Contacts of the helix formed by residues 274 - 297 (chain y) in PDB entry 3J45
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 VAL 274 (chain y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188y SER* 6.0 0.9 - - - +
271y MET* 3.5 37.0 - - + -
272y ALA* 4.5 1.1 - - - +
273y GLY* 1.3 79.1 - - - +
275y ILE* 1.4 78.2 + - + +
276y PRO* 3.5 2.6 - - + +
277y ALA* 4.4 0.5 - - - +
278y ILE* 3.5 26.4 + - + +
411y VAL* 3.3 29.8 - - + +
415y ASP* 3.7 27.1 - - + +
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Residues in contact with ILE 275 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185y ASN* 4.5 18.2 - - - +
187y ILE* 5.3 13.5 - - + -
188y SER* 5.5 3.6 - - - +
274y VAL* 1.4 91.1 - - + +
276y PRO* 1.3 69.3 - - + +
277y ALA 3.3 0.7 + - - -
278y ILE* 3.3 11.4 + - + +
279y PHE* 3.3 30.0 + - + -
332y TYR* 3.3 30.7 - - + +
415y ASP* 4.8 5.2 - - - +
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Residues in contact with PRO 276 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273y GLY* 3.8 12.8 - - - +
274y VAL* 3.5 14.1 - - + +
275y ILE* 1.3 94.7 - - + +
277y ALA* 1.4 56.1 + - - +
279y PHE* 3.6 3.7 + - - +
280y ALA* 3.1 28.2 + - - +
329y CYS* 3.5 31.0 - - + +
332y TYR* 3.5 24.6 - - + +
333y THR* 3.3 26.9 - - + -
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Residues in contact with ALA 277 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273y GLY 3.3 22.0 - - - +
274y VAL 4.0 0.6 + - - +
275y ILE 3.3 0.6 - - - -
276y PRO* 1.4 76.6 - - - +
278y ILE* 1.4 65.3 + - + +
280y ALA* 4.0 1.4 - - - +
281y SER* 3.2 28.8 + - - -
325y ILE* 5.0 3.2 - - + +
329y CYS* 3.6 9.6 - - - -
381y ILE* 3.8 24.9 - - + -
407y LEU* 4.4 15.5 - - + -
408y ILE* 6.1 1.3 - - + -
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Residues in contact with ILE 278 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67y PHE* 6.4 0.7 - - - -
86y ILE* 4.4 3.8 - - + -
187y ILE* 3.5 37.7 - - + -
188y SER* 4.6 18.4 - - - +
191y ILE* 3.8 22.7 - - + -
274y VAL* 3.5 21.5 + - + +
275y ILE* 3.3 12.7 + - + +
277y ALA* 1.4 78.5 - - + +
279y PHE* 1.4 59.6 + - - +
281y SER* 4.0 3.1 - - - -
282y SER* 3.2 21.0 + - - +
408y ILE* 4.4 24.0 - - + -
411y VAL* 5.0 11.4 - - + -
412y VAL* 5.3 6.3 - - + -
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Residues in contact with PHE 279 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G SER* 5.7 9.0 - - - -
86y ILE* 3.4 42.5 - - + +
89y SER* 4.2 20.4 - - - -
90y ILE* 4.1 17.0 - - + +
187y ILE* 3.7 20.0 - - + -
275y ILE* 3.3 26.9 + - + +
276y PRO 3.8 7.2 - - - +
277y ALA 3.4 0.2 - - - -
278y ILE* 1.4 73.9 - - - +
280y ALA* 1.4 58.4 + - - +
282y SER* 3.0 2.9 + - - -
283y ILE* 2.9 32.9 + - - +
332y TYR* 3.2 52.5 - + + -
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Residues in contact with ALA 280 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90y ILE* 6.5 0.2 - - - -
276y PRO 3.1 19.3 + - - +
277y ALA 3.5 3.1 + - - +
278y ILE 3.5 0.2 - - - -
279y PHE* 1.4 74.8 - - - +
281y SER* 1.3 57.9 + - - +
283y ILE* 3.2 18.8 - - - +
284y ILE* 3.7 12.1 + - - +
324y ALA 5.4 0.2 - - - +
325y ILE* 4.2 15.7 - - + +
328y PHE* 3.3 34.8 - - + +
329y CYS* 3.7 19.3 - - - +
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Residues in contact with SER 281 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67y PHE* 4.0 28.3 - - - -
83y MET* 4.5 2.0 - - - +
277y ALA 3.2 16.0 + - - -
278y ILE* 4.0 3.8 - - - -
279y PHE 3.3 0.2 - - - -
280y ALA* 1.3 75.7 - - - +
282y SER* 1.3 64.6 + - - +
283y ILE 3.3 0.2 - - - -
284y ILE* 3.6 9.0 + - - +
285y LEU* 3.6 27.0 + - - +
321y TYR* 3.7 10.3 + - - -
