Contacts of the helix formed by residues 372 - 395 (chain F) in PDB entry 2ACL
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 372 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F LEU* 4.6 6.5 - - + -
283F ASP* 3.2 10.2 + - - +
370F VAL* 4.2 2.9 - - - -
371F GLN* 1.3 77.3 - - + +
373F GLN* 1.3 65.5 + - - +
374F LEU* 3.1 12.2 + - - +
375F GLN* 2.8 41.1 + - + +
376F VAL* 3.1 25.6 + - - +
378F ARG* 4.4 2.5 + - - -
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Residues in contact with GLN 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E THR* 4.7 15.8 + - - +
352E GLU* 3.2 19.8 - - - +
356E LYS* 5.6 3.6 + - - +
365F ALA* 2.9 40.2 - - + +
366F ASP* 4.4 1.6 - - - -
367F ARG 5.9 0.7 - - - -
370F VAL* 3.6 29.3 + - + +
371F GLN 3.1 4.8 + - - +
372F ASP* 1.3 73.2 - - - +
374F LEU* 1.3 56.9 + - - +
376F VAL* 4.5 0.4 - - - -
377F GLU* 3.0 31.9 + - - +
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Residues in contact with LEU 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F ASP* 3.6 8.3 - - - +
373F GLN* 1.3 80.1 - - - +
375F GLN* 1.3 56.6 + - - +
377F GLU* 3.1 36.9 - - - +
378F ARG* 2.8 44.8 + - + +
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Residues in contact with GLN 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F GLY* 5.7 1.8 + - - +
279F LEU* 3.6 21.5 - - + -
372F ASP* 2.8 30.3 + - + +
374F LEU* 1.3 71.4 - - - +
376F VAL* 1.3 67.2 + - - +
377F GLU 3.0 1.1 - - - -
378F ARG* 2.5 49.2 + - - +
379F LEU* 3.0 44.7 + - + +
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Residues in contact with VAL 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F LEU* 4.0 26.9 - - + -
283F ASP* 4.7 1.1 - - - +
287F LEU* 4.0 12.1 - - + -
363F PHE* 3.6 23.6 - - + +
364F SER 3.6 3.8 - - - +
365F ALA* 3.5 26.9 - - - +
370F VAL* 3.9 17.3 - - + -
372F ASP 3.1 17.8 + - - +
373F GLN* 3.9 4.3 - - - +
375F GLN* 1.3 76.0 - - - +
377F GLU* 1.3 63.8 + - - +
379F LEU* 3.5 11.3 + - - +
380F GLN* 3.0 22.3 + - - +
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Residues in contact with GLU 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E LYS* 2.8 39.4 + - - +
421E ARG* 5.1 3.1 + - - +
365F ALA* 4.2 16.8 - - + +
373F GLN* 3.0 14.1 + - - +
374F LEU* 3.1 30.9 - - - +
376F VAL* 1.3 77.6 - - - +
378F ARG* 1.3 58.7 + - + +
380F GLN* 2.9 17.0 + - - +
381F HIS* 2.8 27.3 + - + +
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Residues in contact with ARG 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F ASP* 4.4 3.4 + - - -
374F LEU* 2.8 43.4 + - + +
375F GLN* 2.5 61.6 + - - +
377F GLU* 1.3 79.0 - - + +
379F LEU* 1.3 63.5 + - - +
381F HIS* 3.0 20.8 + - - +
382F THR* 3.3 14.7 + - - -
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Residues in contact with LEU 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F PRO 3.3 25.4 - - - +
275F GLY* 3.5 25.8 - - - +
279F LEU* 4.3 11.7 - - + -
363F PHE* 3.3 36.8 - - + -
375F GLN* 3.0 36.6 + - + +
376F VAL* 3.7 8.7 - - - +
378F ARG* 1.3 77.4 - - - +
380F GLN* 1.3 62.6 + - - +
382F THR* 3.4 9.6 + - - -
383F TYR* 3.0 26.0 - - + -
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Residues in contact with GLN 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E LEU* 4.8 18.3 - - - +
421E ARG* 5.8 1.6 + - - -
360F ILE* 3.0 46.0 + - + +
363F PHE* 3.2 28.2 + - - +
364F SER* 4.4 7.6 + - - +
