Contacts of the helix formed by residues 263 - 286 (chain M) in PDB entry 1JH0
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 263 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H GLU* 4.9 0.7 - - - +
37H ARG* 4.7 8.8 - - - -
62H LYS* 3.2 27.5 + - - +
64H PHE* 3.6 18.2 - - - -
194L VAL* 5.9 2.5 - - + -
195L LEU* 4.0 11.4 - - + +
198L ALA* 4.3 6.3 - - + +
199L ASN* 2.7 31.6 + - - +
238M ILE* 3.0 24.3 - - + +
261M THR* 3.1 3.9 + - - +
262M MET* 1.3 77.5 - - - +
264M GLY* 1.3 64.3 + - - +
266M HIS* 3.3 19.6 + - - +
267M ARG* 3.6 17.8 + - - +
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Residues in contact with GLY 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H GLU 5.0 3.8 - - - -
35H ASN* 3.1 24.9 + - - -
261M THR* 2.9 13.6 + - - -
263M GLU* 1.3 73.5 - - - +
265M ILE* 1.3 56.9 + - - +
266M HIS 2.9 2.2 - - - -
267M ARG* 2.6 40.7 + - - +
268M TRP* 3.1 12.1 + - - -
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Residues in contact with ILE 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ASN* 3.5 3.8 + - - -
215M LEU* 4.2 11.7 - - + -
219M HIS* 3.9 15.3 - - + +
260M ALA* 4.2 4.5 - - + -
261M THR 3.2 16.9 + - - +
262M MET 3.5 3.4 - - - +
264M GLY* 1.3 72.8 - - - +
266M HIS* 1.3 79.4 + - + +
268M TRP* 3.3 11.2 - - + +
269M ALA* 2.9 25.3 + - + +
857M U10 3.4 89.7 - - + -
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Residues in contact with HIS 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L HIS* 2.7 25.3 + + - -
191L GLY* 4.0 6.5 - - - +
194L VAL* 3.4 27.2 - - + +
195L LEU* 3.8 19.4 - - + +
219M HIS* 3.5 7.1 + + - -
234M GLU* 2.8 22.4 + - - -
262M MET 3.1 25.0 + - - -
263M GLU 3.5 8.5 + - - +
264M GLY 2.8 1.0 + - - -
265M ILE* 1.3 79.9 - - + +
267M ARG* 1.3 57.5 + - - +
268M TRP 3.1 1.3 - - - -
269M ALA* 3.5 5.9 - - + +
270M ILE* 2.7 36.2 + - - +
856M FE 2.3 31.2 - - - -
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Residues in contact with ARG 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 3.3 26.3 + - + -
31H LEU* 3.4 15.2 - - + +
34H GLU* 3.7 37.6 + - + -
35H ASN* 5.8 0.2 - - - +
62H LYS* 3.8 7.1 - - - +
195L LEU* 3.8 25.1 - - + +
199L ASN* 3.6 31.7 + - - +
145M HIS* 5.4 6.3 + - - -
263M GLU* 3.7 15.7 + - - +
264M GLY* 2.6 24.6 + - - +
266M HIS* 1.3 72.5 - - - +
268M TRP* 1.3 55.6 + - - +
270M ILE* 2.9 26.9 - - + +
271M TRP* 3.2 17.3 - - + +
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Residues in contact with TRP 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ILE* 5.1 21.1 - - + -
31H LEU* 3.4 41.7 - - + -
32H GLN* 4.1 20.2 - - + -
35H ASN* 2.9 33.2 - - - +
215M LEU* 3.9 13.0 - - + -
258M PHE* 4.5 8.3 - + - -
260M ALA* 4.4 0.9 - - + -
264M GLY 3.1 16.0 + - - -
265M ILE* 3.3 18.2 - - + +
267M ARG* 1.3 75.9 - - - +
269M ALA* 1.3 67.3 + - - +
271M TRP* 3.1 3.1 + - - +
272M MET* 2.9 31.9 + - + +
857M U10 3.7 54.4 - - + +
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Residues in contact with ALA 269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L LEU* 3.7 41.3 - - + +
190L HIS* 5.7 2.2 - - + -
191L GLY* 4.6 6.1 - - - +
215M LEU* 3.6 14.8 - - + +
219M HIS* 5.7 4.7 - - + -
265M ILE* 2.9 16.1 + - + +
266M HIS* 3.2 14.6 + - + +
268M TRP* 1.3 77.8 - - - +
270M ILE* 1.3 63.4 + - - +
271M TRP 3.3 0.2 + - - -
273M ALA* 3.5 16.6 + - - +
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Residues in contact with ILE 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L ALA* 2.9 32.4 - - - +
191L GLY* 4.4 2.4 - - - -
192L ALA* 3.1 33.9 - - + +
195L LEU* 4.1 13.7 - - + -
145M HIS* 5.4 5.2 - - + -
149M ALA* 4.1 13.7 - - + -