325y ILE* 3.6 17.4 - - - +
404y THR* 5.8 0.9 - - - +
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Residues in contact with SER 282 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67y PHE* 6.1 0.2 - - - -
83y MET* 3.7 29.6 - - - +
86y ILE* 3.6 42.2 - - - +
87y SER* 3.7 5.8 + - - -
191y ILE* 5.0 2.3 - - - +
278y ILE* 3.2 13.5 + - - +
279y PHE 3.0 8.7 + - - -
281y SER* 1.3 79.7 - - - +
283y ILE* 1.3 63.2 + - - +
285y LEU 3.8 0.2 + - - -
286y PHE* 3.3 23.0 + - - +
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Residues in contact with ILE 283 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86y ILE* 5.5 0.4 - - - +
87y SER* 4.0 35.2 - - - +
90y ILE* 4.4 17.5 - - + -
91y ILE* 4.1 20.2 - - + -
279y PHE 2.9 14.7 + - - +
280y ALA* 3.2 24.0 - - - +
282y SER* 1.3 79.3 - - - +
284y ILE* 1.3 61.5 + - - +
286y PHE* 3.5 4.5 + - + +
287y PRO* 3.2 22.4 - - + +
328y PHE* 4.2 29.6 - - + -
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Residues in contact with ILE 284 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280y ALA 3.8 11.0 - - - +
281y SER* 3.6 11.0 + - - +
282y SER 3.4 0.4 - - - -
283y ILE* 1.3 80.3 - - + +
285y LEU* 1.4 70.9 + - + +
287y PRO* 3.7 10.0 - - + +
288y ALA* 3.7 12.6 + - - +
310y LEU* 4.4 14.9 - - + +
311y GLN* 3.2 42.8 + - - +
320y LEU 5.5 0.2 - - - +
321y TYR* 4.2 14.8 - - + -
324y ALA* 4.0 27.1 - - + -
328y PHE* 4.9 11.9 - - + -
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Residues in contact with LEU 285 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60y ILE* 4.6 13.0 - - + +
63y MET* 3.8 49.6 - - + -
64y PHE* 4.0 23.1 - - + +
67y PHE* 3.9 29.4 - - + -
83y MET* 4.4 3.1 - - + -
281y SER 3.6 12.7 + - - +
282y SER 4.3 2.0 - - - +
283y ILE 3.4 0.2 - - - -
284y ILE* 1.4 84.4 - - + +
286y PHE* 1.3 63.3 + - - +
287y PRO 3.5 0.4 - - - -
288y ALA* 3.8 2.2 - - + -
289y THR* 3.0 28.0 + - - -
311y GLN* 4.0 18.2 - - + +
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Residues in contact with PHE 286 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64y PHE* 4.9 10.8 - + - -
83y MET* 4.2 4.3 - - + -
84y PRO* 3.6 28.7 - - + -
87y SER* 3.3 31.9 - - - +
127y LEU* 3.9 34.3 - - + -
131y GLN* 3.5 39.3 - - - -
282y SER 3.3 10.5 + - - +
283y ILE* 3.7 5.4 - - + +
284y ILE 3.3 0.2 - - - -
285y LEU* 1.3 78.2 - - - +
287y PRO* 1.4 72.1 - - + +
289y THR* 3.9 4.5 - - - +
290y ILE* 3.6 34.8 + - + +
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Residues in contact with PRO 287 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283y ILE* 3.2 20.6 - - + +
284y ILE* 3.7 8.5 - - + +
286y PHE* 1.4 94.8 - - + +
288y ALA* 1.3 59.5 - - - +
290y ILE* 3.5 5.3 + - + +
291y ALA* 2.9 29.4 + - - +
307y SER* 4.7 0.2 - - - -
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Residues in contact with ALA 288 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60y ILE* 3.5 18.6 - - + -
284y ILE 3.7 13.0 - - - +
285y LEU* 3.5 13.7 - - + +
287y PRO* 1.3 81.3 - - - +
289y THR* 1.3 56.7 + - - +
291y ALA* 3.3 4.2 + - - +
292y SER* 3.0 30.5 + - - -
307y SER* 3.1 29.7 + - - +
310y LEU* 6.1 1.1 - - + -
311y GLN* 5.4 3.6 - - + -
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Residues in contact with THR 289 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60y ILE* 3.7 11.2 - - - -
61y ILE* 4.1 8.8 - - - -
64y PHE* 3.2 58.5 - - + +
131y GLN* 5.1 1.3 - - - +
285y LEU* 3.0 15.9 + - - +
286y PHE* 3.9 8.1 - - + +
288y ALA* 1.3 74.0 - - - +
290y ILE* 1.4 76.8 + - + +
292y SER* 3.4 3.9 + - - -
293y TRP* 3.2 43.2 + - + -
