Contacts of the helix formed by residues 364 - 389 (chain W) in PDB entry 3FKS
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 GLY 364 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360W ALA* 3.2 15.7 + - - -
362W VAL 3.2 5.7 - - - -
363W VAL* 1.3 81.4 - - - +
365W GLN* 1.3 61.5 + - - -
366W GLU* 3.3 3.1 - - - -
367W HIS* 3.4 3.0 + - - -
368W TYR* 3.0 30.0 + - - +
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Residues in contact with GLN 365 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360W ALA* 3.5 28.1 + - + +
364W GLY* 1.3 69.2 - - - -
366W GLU* 1.3 67.3 + - - +
368W TYR* 4.2 7.9 - - - -
369W ASP* 3.1 62.1 + - - +
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Residues in contact with GLU 366 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364W GLY* 3.3 1.1 - - - -
365W GLN* 1.3 79.3 - - - +
367W HIS* 1.3 63.8 + - - +
369W ASP* 3.9 5.0 - - - +
370W VAL* 3.3 27.0 + - - +
438W VAL* 4.0 15.8 - - + +
439W ALA* 5.7 2.6 + - - +
442W LYS* 2.7 38.3 + - - +
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Residues in contact with HIS 367 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142W ASP 3.2 21.0 + - - -
143W LEU* 3.1 36.4 - - + +
146W PRO* 4.9 1.5 - - + +
358W LEU* 4.7 5.6 - - + +
363W VAL* 3.5 43.8 - - + +
364W GLY* 3.4 10.0 + - - +
366W GLU* 1.3 76.3 - - - +
368W TYR* 1.3 67.6 + - - +
369W ASP 2.9 1.7 + - - -
370W VAL* 3.1 4.4 + - - +
371W ALA* 3.0 22.8 + - + +
434W LEU* 3.3 19.0 - - + +
438W VAL* 3.5 33.9 - - + +
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Residues in contact with TYR 368 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364T ARG* 5.8 2.1 + - - -
358W LEU* 3.3 35.7 - - + -
359W ASP* 3.9 10.5 - - - -
360W ALA* 3.5 33.9 - - + -
363W VAL* 4.1 1.5 - - + +
364W GLY 3.0 14.7 + - - +
365W GLN* 3.9 11.7 - - - +
367W HIS* 1.3 82.2 + - - +
369W ASP* 1.3 61.9 + - - +
371W ALA* 3.7 4.0 + - - +
372W SER* 2.9 52.6 + - - -
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Residues in contact with ASP 369 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365W GLN* 3.1 45.5 + - - +
366W GLU* 3.9 4.9 - - - +
367W HIS 2.9 1.6 + - - -
368W TYR* 1.3 78.3 - - - +
370W VAL* 1.3 68.1 + - + +
371W ALA 3.2 1.0 + - - -
372W SER* 3.3 5.9 + - - -
373W LYS* 3.2 32.1 + - - +
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Residues in contact with VAL 370 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143W LEU* 4.5 9.2 - - + -
366W GLU 3.3 15.0 + - - +
367W HIS* 3.1 6.1 + - - +
369W ASP* 1.3 78.1 - - + +
371W ALA* 1.3 63.7 + - - +
373W LYS* 4.8 2.7 - - - -
374W VAL* 3.3 16.6 + - + +
438W VAL* 3.9 13.5 - - + +
441W PHE* 3.8 16.8 - - + -
442W LYS* 3.5 61.5 - - + +
445W LEU* 3.3 15.4 - - + +
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Residues in contact with ALA 371 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143W LEU* 3.7 37.0 - - + +
144W LEU* 4.2 6.0 - - + +
358W LEU* 4.5 13.7 - - + -
367W HIS* 3.0 20.1 + - - +
368W TYR 4.0 3.1 - - - +
370W VAL* 1.3 76.3 - - - +
372W SER* 1.3 58.4 + - - +
374W VAL* 2.8 28.4 + - - +
375W GLN* 3.0 16.9 + - + +
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Residues in contact with SER 372 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358W LEU* 5.8 2.8 - - - +
368W TYR* 2.9 44.8 + - - -
369W ASP* 3.3 4.9 + - - -
371W ALA* 1.3 76.9 - - - +
373W LYS* 1.3 58.4 + - - +