365F ALA* 5.0 4.7 + - - +
376F VAL 3.0 7.5 + - - +
377F GLU* 2.9 18.9 + - - +
379F LEU* 1.3 76.3 - - - +
381F HIS* 1.3 66.9 + - - +
383F TYR* 3.0 18.1 + - - +
384F VAL* 3.1 21.8 + - + +
409F LEU* 4.9 3.8 - - - +
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Residues in contact with HIS 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413E GLY* 5.8 2.8 + - - -
377F GLU 2.8 11.3 + - - +
378F ARG* 3.0 14.8 + - - +
380F GLN* 1.3 76.1 - - - +
382F THR* 1.3 63.4 + - - +
384F VAL* 3.2 9.1 + - + +
385F GLU* 3.1 49.8 + - + +
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Residues in contact with THR 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F GLN* 5.2 1.0 + - - -
211F MET* 3.2 33.0 - - + -
378F ARG 3.3 9.6 + - - -
379F LEU* 3.5 11.9 + - - -
380F GLN 3.0 0.6 + - - -
381F HIS* 1.3 80.8 + - - +
383F TYR* 1.3 62.0 + - + +
385F GLU* 3.5 4.6 + - - +
386F ALA* 3.2 20.8 + - - +
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Residues in contact with TYR 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F MET* 3.4 31.2 - - + -
215F LEU* 4.1 18.6 - - + -
273F LEU* 3.2 34.3 - - + +
274F PRO* 3.2 30.8 + - + +
356F LEU* 3.9 8.9 - - + +
359F ALA* 3.7 14.1 - - + -
360F ILE* 3.7 22.1 - - + +
363F PHE* 3.6 25.4 - + - -
379F LEU* 3.0 30.3 - - + -
380F GLN* 3.0 5.7 + - - +
382F THR* 1.3 75.7 - - - +
384F VAL* 1.3 60.9 + - - +
386F ALA* 3.9 6.0 - - - +
387F LEU* 3.0 30.8 + - - +
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Residues in contact with VAL 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416E ALA* 4.0 15.9 - - + -
420E LEU* 4.3 20.0 - - + -
360F ILE* 3.6 31.2 - - + -
380F GLN* 3.1 23.1 + - + +
381F HIS* 3.2 13.4 + - + +
383F TYR* 1.3 76.2 - - - +
385F GLU* 1.3 65.3 + - - +
387F LEU* 3.5 0.4 + - - -
388F HIS* 2.9 26.9 + - - +
402F PHE* 3.6 24.9 - - + -
406F LEU* 4.6 6.1 - - + -
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Residues in contact with GLU 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412E PRO* 5.2 5.4 - - - +
413E GLY* 3.9 25.8 + - - +
416E ALA* 4.6 5.2 - - - +
208F GLN* 4.0 11.2 - - - +
381F HIS* 3.1 46.4 + - + +
382F THR* 4.0 4.5 - - - +
384F VAL* 1.3 81.9 - - - +
386F ALA* 1.3 66.6 + - - +
388F HIS* 3.1 13.8 + - - +
389F ALA* 2.8 25.6 + - - +
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Residues in contact with ALA 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F LEU* 4.2 1.9 - - - +
208F GLN* 3.6 27.9 - - + +
211F MET* 4.2 14.8 - - - -
212F ILE* 4.9 7.0 - - + -
356F LEU* 4.1 15.9 - - + -
382F THR 3.2 16.1 + - - +
383F TYR 3.9 3.6 - - - +
385F GLU* 1.3 78.8 - - - +
387F LEU* 1.3 52.1 + - - +
389F ALA* 3.3 1.6 + - - +
390F TYR* 2.6 39.2 + - - +
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Residues in contact with LEU 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F GLU* 4.3 14.1 - - + +
356F LEU* 3.6 35.6 - - + +
357F LEU* 5.3 8.5 - - + +
360F ILE* 4.2 16.8 - - + -
383F TYR 3.0 19.5 + - - +
384F VAL 3.7 3.1 - - - +
386F ALA* 1.3 73.0 - - - +
388F HIS* 1.3 66.5 + - - +
390F TYR* 4.1 1.6 - - + -
391F VAL* 2.8 34.1 + - + +
402F PHE* 4.0 14.8 - - + -
405F MET* 3.3 42.0 - - + -
406F LEU* 4.9 4.5 - - + -
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Residues in contact with HIS 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401E GLU* 4.0 19.8 + - - -
