Contacts of the helix formed by residues 278 - 301 (chain A) in PDB entry 2DOU
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 PRO 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LYS 3.3 6.9 - - - +
277A THR* 1.3 97.0 - - + +
279A LYS* 1.3 63.0 + - - +
280A GLU* 2.9 13.9 + - + +
281A VAL* 3.0 24.5 + - + +
282A VAL* 3.7 2.8 + - - +
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Residues in contact with LYS 279 (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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79A ARG* 5.1 20.3 - - - +
207A GLY 5.0 7.1 + - - -
208A GLU* 6.0 1.2 + - - +
277A THR 3.1 5.6 + - - -
278A PRO* 1.3 70.7 - - - +
280A GLU* 1.3 65.6 + - - +
281A VAL 3.3 0.2 - - - -
282A VAL* 3.9 10.2 - - + +
283A ARG* 3.1 53.6 + - + +
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Residues in contact with GLU 280 (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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278A PRO* 2.9 9.6 - - + +
279A LYS* 1.3 82.9 - - - +
281A VAL* 1.3 58.5 + - + +
283A ARG* 3.5 3.8 + - - +
284A GLY* 3.0 24.1 + - - -
287A ARG* 3.8 22.8 + - - +
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Residues in contact with VAL 281 (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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40A PRO* 4.7 7.6 - - + -
277A THR* 3.8 19.3 - - + -
278A PRO* 3.0 24.3 + - + +
280A GLU* 1.3 77.9 - - + +
282A VAL* 1.3 65.5 + - - +
284A GLY* 3.1 11.1 + - - -
285A TYR* 3.2 44.1 + - + +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 5.4 4.3 - - - +
202A ASP* 3.5 41.9 - - + +
231A SER* 4.1 14.1 - - - +
232A TYR* 3.7 31.6 - - + +
277A THR* 4.3 7.9 - - + +
278A PRO 3.7 10.5 + - - +
279A LYS* 3.5 11.4 + - + +
280A GLU 3.4 0.2 - - - -
281A VAL* 1.3 76.5 - - - +
283A ARG* 1.3 67.0 + - + +
285A TYR* 3.3 24.8 + - + +
286A ALA* 3.4 6.8 + - - +
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Residues in contact with ARG 283 (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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202A ASP* 3.6 23.2 + - - +
204A VAL* 3.0 40.0 + - - +
205A TYR 3.3 20.4 + - - -
207A GLY 4.0 19.3 + - - +
279A LYS* 3.1 53.6 + - + +
280A GLU* 4.0 6.5 - - - +
282A VAL* 1.3 79.7 - - + +
284A GLY* 1.3 60.7 + - - +
286A ALA* 3.3 13.2 + - - +
287A ARG* 2.9 50.9 + - - +
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Residues in contact with GLY 284 (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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280A GLU 3.0 13.5 + - - -
281A VAL* 3.1 6.8 + - - -
283A ARG* 1.3 78.6 - - - +
285A TYR* 1.3 61.9 + - - +
287A ARG* 3.0 35.4 - - - +
288A VAL* 3.1 14.4 + - - +
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Residues in contact with TYR 285 (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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37A LEU* 4.2 20.9 - - + -
38A PRO* 3.1 29.4 + - + -
39A PRO 3.8 0.7 - - - -
40A PRO* 3.4 22.3 - - + +
202A ASP 6.0 0.2 - - - +
203A GLN* 6.3 1.3 - - + -
230A LYS 5.0 2.7 - - - +
231A SER* 3.4 27.6 - - - -
232A TYR* 4.3 6.3 - + - -
233A ASN* 3.6 19.1 - - - +
281A VAL* 3.2 35.2 + - + +
282A VAL* 3.4 13.7 - - + +
283A ARG 3.2 0.2 - - - -
284A GLY* 1.3 76.6 - - - +
286A ALA* 1.3 58.8 + - - +
288A VAL* 2.9 24.4 + - + +
289A TYR* 3.2 22.7 + - + +
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Residues in contact with ALA 286 (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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202A ASP 3.7 19.7 + - - +
203A GLN* 4.2 6.7 - - - +
204A VAL 3.7 23.6 - - - +
205A TYR* 4.0 5.7 - - - -
282A VAL 3.4 4.2 + - - +