375W GLN* 3.6 16.8 + - - +
376W GLU* 3.0 30.5 + - - +
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Residues in contact with LYS 373 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369W ASP* 3.2 19.6 + - - +
370W VAL* 3.6 3.1 - - - +
371W ALA 3.1 0.6 - - - -
372W SER* 1.3 75.5 - - - +
374W VAL* 1.3 55.7 + - - +
376W GLU* 2.9 15.3 + - - +
377W THR* 2.6 40.4 + - - +
445W LEU* 3.5 35.1 - - + +
446W GLU* 6.0 3.8 - - - +
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Residues in contact with VAL 374 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143W LEU* 4.3 9.4 - - + -
144W LEU* 3.7 23.8 - - + -
370W VAL 3.4 15.5 - - - +
371W ALA* 2.8 13.1 + - - +
373W LYS* 1.3 73.2 - - - +
375W GLN* 1.3 63.6 + - - +
377W THR* 3.3 5.3 + - - -
378W LEU* 3.1 45.1 + - + +
410W ILE* 3.9 15.9 - - + -
414W LEU* 5.1 0.9 - - + -
441W PHE* 3.9 26.2 - - + -
445W LEU* 3.8 15.2 - - + +
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Residues in contact with GLN 375 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144W LEU* 4.0 26.9 + - + +
350W PRO 4.6 11.5 + - - +
351W LEU* 3.5 28.1 + - + +
353W SER 4.6 5.7 + - - -
354W LYS* 5.4 5.3 - - - +
358W LEU* 3.8 28.7 - - - +
371W ALA* 3.0 13.3 + - - +
372W SER* 3.8 17.6 + - - +
374W VAL* 1.3 77.9 - - - +
376W GLU* 1.3 57.3 + - - +
378W LEU* 4.8 1.3 - - - -
379W GLN* 3.0 30.0 + - - +
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Residues in contact with GLU 376 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372W SER* 3.0 16.6 + - - +
373W LYS* 2.9 20.0 + - - +
375W GLN* 1.3 76.0 - - - +
377W THR* 1.3 64.4 + - - +
379W GLN* 3.2 5.7 + - + +
380W THR* 3.1 35.3 + - + +
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Residues in contact with THR 377 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373W LYS* 2.6 23.1 + - - +
374W VAL* 3.8 5.6 - - - -
376W GLU* 1.3 72.2 - - - +
378W LEU* 1.3 59.2 + - - +
380W THR* 2.8 21.5 + - - -
381W TYR* 3.2 12.8 + - - +
403W THR* 3.4 36.1 - - + +
406W ARG* 4.8 5.6 - - + -
407W ALA* 3.6 17.6 - - + +
410W ILE* 5.1 4.0 - - + -
445W LEU* 3.6 20.5 - - + +
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Residues in contact with LEU 378 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144W LEU* 5.1 0.2 - - + -
350W PRO* 4.0 26.0 - - + -
351W LEU* 4.4 13.4 - - + +
374W VAL* 3.1 37.7 + - + +
375W GLN* 4.2 5.2 - - - +
377W THR* 1.3 76.1 - - - +
379W GLN* 1.3 60.9 + - - +
381W TYR* 3.5 9.5 + - + +
382W LYS* 3.0 27.5 + - - +
407W ALA* 3.6 33.0 - - + +
410W ILE* 4.4 4.3 - - + -
411W GLN* 4.1 27.6 - - + +
414W LEU* 4.2 10.5 - - + -
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Residues in contact with GLN 379 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360T TYR* 4.9 12.3 + - - -
351W LEU* 3.5 34.2 - - - +
375W GLN 3.0 18.0 + - - +
376W GLU* 3.2 7.6 + - + +
378W LEU* 1.3 77.6 - - - +
380W THR* 1.3 63.5 + - + +
382W LYS* 3.3 18.9 + - - +
383W SER* 3.2 19.6 + - - -
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Residues in contact with THR 380 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376W GLU* 3.1 19.8 + - + +
377W THR* 2.8 24.3 + - - -
379W GLN* 1.3 74.8 - - + +
381W TYR* 1.3 65.8 + - - +
383W SER* 2.8 26.8 + - - +
384W LEU* 2.9 23.0 + - - +
403W THR* 4.7 11.8 + - - -
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Residues in contact with TYR 381 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377W THR 3.2 13.2 + - - +
