Contacts of the helix formed by residues 372 - 395 (chain D) in PDB entry 3FAL
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D LEU* 4.7 6.5 - - + +
283D ASP* 2.9 14.5 + - - +
370D VAL* 4.1 4.0 - - - -
371D GLN* 1.3 80.7 - - + +
373D GLN* 1.3 62.7 + - - +
374D LEU* 3.1 7.4 + - - +
375D GLN* 3.2 35.3 + - + +
376D VAL* 3.0 22.9 + - - +
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Residues in contact with GLN 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C THR* 4.0 22.6 + - - +
352C GLU* 3.9 17.0 + - - +
365D ALA* 3.5 25.8 + - + +
366D ASP* 5.3 1.0 - - - +
367D ARG 5.6 1.4 + - - -
370D VAL* 3.9 28.8 + - + +
371D GLN 3.0 11.5 + - - +
372D ASP* 1.3 72.1 + - - +
374D LEU* 1.3 57.4 + - - +
376D VAL* 3.5 0.8 + - - -
377D GLU* 3.0 46.0 + - - +
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Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D ASP* 3.1 6.8 + - - +
373D GLN* 1.3 77.2 - - - +
375D GLN* 1.3 59.6 + - - +
377D GLU* 3.5 15.8 + - + +
378D ARG* 3.0 76.8 + - + +
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Residues in contact with GLN 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLY* 5.5 3.4 + - - -
278D GLN* 6.4 0.4 - - - +
279D LEU* 4.0 17.0 - - + -
372D ASP* 3.2 32.4 + - + +
374D LEU* 1.3 74.7 - - - +
376D VAL* 1.3 60.5 + - - +
378D ARG* 3.3 20.1 + - - +
379D LEU* 2.9 62.1 + - + +
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Residues in contact with VAL 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU* 4.0 20.2 - - + -
283D ASP* 4.9 1.8 - - - +
287D LEU* 4.2 17.5 - - + -
363D PHE* 3.7 31.9 - - + +
364D SER 3.8 3.1 - - - +
365D ALA* 3.7 20.6 - - + +
370D VAL* 4.0 16.4 - - + -
372D ASP 3.0 16.7 + - - +
373D GLN* 3.8 4.3 - - - +
375D GLN* 1.3 76.3 - - - +
377D GLU* 1.3 56.5 + - - +
379D LEU* 3.2 10.8 + - - +
380D GLN* 2.9 26.2 + - - +
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Residues in contact with GLU 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C GLU* 5.5 0.7 - - - +
356C LYS* 2.8 35.5 + - - +
421C ARG* 6.1 2.9 - - - +
365D ALA* 3.5 19.5 - - + +
373D GLN* 3.0 33.3 + - - +
374D LEU* 3.6 16.4 + - + +
376D VAL* 1.3 71.6 - - - +
378D ARG* 1.3 63.3 + - + +
380D GLN* 3.1 10.5 + - - +
381D HIS* 2.8 32.8 + - - +
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Residues in contact with ARG 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU* 3.0 62.6 + - + +
375D GLN* 3.3 23.8 + - - +
377D GLU* 1.3 77.0 - - + +
379D LEU* 1.3 64.9 + - + +
381D HIS* 3.5 10.7 + - - +
382D THR* 3.4 19.8 + - - -
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Residues in contact with LEU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D PRO 4.0 15.5 - - - +
275D GLY* 3.8 26.5 - - - +
279D LEU* 4.3 11.0 - - + -
363D PHE* 3.5 38.4 - - + -
375D GLN* 2.9 41.6 + - + +
376D VAL* 3.4 7.6 - - - +
378D ARG* 1.3 78.1 - - + +
380D GLN* 1.3 62.2 + - - +
382D THR* 3.2 17.1 + - - +
383D TYR* 3.2 19.4 - - + -
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Residues in contact with GLN 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C LEU* 4.4 18.5 - - - +
421C ARG* 5.7 2.6 + - - -
360D ILE* 2.9 43.2 + - + +
363D PHE* 3.0 32.9 + - + +