266M HIS 2.7 18.2 + - - +
267M ARG* 2.9 24.0 - - - +
269M ALA* 1.3 72.9 - - - +
271M TRP* 1.3 78.8 + - + +
273M ALA* 4.4 1.6 - - - +
274M VAL* 3.2 33.1 + - + +
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Residues in contact with TRP 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H PHE* 4.3 24.2 - + - -
27H LEU* 3.8 44.5 - - + +
30H TYR* 4.6 12.6 - + - -
31H LEU* 4.2 13.0 - - + -
267M ARG* 3.2 24.8 - - - +
268M TRP 3.1 2.7 + - - +
270M ILE* 1.3 89.7 - - + +
272M MET* 1.3 69.5 + - - +
273M ALA 2.9 3.1 + - - -
274M VAL* 2.9 34.3 + - + -
275M LEU* 2.9 29.8 + - + +
278M LEU* 5.0 3.8 - - + -
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Residues in contact with MET 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L LEU* 4.3 0.7 - - + -
853L BCL 5.2 6.3 - - + -
208M PHE* 3.4 46.7 - - + +
211M GLY* 3.7 29.4 - - - +
212M SER* 3.4 25.7 + - - +
215M LEU* 3.8 17.7 - - + -
268M TRP* 2.9 26.5 + - + +
269M ALA 3.9 2.2 - - - +
271M TRP* 1.3 74.0 - - - +
273M ALA* 1.3 60.1 + - - +
275M LEU* 3.8 8.1 + - - +
857M U10 3.7 30.3 - - + -
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Residues in contact with ALA 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L ALA* 3.7 25.4 - - - +
187L LEU* 4.2 4.9 - - + -
188L ALA* 3.9 19.7 - - + +
212M SER* 3.3 16.8 - - - +
269M ALA 3.5 9.9 + - - +
271M TRP 2.9 1.0 + - - -
272M MET* 1.3 77.0 - - - +
274M VAL* 1.3 66.5 + - - +
275M LEU 3.1 2.0 - - - -
276M VAL* 2.9 18.2 + - - +
854M BPH 3.1 15.8 - - + +
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Residues in contact with VAL 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L ALA* 5.2 2.5 - - + -
148M TRP 6.1 0.2 - - - +
149M ALA* 3.8 38.8 - - + +
152M SER* 2.6 33.0 + - - +
270M ILE* 3.2 24.5 + - + +
271M TRP* 2.9 32.2 + - + +
273M ALA* 1.3 74.9 - - - +
275M LEU* 1.3 63.9 + - - +
276M VAL 3.3 0.5 + - - -
277M THR* 3.5 1.7 + - - -
278M LEU* 3.2 14.3 + - + +
854M BPH 3.9 8.0 - - + +
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Residues in contact with LEU 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H PHE* 4.3 9.2 - - + -
23H PHE* 4.1 16.8 - - + -
24H LEU* 4.3 8.1 - - + -
27H LEU* 3.9 22.2 - - + -
208M PHE* 3.5 41.3 - - + -
271M TRP* 2.9 32.5 + - + +
272M MET* 4.0 1.8 - - - +
274M VAL* 1.3 73.5 - - - +
276M VAL* 1.3 66.0 + - - +
278M LEU* 3.3 32.1 - - + -
279M THR* 2.9 26.7 + - - +
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Residues in contact with VAL 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L ALA* 5.2 2.9 - - + -
205M SER* 2.9 31.7 + - - +
208M PHE* 3.3 31.4 - - + +
209M LEU* 3.3 29.4 - - + +
212M SER* 4.0 6.1 - - - +
272M MET 3.8 3.1 - - - +
273M ALA* 2.9 18.6 + - - +
275M LEU* 1.3 81.4 - - - +
277M THR* 1.3 62.1 + - + +
280M GLY* 3.1 8.5 + - - -
852M BCL 3.7 31.9 - - + +
854M BPH 4.7 5.4 - - + -
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Residues in contact with THR 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152M SER* 2.8 43.1 + - - +
153M ALA* 3.6 5.3 + - - -
155M TRP* 3.2 12.5 - - - -
156M LEU* 4.0 28.2 - - + +
273M ALA 4.1 0.2 + - - -
274M VAL 3.5 1.8 + - - -
276M VAL* 1.3 83.3 - - + +
278M LEU* 1.3 60.5 + - - +
280M GLY* 4.3 1.8 - - - +
281M GLY* 3.1 20.1 + - - +
852M BCL 4.2 11.0 - - + +
854M BPH 3.6 32.3 - - + +
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Residues in contact with LEU 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H PHE* 4.6 9.6 - - + -
23H PHE* 4.7 11.0 - - + -
152M SER* 4.2 8.1 - - - +
155M TRP* 3.2 29.3 + - + +
271M TRP* 5.0 3.6 - - + -
274M VAL* 3.2 25.7 + - + +
275M LEU* 3.1 34.2 + - + +