405E LYS* 6.0 3.7 - - - -
412E PRO 5.2 9.9 + - - -
413E GLY* 5.6 1.3 - - - -
415E PHE* 5.2 2.8 - - - +
416E ALA* 4.9 4.3 - - + -
384F VAL 2.9 15.8 + - - +
385F GLU* 3.3 23.3 - - - +
387F LEU* 1.3 74.9 - - - +
389F ALA* 1.3 52.3 + - - +
391F VAL* 2.9 6.5 - - - +
392F SER* 2.8 43.4 + - - -
399F PRO 6.1 0.2 - - - -
402F PHE* 3.3 52.1 - + + +
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Residues in contact with ALA 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F VAL* 4.4 20.0 - - + +
203F GLN 5.2 0.2 - - - -
204F LEU* 4.3 9.6 - - + +
208F GLN* 3.9 21.8 - - - +
385F GLU 2.8 18.1 + - - +
386F ALA 3.6 2.9 - - - +
388F HIS* 1.3 74.0 - - - +
390F TYR* 1.3 63.9 + - - +
392F SER* 3.2 8.3 - - - -
393F ILE* 3.0 29.5 + - - +
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Residues in contact with TYR 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F LEU* 3.7 22.4 - - + +
209F LEU* 6.3 1.3 - - + -
212F ILE* 3.3 30.5 - - + -
350F ASN* 3.1 24.7 + - - -
352F ALA* 3.7 20.4 - - + +
353F GLU* 2.8 36.6 - - + -
356F LEU* 4.4 5.2 - - + -
386F ALA 2.6 21.0 + - - +
387F LEU* 3.6 7.4 - - - +
388F HIS 3.2 0.2 - - - -
389F ALA* 1.3 73.6 - - - +
391F VAL* 1.3 60.4 + - + +
393F ILE 3.3 1.6 + - - -
394F ASN* 2.5 60.8 + - + +
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Residues in contact with VAL 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F GLU* 3.8 19.1 - - + +
387F LEU* 2.8 26.8 + - + +
388F HIS* 2.9 18.8 - - - +
390F TYR* 1.3 72.6 - - + +
392F SER* 1.3 67.8 + - - +
395F HIS* 3.0 37.2 + - - +
398F ASP 5.3 0.2 - - - +
401F MET* 3.9 17.5 - - + -
402F PHE* 4.2 22.0 - - + +
405F MET* 3.4 26.9 - - + -
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Residues in contact with SER 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F VAL 5.3 4.0 + - - -
388F HIS* 2.8 27.3 + - - -
389F ALA* 3.2 12.8 - - - -
391F VAL* 1.3 81.7 - - - +
393F ILE* 1.3 61.9 + - - +
395F HIS 4.1 1.9 - - - -
396F PRO* 3.9 17.8 - - - +
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Residues in contact with ILE 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F VAL 5.4 0.4 - - - +
203F GLN* 3.7 28.5 - - + +
204F LEU* 3.0 55.9 - - + +
389F ALA 3.0 9.5 + - - +
390F TYR 3.6 1.6 - - - +
392F SER* 1.3 79.1 - - - +
394F ASN* 1.3 72.6 + - - +
396F PRO* 3.5 18.9 - - - +
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Residues in contact with ASN 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F LEU* 5.0 2.1 - - - +
350F ASN* 6.2 0.7 - - - +
390F TYR* 2.5 57.8 + - + +
393F ILE* 1.3 86.3 - - - +
395F HIS* 1.3 82.1 + - + +
396F PRO* 3.4 5.9 - - - +
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Residues in contact with HIS 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F LEU 5.5 0.6 + - - -
348F GLN 5.6 2.8 + - - -
350F ASN* 5.6 1.6 - - - -
353F GLU* 3.3 30.0 + - - -
390F TYR* 5.1 0.2 - + - -
391F VAL* 3.0 31.0 + - + +
392F SER* 4.1 1.6 - - - +
393F ILE 3.4 0.2 - - - -
394F ASN* 1.3 100.8 + - + +
396F PRO* 1.3 68.0 - - - +
397F HIS 3.2 3.6 - - - -
398F ASP* 3.1 37.5 + - + +
399F PRO* 4.1 1.4 - - - +
401F MET* 3.4 35.8 - - + +
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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) + - + + + + + -
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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