364D SER* 3.9 11.1 + - - +
365D ALA 5.6 1.0 + - - -
376D VAL 2.9 10.6 + - - +
377D GLU* 3.1 9.9 + - - +
379D LEU* 1.3 73.8 - - - +
381D HIS* 1.3 67.1 + - - +
383D TYR* 3.0 9.3 + - - +
384D VAL* 3.0 31.1 + - + +
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Residues in contact with HIS 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C GLY* 5.9 7.9 - - - -
417C LYS* 6.4 0.2 - - - -
420C LEU* 6.3 1.1 - - - -
377D GLU 2.8 20.1 + - - +
378D ARG* 3.6 10.8 - - - +
379D LEU 3.3 0.2 - - - -
380D GLN* 1.3 73.5 + - - +
382D THR* 1.3 62.1 - - - +
384D VAL* 3.3 8.6 + - - +
385D GLU* 2.9 55.6 + - + +
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Residues in contact with THR 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D GLU* 6.5 1.1 - - + -
208D GLN* 5.2 2.8 + - + +
211D MET* 3.8 19.3 - - + -
378D ARG 3.4 10.5 + - - -
379D LEU* 3.2 13.1 + - - +
380D GLN 3.1 1.0 - - - -
381D HIS* 1.3 85.7 - - - +
383D TYR* 1.3 61.9 + - + +
385D GLU* 3.6 11.4 + - - +
386D ALA* 3.1 25.1 + - - +
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Residues in contact with TYR 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D MET* 3.4 38.6 - - + -
215D LEU* 3.8 19.3 - - + -
273D LEU* 3.9 5.5 - - + +
274D PRO* 3.1 39.7 + - - +
356D LEU* 4.1 9.6 - - + +
359D ALA* 3.8 19.3 - - + -
360D ILE* 3.8 20.2 - - + +
363D PHE* 3.5 32.4 - + - -
379D LEU* 3.2 26.7 - - + -
380D GLN* 3.0 6.7 + - - +
382D THR* 1.3 80.3 - - + +
384D VAL* 1.3 59.5 + - - +
386D ALA* 3.6 2.2 - - - +
387D LEU* 2.8 30.8 + - - +
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Residues in contact with VAL 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ALA* 3.9 21.3 - - + -
420C LEU* 3.8 33.7 - - + -
360D ILE* 3.9 28.7 - - + -
380D GLN* 3.0 29.2 + - + +
381D HIS* 3.8 9.6 - - - +
383D TYR* 1.3 74.4 - - - +
385D GLU* 1.3 58.6 + - - +
387D LEU* 3.2 3.2 + - - +
388D HIS* 2.9 28.8 + - + +
402D PHE* 4.0 10.7 - - + -
406D LEU* 4.8 5.4 - - + -
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Residues in contact with GLU 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D GLN* 3.8 15.0 + - - +
381D HIS* 2.9 44.5 + - + +
382D THR* 3.7 10.8 + - - +
384D VAL* 1.3 79.1 - - - +
386D ALA* 1.3 60.0 + - - +
388D HIS* 3.5 7.8 + - - +
389D ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D LEU* 4.0 2.6 - - - +
208D GLN* 3.8 26.4 - - + +
211D MET* 3.6 21.8 - - + -
212D ILE* 4.6 6.3 - - + -
356D LEU* 4.2 11.0 - - + -
382D THR 3.1 17.2 + - - +
383D TYR 3.2 5.6 + - - +
385D GLU* 1.3 75.4 - - - +
387D LEU* 1.3 60.2 + - - +
389D ALA* 3.4 2.8 + - - +
390D TYR* 2.9 31.0 + - - +
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Residues in contact with LEU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D GLU* 4.2 14.4 - - + +
356D LEU* 3.6 29.4 - - + +
357D LEU* 4.1 16.6 - - + -
360D ILE* 3.9 22.2 - - + -
383D TYR 2.8 16.3 + - - +
384D VAL 3.5 4.7 - - - +
386D ALA* 1.3 76.2 - - - +
388D HIS* 1.3 65.6 + - - +
390D TYR* 3.2 3.9 + - + +
391D VAL* 2.8 30.7 + - + +
402D PHE* 3.8 18.2 - - + -
405D MET* 3.9 35.4 - - + -
406D LEU* 4.6 4.5 - - + -
