + - - +
204A TRP* 1.3 89.5 - - + +
206A ARG* 1.3 58.8 + - - +
207A GLN 3.3 0.2 - - - -
208A GLN* 3.5 9.6 + - - +
209A GLN* 3.0 27.8 + - - +
274A LEU* 4.7 13.5 - - + +
408A LEU* 5.3 2.1 - - - +
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Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLN 3.3 10.5 + - - +
203A ILE* 3.6 10.3 - - - +
204A TRP 3.3 0.2 - - - -
205A LYS* 1.3 76.9 - - - +
207A GLN* 1.3 58.9 + - + +
209A GLN* 3.0 26.0 + - - +
210A LEU* 3.1 48.2 + - + +
430A ASN 2.6 28.7 + - - -
431A ALA 3.0 23.2 + - - -
432A PHE* 4.6 0.2 - - - +
433A SER 3.6 26.1 + - - +
434A GLU 5.8 0.2 - - - -
435A MET* 4.0 30.8 - - + +
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Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG* 4.0 7.4 + - - +
203A ILE* 3.3 25.2 + - + +
204A TRP* 3.4 17.3 - - - +
205A LYS 3.3 0.4 - - - -
206A ARG* 1.3 80.2 - - + +
208A GLN* 1.3 59.3 + - - +
210A LEU* 3.4 7.9 + - + +
211A ALA* 3.2 22.3 + - - +
215A ALA* 5.3 0.9 - - - +
217A PHE* 3.6 19.6 + - + +
219A GLU* 3.2 33.6 + - - +
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Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TRP* 3.1 30.8 + - + +
205A LYS* 3.7 10.3 - - - +
207A GLN* 1.3 72.6 - - - +
209A GLN* 1.3 64.7 + - - +
211A ALA* 3.6 3.2 + - - +
212A GLY* 3.6 14.2 + - - -
217A PHE* 3.5 31.4 - - + -
275A VAL 3.2 16.5 + - - +
276A GLU 3.0 28.3 + - - -
278A GLN* 3.3 34.0 + - + +
408A LEU* 4.5 5.4 - - - +
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS 3.0 17.0 + - - +
206A ARG* 3.0 35.0 + - - +
208A GLN* 1.3 77.7 - - - +
210A LEU* 1.3 61.8 + - - +
212A GLY 3.3 8.7 + - - -
408A LEU* 3.9 34.2 - - + +
429A ASP* 3.8 4.6 + - - -
430A ASN* 3.5 40.9 + - - +
433A SER* 3.6 21.6 + - - -
434A GLU 5.6 0.7 - - - +
437A ARG* 3.9 14.6 - - - +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 3.1 50.3 + - + +
207A GLN* 3.4 8.3 + - + +
208A GLN 3.3 0.2 - - - -
209A GLN* 1.3 76.3 - - - +
211A ALA* 1.3 54.3 - - - +
212A GLY 3.1 1.3 - - - -
213A ASN* 3.1 23.5 + - + +
215A ALA* 3.2 26.6 + - + +
430A ASN* 3.6 16.6 - - - +
431A ALA* 4.1 14.1 - - + +
454A THR* 6.1 0.2 - - - +
457A LEU* 5.6 2.8 - - + +
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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
----------------------------------------------------------
207A GLN 3.2 16.7 + - - +
208A GLN 3.6 8.1 - - - +
210A LEU* 1.3 70.0 - - - +
212A GLY* 1.3 58.6 + - - +
213A ASN 3.2 1.6 - - - -
214A GLY* 3.0 16.7 + - - -
215A ALA* 3.6 24.2 - - - +
217A PHE* 3.8 23.6 - - + -
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLN 3.6 6.7 + - - -
209A GLN* 3.3 11.6 + - - -
210A LEU 3.1 0.8 - - - -
211A ALA* 1.3 77.9 - - - +
213A ASN* 1.3 65.3 + - - +
214A GLY 3.5 0.2 - - - -
281A GLN* 4.5 7.7 - - - +
408A LEU* 5.8 0.4 - - - -
426A ILE* 5.7 1.6 - - - +
430A ASN* 3.8 10.6 + - - -
458A LYS* 5.1 5.2 + - - -
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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