283A ARG* 3.3 20.1 + - - +
285A TYR* 1.3 79.1 - - - +
287A ARG* 1.3 57.2 + - - +
289A TYR* 3.3 14.4 + - - +
290A ARG* 2.9 30.1 + - - +
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Residues in contact with ARG 287 (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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280A GLU* 3.8 25.8 + - - -
283A ARG* 2.9 38.9 + - - +
284A GLY* 3.0 32.1 - - - +
285A TYR 3.0 0.2 - - - -
286A ALA* 1.3 74.7 - - - +
288A VAL* 1.3 62.9 + - + +
290A ARG* 3.3 12.5 + - + +
291A GLU* 3.0 24.3 + - - +
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Residues in contact with VAL 288 (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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37A LEU* 4.1 26.5 - - + -
284A GLY 3.1 15.1 + - - +
285A TYR* 2.9 9.9 + - + +
287A ARG* 1.3 77.9 - - + +
289A TYR* 1.3 62.4 + - + +
291A GLU* 3.3 13.6 + - - +
292A ARG* 3.0 58.3 + - - +
502A SO4 4.5 5.6 - - - +
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Residues in contact with TYR 289 (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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35A THR* 2.7 34.1 + - - +
36A ASP* 5.1 0.4 - - - -
37A LEU* 3.4 21.8 - - + +
203A GLN* 3.6 29.6 + - + -
205A TYR* 4.0 5.8 - - + -
230A LYS 5.5 1.5 + - - -
233A ASN* 4.3 4.9 + - - -
285A TYR* 3.2 22.6 + - + +
286A ALA* 3.7 12.3 - - - +
288A VAL* 1.3 76.9 - - + +
290A ARG* 1.3 60.8 + - - +
292A ARG* 3.7 9.0 - - - +
293A ALA* 2.8 33.4 + - - +
312A THR 4.0 15.5 - - - +
313A MET* 3.7 30.2 - - + -
357A LEU* 3.8 26.7 - - + +
358A VAL* 5.4 1.1 - - + -
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Residues in contact with ARG 290 (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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205A TYR* 3.7 46.9 - - + +
206A GLU* 2.9 30.8 + - - +
286A ALA 2.9 17.6 + - - +
287A ARG* 3.5 12.6 - - - +
288A VAL 3.2 0.2 - - - -
289A TYR* 1.3 76.2 - - - +
291A GLU* 1.3 65.3 + - - +
293A ALA* 3.4 0.7 + - - +
294A LEU* 3.1 55.0 + - + +
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Residues in contact with GLU 291 (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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287A ARG 3.0 12.7 + - - +
288A VAL* 3.3 19.8 - - - +
290A ARG* 1.3 80.6 - - - +
292A ARG* 1.3 60.4 + - - +
294A LEU* 4.2 3.6 - - - +
295A GLY* 3.1 20.6 + - - -
361A LEU* 3.9 25.8 - - + +
502A SO4 2.9 41.2 + - - -
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Residues in contact with ARG 292 (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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36A ASP* 2.9 41.6 + - - -
37A LEU* 4.4 4.8 - - - +
288A VAL* 3.0 39.7 + - - +
289A TYR* 3.7 8.3 - - - +
291A GLU* 1.3 77.9 - - - +
293A ALA* 1.3 63.8 + - - +
295A GLY* 4.0 0.2 - - - -
296A MET* 3.0 28.8 + - - +
357A LEU* 3.1 34.9 + - + -
359A ARG 3.2 23.1 + - - +
360A PRO* 3.7 5.7 - - - +
361A LEU* 4.1 7.9 - - - +
364A LEU* 3.4 18.9 - - + +
502A SO4 2.8 43.1 + - - +
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Residues in contact with ALA 293 (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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205A TYR* 3.2 39.5 - - + +
289A TYR 2.8 15.5 + - - +
290A ARG 3.8 0.7 - - - +
292A ARG* 1.3 74.0 - - - +
294A LEU* 1.3 57.5 + - - +
297A ALA* 3.0 32.1 + - - +
309A PRO* 3.9 11.5 - - + +
315A LEU* 3.9 10.4 - - + +
357A LEU* 3.5 16.5 - - + +
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Residues in contact with LEU 294 (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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205A TYR* 5.3 1.3 - - + -
