Contacts of the helix formed by residues 357 - 379 (chain A) in PDB entry 4ORA
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 ASP 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A TRP* 6.3 1.1 - - - -
352A LEU* 4.1 0.9 - - - -
355A PHE 3.7 2.4 + - - -
356A MET* 1.3 76.8 - - - +
358A VAL* 1.3 61.0 + - - +
359A PHE* 3.1 32.7 + - - +
360A THR* 2.5 27.1 + - - -
361A TRP* 3.0 25.6 + - - +
131B ILE* 6.4 0.2 - - - -
135B THR* 3.2 24.0 - - + +
138B ASN* 6.5 0.7 - - + -
155B VAL* 3.2 20.9 - - - +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.3 1.8 - - + -
357A ASP* 1.3 71.9 - - - +
359A PHE* 1.3 54.9 + - + +
361A TRP* 3.7 8.3 - - - +
362A SER* 2.5 38.8 + - - -
111B LEU* 3.6 39.9 - - + -
115B LEU* 3.6 19.2 - - + +
131B ILE* 3.6 45.3 - - + +
132B VAL* 4.1 2.7 - - + +
135B THR* 2.9 21.4 + - + +
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Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASP* 3.1 16.7 + - - +
358A VAL* 1.3 75.4 - - + +
360A THR* 1.3 62.5 + - - +
361A TRP 3.0 1.6 - - - -
362A SER* 3.1 2.2 + - - -
363A LEU* 2.7 39.2 + - + +
98B TYR* 4.0 16.8 - + - -
106B ILE* 4.0 21.3 - - + -
111B LEU* 3.8 33.7 - - + -
135B THR* 3.9 18.8 - - + -
139B ALA* 5.3 4.9 - - + -
147B ILE* 4.4 20.4 - - + -
152B PHE* 3.6 38.1 - + + -
155B VAL* 4.5 11.2 - - + -
156B VAL* 3.6 15.9 - - + -
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Residues in contact with THR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A MET* 3.9 26.0 - - + +
357A ASP* 2.5 29.5 + - - -
359A PHE* 1.3 77.8 - - - +
361A TRP* 1.3 61.0 + - - +
364A PRO* 3.3 20.4 - - - +
155B VAL* 4.3 9.0 + - - +
156B VAL* 4.6 1.1 - - - +
159B LEU* 3.7 38.5 - - + +
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Residues in contact with TRP 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 3.5 34.3 - - + +
356A MET* 4.0 23.8 - - + +
357A ASP 3.0 17.9 + - - +
358A VAL* 3.7 5.4 - - - +
359A PHE 3.0 0.2 - - - -
360A THR* 1.3 80.3 - - - +
362A SER* 1.3 58.7 + - - +
364A PRO* 4.1 6.4 - - - +
365A PHE 5.0 0.3 + - - -
419A LEU* 3.6 27.5 - - + +
420A SER 3.3 19.2 + - - -
421A VAL* 3.5 26.7 - - - -
422A LEU* 4.1 14.9 - - + +
115B LEU* 3.7 31.4 - - + -
119B VAL* 3.4 24.7 - - + -
123B LEU* 3.9 18.4 - - + -
131B ILE* 4.1 8.7 - - + -
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL 2.5 24.0 + - - -
359A PHE* 3.4 1.0 + - - -
361A TRP* 1.3 77.0 - - - +
363A LEU* 1.3 57.2 + - - +
364A PRO* 3.2 2.7 - - - -
365A PHE* 2.7 29.5 + - - +
366A VAL* 2.9 10.4 + - - +
419A LEU* 3.7 25.4 - - - -
98B TYR* 2.7 28.8 + - - -
115B LEU* 4.2 5.6 - - - +
118B MET* 3.9 14.6 - - - -
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Residues in contact with LEU 363 (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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359A PHE* 2.7 22.8 + - - +
360A THR* 4.9 0.9 - - - -
362A SER* 1.3 72.7 + - - +
364A PRO* 1.4 58.2 - - + +
366A VAL* 3.1 9.0 + - + +
367A GLY* 2.7 34.5 + - - +
91B LEU* 5.0 7.0 - - + -
94B ALA* 3.6 29.6 - - + -
98B TYR* 3.7 13.7 - - - +
152B PHE* 4.7 7.0 - - + -
156B VAL* 3.6 40.4 - - + +
159B LEU* 4.5 4.5 - - + -
161B ILE* 4.0 29.3 - - + +
165B MET* 5.6 2.0 - - - -
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Residues in contact with PRO 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A THR 3.3 22.9 - - - +