277M THR* 1.3 75.7 - - - +
279M THR* 1.3 66.9 + - - +
281M GLY 3.2 8.7 + - - -
282M ILE* 3.4 14.2 + - + +
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Residues in contact with THR 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H PHE* 3.4 40.4 - - + -
201M PHE* 3.5 29.5 - - + +
204M LEU* 4.4 4.5 - - + -
205M SER* 3.3 23.0 - - - -
208M PHE* 3.5 13.9 - - + -
275M LEU* 2.9 21.9 + - + +
278M LEU* 1.3 76.6 - - + +
280M GLY* 1.3 73.0 + - - +
281M GLY 3.2 0.5 + - - -
282M ILE* 3.2 5.6 + - - +
283M GLY 3.0 19.6 + - - -
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Residues in contact with GLY 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M LEU* 4.1 0.9 - - - -
205M SER* 3.5 11.4 - - - -
276M VAL 3.1 9.6 + - - -
277M THR* 4.3 1.1 - - - -
278M LEU 3.2 0.2 - - - -
279M THR* 1.3 85.0 + - - +
281M GLY* 1.3 61.8 + - - +
284M ILE* 3.2 11.8 + - - +
852M BCL 3.1 49.9 - - - +
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Residues in contact with GLY 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M TRP* 3.4 26.0 - - - -
156M LEU* 3.9 17.2 - - - +
159M VAL* 3.8 6.1 - - - +
277M THR 3.1 13.6 + - - -
278M LEU 3.2 0.2 + - - -
279M THR 3.1 0.6 - - - -
280M GLY* 1.3 77.7 - - - +
282M ILE* 1.3 61.8 + - - +
284M ILE* 3.3 4.9 + - - +
285M LEU* 3.0 22.0 + - - +
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Residues in contact with ILE 282 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ALA* 4.8 5.4 - - + -
20H PHE* 6.2 2.9 - - + -
155M TRP* 3.5 26.9 - - + +
201M PHE* 4.0 23.1 - - + -
278M LEU* 3.4 17.9 + - + +
279M THR* 3.2 8.9 + - - +
281M GLY* 1.3 74.3 - - - +
283M GLY* 1.3 57.3 + - - +
285M LEU* 2.7 33.5 + - + +
286M LEU* 3.0 37.0 + - + +
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Residues in contact with GLY 283 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199M ASN* 3.0 18.4 + - - -
201M PHE* 3.5 27.1 - - - +
279M THR 3.0 9.3 + - - -
280M GLY 4.0 1.8 - - - -
282M ILE* 1.3 80.5 - - - +
284M ILE* 1.3 59.5 + - - +
286M LEU* 3.8 3.5 + - - -
287M SER* 3.0 24.6 + - - -
294M TRP* 4.2 0.9 - - - -
852M BCL 4.6 3.4 - - - -
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Residues in contact with ILE 284 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M LEU* 4.3 5.2 - - + -
159M VAL* 4.1 11.9 - - + -
160M LEU* 3.6 23.3 - - + -
164M ARG* 3.4 19.8 - - - -
189M PHE* 4.0 30.5 - - + -
196M LEU* 4.0 8.3 - - + -
280M GLY 3.2 18.3 + - - +
281M GLY 3.8 3.6 - - - +
282M ILE 3.1 1.0 - - - -
283M GLY* 1.3 75.7 - - - +
285M LEU* 1.3 65.7 + - - +
287M SER* 3.3 12.3 + - - -
852M BCL 3.0 52.5 - - + +
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Residues in contact with LEU 285 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M TRP* 4.2 20.4 - - + -
159M VAL* 3.8 15.7 - - + +
163M ILE* 3.4 33.0 - - + -
164M ARG* 4.6 7.4 - - - +
167M LEU* 3.8 19.3 - - + -
281M GLY 3.0 13.6 + - - +
282M ILE* 2.7 21.4 + - + +
284M ILE* 1.3 74.5 - - - +
286M LEU* 1.3 58.0 + - + +
287M SER 3.1 1.8 + - - -
289M THR* 2.6 34.4 + - + +
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Residues in contact with LEU 286 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 4.9 15.0 - - + -
13H ALA* 4.3 14.1 - - + -
16H ALA* 4.2 14.4 - - + -
201M PHE* 3.8 20.6 - - + -
282M ILE* 3.0 38.5 + - + +
283M GLY 3.8 1.3 + - - +
284M ILE 3.3 0.2 - - - -
285M LEU* 1.3 85.1 - - + +
287M SER* 1.3 60.2 + - - +
289M THR* 3.7 6.7 - - - +
290M VAL* 4.3 22.2 - - + -
291M VAL* 3.1 32.6 + - + +
294M TRP* 3.7 13.0 - - + -
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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