290A ARG* 3.1 59.6 + - + +
291A GLU* 4.3 3.4 - - - +
293A ALA* 1.3 72.7 - - - +
295A GLY* 1.3 65.9 + - - +
297A ALA* 3.8 3.3 - - + +
298A GLU* 3.1 22.3 + - - +
309A PRO* 4.1 35.7 - - + +
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Residues in contact with GLY 295 (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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291A GLU 3.1 16.6 + - - -
292A ARG 4.0 0.4 - - - -
294A LEU* 1.3 77.7 - - - +
296A MET* 1.3 63.7 + - - +
298A GLU* 3.0 17.8 + - - +
299A ALA* 3.2 11.4 + - - +
361A LEU* 4.1 15.3 - - - -
365A LEU* 4.3 6.6 - - - +
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Residues in contact with MET 296 (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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30A LEU* 3.9 23.3 - - + -
292A ARG 3.0 17.2 + - - +
295A GLY* 1.3 74.4 - - - +
297A ALA* 1.3 63.1 + - - +
299A ALA* 3.0 8.8 + - - +
300A LEU* 2.9 31.1 + - + +
315A LEU* 4.2 9.4 - - + -
355A ILE* 3.8 24.5 - - + -
357A LEU* 4.2 9.9 - - - -
361A LEU* 4.1 3.6 - - - +
364A LEU* 3.4 43.1 - - + +
365A LEU* 4.6 4.7 - - - -
368A ALA* 3.9 15.9 - - + +
371A ILE* 4.0 19.7 - - + -
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Residues in contact with ALA 297 (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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293A ALA 3.0 22.6 + - - +
294A LEU* 3.8 5.6 - - + +
295A GLY 3.2 0.2 - - - -
296A MET* 1.3 76.4 - - - +
298A GLU* 1.3 62.5 + - - +
300A LEU* 3.2 9.7 + - - +
301A LYS* 3.2 13.2 + - - +
306A LEU* 3.6 28.1 - - + +
309A PRO* 3.9 21.1 - - + -
315A LEU* 4.3 2.8 - - + +
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Residues in contact with GLU 298 (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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294A LEU 3.1 13.7 + - - +
295A GLY* 3.0 13.3 + - - +
297A ALA* 1.3 78.1 - - - +
299A ALA* 1.3 61.7 + - - +
301A LYS* 3.3 19.1 + - - +
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Residues in contact with ALA 299 (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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295A GLY 3.2 6.9 + - - +
296A MET 3.0 8.9 + - - +
298A GLU* 1.3 80.9 - - - +
300A LEU* 1.3 61.0 + - - +
301A LYS 3.4 2.2 - - - +
303A VAL* 4.4 0.7 - - - +
365A LEU* 4.4 14.6 - - + +
368A ALA* 3.6 20.0 - - + -
372A ARG* 3.3 30.8 + - - +
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Residues in contact with LEU 300 (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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296A MET* 2.9 30.2 + - + +
297A ALA 3.2 0.8 + - - -
299A ALA* 1.3 74.2 - - - +
301A LYS* 1.3 68.6 + - - +
302A GLY 3.1 0.2 + - - -
303A VAL* 2.8 25.2 + - + -
304A LEU* 3.0 24.9 + - + +
306A LEU* 3.7 30.1 - - + -
315A LEU* 4.5 2.9 - - + -
355A ILE* 3.7 27.8 - - + -
368A ALA* 3.9 29.8 - - + +
371A ILE* 4.1 23.1 - - + -
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Residues in contact with LYS 301 (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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297A ALA 3.2 9.9 + - - +
298A GLU* 3.3 18.6 + - - +
299A ALA 3.4 2.5 - - - +
300A LEU* 1.3 76.6 - - - +
302A GLY* 1.3 58.7 + - - +
303A VAL* 3.4 5.7 + - - +
304A LEU 4.6 3.6 - - - -
306A LEU* 6.0 0.2 - - - -
372A ARG* 5.5 1.9 - - - -
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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
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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) + - + + + + + -
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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