361A TRP 4.1 4.3 - - - +
362A SER 3.4 3.8 - - - +
363A LEU* 1.4 93.5 - - + +
365A PHE* 1.3 56.3 + - - +
367A GLY* 3.7 0.7 - - - +
368A GLU* 2.9 31.9 + - - +
159B LEU* 5.0 3.4 - - + -
161B ILE* 4.1 28.0 - - + +
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Residues in contact with PHE 365 (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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361A TRP 5.0 0.6 + - - +
362A SER 2.7 15.4 + - - +
364A PRO* 1.3 72.7 - - - +
366A VAL* 1.3 64.4 + - - +
368A GLU* 3.2 10.2 + - - +
369A LYS* 2.9 67.3 + - + +
416A ALA* 4.1 11.7 - - + -
418A TYR* 3.7 15.7 - - - -
419A LEU* 3.7 46.0 - - + -
52B PRO* 4.0 16.6 - - + -
53B LEU* 4.7 2.2 - - + -
118B MET* 3.6 43.3 - - + -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER 2.9 11.0 + - - +
363A LEU* 3.3 17.7 - - + +
365A PHE* 1.3 75.8 - - - +
367A GLY* 1.3 65.5 + - - +
369A LYS* 3.7 0.2 - - - -
370A VAL* 3.0 34.3 + - + +
53B LEU* 3.8 11.9 - - + -
94B ALA* 4.8 8.1 - - + +
97B ILE* 4.0 33.0 - - + -
98B TYR* 3.6 24.5 - - + +
118B MET* 3.8 25.1 - - + -
165B MET* 5.7 1.1 - - + -
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Residues in contact with GLY 367 (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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363A LEU* 2.7 19.6 + - - +
364A PRO 3.7 1.6 - - - -
366A VAL* 1.3 75.1 - - - +
368A GLU* 1.3 59.9 + - - +
370A VAL* 4.4 2.9 - - - -
371A THR* 2.6 32.1 + - - -
161B ILE* 4.4 9.2 - - - -
164B LYS* 5.1 6.1 - - - +
165B MET* 4.2 22.9 - - - -
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PRO 2.9 19.3 + - - +
365A PHE* 3.7 10.1 - - - +
366A VAL 3.2 0.2 - - - -
367A GLY* 1.3 75.8 - - - +
369A LYS* 1.3 70.3 + - - +
371A THR* 3.9 2.6 - - - -
372A GLU* 3.0 39.5 + - - +
416A ALA 3.7 23.1 + - - -
164B LYS* 6.0 0.6 - - - +
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Residues in contact with LYS 369 (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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365A PHE* 2.9 50.5 + - + +
368A GLU* 1.3 84.5 + - + +
370A VAL* 1.3 61.6 + - - +
372A GLU* 3.6 28.9 + - - +
373A MET* 3.1 13.5 + - - +
416A ALA 3.9 7.8 - - - +
417A ARG* 3.2 39.3 - - - +
50B GLN 5.1 2.4 + - - -
51B ASN* 2.9 41.1 + - - +
52B PRO* 4.9 6.1 - - + +
53B LEU* 3.8 16.4 - - + -
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL* 3.0 23.1 + - + +
367A GLY 3.9 4.7 - - - +
369A LYS* 1.3 73.8 - - - +
371A THR* 1.3 69.6 + - - +
373A MET* 3.2 8.0 + - - +
374A LEU* 3.0 27.6 + - + +
53B LEU* 4.0 18.2 - - + -
57B VAL* 3.7 28.0 - - + -
81B PHE* 3.7 27.4 - - + -
93B PHE* 4.5 3.1 - - + -
97B ILE* 4.0 16.2 - - + -
165B MET* 4.1 13.7 - - + -
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Residues in contact with THR 371 (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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367A GLY 2.6 23.2 + - - -
368A GLU* 4.0 3.1 - - - -
370A VAL* 1.3 78.9 - - - +
372A GLU* 1.3 62.2 + - - +
374A LEU* 3.5 3.5 + - - +
375A VAL* 3.0 28.7 + - + +
81B PHE* 3.9 10.7 - - + -
164B LYS 3.7 16.9 + - - +
165B MET* 3.5 19.8 - - - +
166B VAL 3.7 21.1 - - - +
167B VAL* 4.2 7.2 - - + -