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Residues in contact with HIS 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C GLU* 4.2 19.2 + - - -
405C LYS* 6.3 0.4 - - - -
412C PRO 4.9 12.9 + - - -
415C PHE* 5.5 2.0 - + - -
416C ALA* 6.0 1.1 - - + -
384D VAL 2.9 12.2 + - - +
385D GLU* 3.7 8.1 - - + +
386D ALA 3.3 0.2 - - - -
387D LEU* 1.3 77.5 - - - +
389D ALA* 1.3 66.2 + - - +
391D VAL* 3.2 2.0 + - + +
392D SER* 3.0 35.0 + - - -
402D PHE* 3.1 54.1 - + + +
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D GLN 5.3 2.0 - - - +
204D LEU* 3.9 21.1 - - + +
208D GLN* 4.2 14.8 - - - +
385D GLU 3.1 17.1 + - - +
386D ALA 3.8 3.6 - - - +
388D HIS* 1.3 79.1 - - - +
390D TYR* 1.3 63.5 + - - +
392D SER* 3.3 5.9 + - - -
393D ILE* 2.9 31.1 + - + +
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Residues in contact with TYR 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D LEU* 3.8 18.1 - - + +
209D LEU* 6.0 2.5 - - + -
212D ILE* 3.7 26.2 - - + -
350D ASN* 2.9 26.5 + - - -
352D ALA* 3.6 21.1 - - + +
353D GLU* 3.6 36.3 - - + -
356D LEU* 4.6 4.9 - - + -
386D ALA 2.9 19.0 + - - +
387D LEU* 3.6 7.4 - - + +
389D ALA* 1.3 78.0 - - - +
391D VAL* 1.3 57.1 + - + +
394D ASN* 2.8 63.1 + - + +
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Residues in contact with VAL 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D GLU* 4.5 9.9 - - + +
387D LEU* 2.8 28.1 + - + +
388D HIS* 3.8 3.1 - - - +
390D TYR* 1.3 72.2 - - - +
392D SER* 1.3 62.0 + - - +
395D HIS* 2.7 38.6 + - + +
398D ASP 4.8 1.3 - - - +
399D PRO* 4.7 4.9 - - + +
401D MET* 4.1 16.2 - - + -
402D PHE* 3.8 33.7 - - + +
405D MET* 2.9 34.5 - - + -
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Residues in contact with SER 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D PRO 5.7 0.3 + - - -
388D HIS* 3.0 28.6 + - - -
389D ALA* 3.7 6.4 + - - -
391D VAL* 1.3 83.7 - - - +
393D ILE* 1.3 62.9 + - - +
395D HIS 4.8 2.5 - - - -
396D PRO* 3.7 19.8 - - - +
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Residues in contact with ILE 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D PRO 4.1 12.3 - - - +
203D GLN* 3.2 31.4 - - + +
204D LEU* 3.0 52.3 - - + +
389D ALA* 2.9 17.0 + - + +
390D TYR 4.1 1.8 - - - +
392D SER* 1.3 82.4 - - - +
394D ASN* 1.3 74.8 + - - +
395D HIS 3.6 0.2 - - - -
396D PRO* 3.5 16.9 - - - +
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Residues in contact with ASN 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 4.3 3.3 - - - +
350D ASN* 5.9 0.9 - - - +
390D TYR* 2.8 63.6 + - + +
393D ILE* 1.3 85.4 + - - +
395D HIS* 1.3 77.3 + - + +
396D PRO* 3.3 8.8 - - - +
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Residues in contact with HIS 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU 5.3 1.6 - - - -
348D GLN 4.8 10.3 - - - -
349D LEU* 5.8 0.2 - - - -
350D ASN* 5.5 1.4 + - - -
353D GLU* 2.6 34.7 + - - -
390D TYR* 5.1 0.2 - - - -
391D VAL* 2.7 32.8 + - - +
392D SER* 4.8 1.6 - - - -
394D ASN* 1.3 91.0 + - + +
396D PRO* 1.3 65.0 - - - +
397D HIS 3.2 2.7 - - - -
398D ASP* 3.0 40.2 + - + +
399D PRO* 4.7 1.2 - - - +
401D MET* 3.9 30.1 - - + +
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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