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Residues in contact with ILE 290 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130y PHE* 3.7 35.4 - - + -
131y GLN* 3.4 39.3 - - + +
286y PHE* 3.6 31.2 + - + +
287y PRO* 3.5 8.4 + - + +
288y ALA 3.3 0.4 - - - -
289y THR* 1.4 84.5 - - + +
291y ALA* 1.4 63.1 + - - +
293y TRP* 3.1 20.4 + - + +
294y PHE* 3.1 40.6 + - + -
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Residues in contact with ALA 291 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287y PRO 2.9 18.6 + - - +
288y ALA 3.5 5.2 - - - +
289y THR 3.2 0.2 - - - -
290y ILE* 1.4 76.5 - - - +
292y SER* 1.4 52.9 + - - +
294y PHE* 3.3 6.7 + - - +
295y GLY 3.2 17.8 + - - -
300y TRP* 4.0 4.9 - - - +
303y LEU* 3.5 25.6 - - + +
304y THR* 2.5 38.8 + - - +
307y SER* 4.2 3.1 - - - +
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Residues in contact with SER 292 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57y ARG* 4.7 12.7 - - - +
58y GLY* 5.1 2.2 - - - -
60y ILE* 3.5 22.0 - - - +
61y ILE* 3.9 23.1 - - - -
288y ALA 3.0 13.2 + - - -
289y THR 3.5 10.3 - - - -
290y ILE 3.3 0.2 - - - -
291y ALA* 1.4 71.7 - - - +
293y TRP* 1.3 60.1 + - - +
295y GLY 3.3 0.9 + - - -
296y GLY* 2.9 28.2 + - - -
304y THR* 2.9 24.0 + - - +
307y SER* 5.1 0.2 - - - -
308y LEU* 5.6 0.2 - - - +
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Residues in contact with TRP 293 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53y LEU* 5.9 0.4 - - - +
57y ARG* 3.4 37.5 + - - +
61y ILE* 3.6 24.9 - - + +
64y PHE* 3.9 26.2 - + - -
72y LEU* 4.5 7.2 - - + -
80y LEU* 4.1 15.7 - - + -
131y GLN* 3.7 35.7 - - + -
134y GLY 4.6 10.5 - - - +
135y ILE* 3.7 50.5 - - + +
138y GLY* 4.2 6.6 - - - -
289y THR* 3.2 25.2 + - + -
290y ILE* 3.1 22.8 + - + +
292y SER* 1.3 76.2 - - - +
294y PHE* 1.4 64.5 + - + +
297y GLY* 3.2 19.6 + - - -
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Residues in contact with PHE 294 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130y PHE* 4.3 24.5 - + - -
133y ILE* 5.0 6.7 - - + -
134y GLY* 3.3 38.1 - - - -
137y THR* 6.2 2.7 - - - -
138y GLY* 5.8 2.2 - - - -
290y ILE* 3.1 41.8 + - + +
291y ALA* 3.3 7.2 + - - +
292y SER 3.3 0.2 - - - -
293y TRP* 1.4 78.4 - - + +
295y GLY* 1.3 58.9 + - - +
297y GLY 3.1 9.6 - - - +
298y THR 3.9 17.0 - - - -
299y GLY* 3.1 30.0 + - - -
300y TRP* 3.7 26.5 - + + +
303y LEU* 6.3 0.2 - - + -
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Residues in contact with GLY 295 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142y MET* 5.4 2.4 - - - +
291y ALA 3.2 9.1 + - - -
292y SER 3.3 1.7 + - - -
294y PHE* 1.3 76.0 - - - +
296y GLY* 1.4 62.4 + - - +
297y GLY 3.3 5.8 - - - +
300y TRP 2.6 26.9 + - - -
301y ASN* 3.8 15.9 - - - +
304y THR* 4.3 5.8 - - - -
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Residues in contact with GLY 296 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57y ARG* 4.1 24.2 - - - -
142y MET* 3.4 26.0 - - - +
143y PRO* 3.7 18.5 - - - +
292y SER 2.9 19.7 + - - -
295y GLY* 1.4 67.0 - - - +
297y GLY* 1.3 64.7 + - - +
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Residues in contact with GLY 297 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57y ARG* 4.8 0.8 - - - +
138y GLY* 3.5 26.1 + - - -
141y ASN* 5.7 1.8 - - - -
142y MET* 5.3 4.7 - - - +
143y PRO* 4.6 3.1 - - - -
293y TRP 3.2 14.7 + - - -
294y PHE 3.1 11.9 - - - +
295y GLY* 3.3 7.6 - - - +
296y GLY* 1.3 81.9 - - - +
298y THR* 1.3 61.0 + - - +
299y GLY 3.8 1.0 + - - -
301y ASN* 5.2 1.0 - - - +
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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