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Residues in contact with GLU 372 (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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368A GLU* 3.0 28.7 + - + +
369A LYS* 3.6 36.5 + - - +
370A VAL 3.2 0.2 - - - -
371A THR* 1.3 77.4 - - - +
373A MET* 1.3 58.5 + - - +
375A VAL* 3.3 5.0 + - - +
376A ASN* 2.5 46.9 + - - +
47B GLU 4.7 8.5 - - - +
51B ASN* 4.6 9.1 + - - +
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Residues in contact with MET 373 (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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369A LYS 3.1 15.1 + - - +
370A VAL* 3.2 8.5 + - - +
372A GLU* 1.3 78.4 - - - +
374A LEU* 1.3 62.1 + - + +
376A ASN* 3.2 3.4 + - - +
377A VAL* 2.8 31.7 + - + +
42B PHE* 4.3 24.7 - - + -
48B LEU* 3.9 21.2 - - + +
51B ASN* 3.7 11.2 - - - +
53B LEU 4.9 0.2 - - - -
54B VAL* 3.7 39.5 - - + +
57B VAL* 3.5 47.8 - - + -
58B ILE* 4.3 4.5 - - + -
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Residues in contact with LEU 374 (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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370A VAL* 3.0 17.9 + - + +
371A THR* 3.9 4.3 - - - +
373A MET* 1.3 87.9 - - + +
375A VAL* 1.3 57.7 + - - +
377A VAL* 3.7 12.0 - - + +
378A LEU* 2.8 41.5 + - + +
42B PHE* 6.3 0.9 - - + -
57B VAL* 4.6 8.5 - - + -
61B PHE* 4.1 27.4 - - + -
74B PHE* 6.4 0.9 - - + -
78B VAL* 4.6 13.5 - - + -
81B PHE* 3.3 50.5 - - + -
167B VAL* 4.0 12.8 - - + -
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A THR* 3.0 27.0 + - + +
372A GLU* 3.8 6.1 - - - +
373A MET 3.2 0.2 - - - -
374A LEU* 1.3 76.8 - - - +
376A ASN* 1.3 66.0 + - - +
378A LEU* 3.4 6.0 + - - +
379A SER* 3.1 27.0 + - - -
166B VAL 5.1 0.9 - - - +
167B VAL* 3.9 22.0 - - + -
168B ASP 5.8 0.7 - - - +
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Residues in contact with ASN 376 (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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372A GLU* 2.5 50.5 + - - +
373A MET* 3.6 5.1 - - - +
375A VAL* 1.3 80.8 - - - +
377A VAL* 1.3 60.3 + - - +
379A SER* 2.9 21.1 + - - -
380A ILE* 3.9 2.9 + - - -
45B LEU* 3.9 10.6 - - - +
47B GLU* 3.3 41.9 + - + +
48B LEU* 3.9 14.8 - - + +
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A MET* 2.8 29.4 + - + +
374A LEU* 3.7 13.0 - - + +
375A VAL 3.3 0.2 - - - -
376A ASN* 1.3 74.3 - - - +
378A LEU* 1.3 68.1 + - + +
380A ILE* 3.1 26.9 + - - +
25B ARG* 4.9 0.2 - - - +
29B LEU* 3.5 25.0 - - + +
42B PHE* 4.1 19.1 - - + -
45B LEU* 4.0 10.3 - - + -
48B LEU* 4.0 24.7 - - + -
74B PHE* 4.4 18.2 - - + -
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 2.8 29.8 + - + +
375A VAL* 4.0 5.2 - - + +
377A VAL* 1.3 74.5 - - + +
379A SER* 1.3 56.9 + - - +
380A ILE 3.1 3.8 + - - -
381A CYS 3.8 3.5 - - - +
22B LEU* 3.6 30.1 - - + -
25B ARG* 2.7 54.2 + - - +
74B PHE* 4.6 13.2 - - + -
78B VAL* 4.4 14.1 - - + -
167B VAL* 3.8 26.0 - - + -
168B ASP 3.8 20.2 - - - +
169B VAL* 4.7 1.3 - - + -
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.1 16.9 + - - -
376A ASN* 2.9 22.5 + - - -
377A VAL 3.1 0.2 - - - -
378A LEU* 1.3 75.0 - - - +
380A ILE* 1.3 65.2 + - - +
381A CYS 3.2 13.8 - - - +
382A SER* 4.4 5.9 + - - -
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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