378W LEU* 3.6 10.8 - - + +
380W THR* 1.3 81.2 + - - +
382W LYS* 1.3 65.5 + - - +
384W LEU* 3.3 18.1 + - - +
385W GLN* 3.3 39.2 + - + +
388W ILE* 5.5 3.5 - - + +
403W THR 5.4 0.2 - - - +
404W VAL* 4.0 25.8 - - + -
407W ALA* 3.8 23.1 - - + -
408W ARG* 3.5 42.8 + - + +
411W GLN* 4.2 25.0 + - - -
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Residues in contact with LYS 382 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351W LEU* 4.0 15.8 - - + +
378W LEU 3.0 14.7 + - - +
379W GLN* 3.3 28.9 - - - +
380W THR 3.1 0.2 - - - -
381W TYR* 1.3 81.5 - - + +
383W SER* 1.3 57.8 + - - +
384W LEU 3.2 0.9 + - - -
385W GLN* 3.7 21.8 + - + +
386W ASP* 5.0 1.9 + - - +
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Residues in contact with SER 383 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379W GLN 3.2 6.3 + - - -
380W THR* 2.8 27.4 + - - +
382W LYS* 1.3 77.8 - - - +
384W LEU* 1.3 64.8 + - - +
385W GLN 3.4 0.7 - - - -
386W ASP* 4.2 14.2 - - - +
387W ILE* 3.9 9.7 - - - +
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Residues in contact with LEU 384 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380W THR* 2.9 28.6 + - - +
381W TYR* 3.7 7.9 - - - +
382W LYS 3.2 0.6 - - - -
383W SER* 1.3 78.4 - - - +
385W GLN* 1.3 65.9 + - - +
386W ASP 3.1 3.8 + - - -
387W ILE* 3.5 22.2 - - + +
388W ILE* 3.0 39.3 + - + +
396W LEU* 4.5 16.2 - - + -
400W ASP* 4.5 23.6 - - - +
403W THR* 4.9 3.4 - - - +
404W VAL* 3.5 27.1 - - + -
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Residues in contact with GLN 385 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381W TYR* 3.3 49.2 + - + +
382W LYS* 3.7 17.5 - - + +
383W SER 3.4 0.6 - - - -
384W LEU* 1.3 77.9 - - - +
386W ASP* 1.3 59.3 + - - +
388W ILE* 3.8 16.3 - - - +
389W ALA* 2.8 35.9 + - - +
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Residues in contact with ASP 386 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382W LYS 5.6 1.3 - - - -
383W SER* 4.2 11.8 - - - +
384W LEU 3.1 1.0 + - - -
385W GLN* 1.3 79.3 - - - +
387W ILE* 1.3 67.9 + - + +
389W ALA* 3.0 20.2 + - - +
390W ILE* 3.4 18.5 + - - +
24Y LYS* 5.7 6.4 + - - +
234Y ARG* 5.8 2.9 - - - +
238Y ASP* 5.2 7.6 - - - +
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Residues in contact with ILE 387 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383W SER 3.9 8.1 - - - +
384W LEU* 3.5 40.2 - - + +
386W ASP* 1.3 81.2 - - + +
388W ILE* 1.3 62.4 + - + +
390W ILE* 3.8 5.6 - - - +
391W LEU* 2.9 51.4 + - + +
392W GLY 3.6 1.3 + - - +
395W GLU* 6.3 0.2 - - + -
396W LEU* 5.5 4.5 - - + -
173Y LEU* 4.3 33.7 - - + -
234Y ARG* 5.8 4.5 - - - +
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Residues in contact with ILE 388 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381W TYR* 5.5 3.1 - - + +
384W LEU* 3.0 39.2 + - + +
385W GLN* 3.8 19.7 - - - +
386W ASP 3.1 0.8 - - - -
387W ILE* 1.3 77.9 - - + +
389W ALA* 1.3 59.6 + - - +
390W ILE 3.1 6.0 + - - -
392W GLY* 3.5 32.5 + - - +
393W MET* 5.6 3.4 - - + -
396W LEU* 4.1 29.2 - - + -
404W VAL* 4.6 13.5 - - + -
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Residues in contact with ALA 389 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385W GLN* 2.8 22.9 + - - +
386W ASP* 3.0 7.4 + - - +
388W ILE* 1.3 76.9 - - - +
390W ILE* 1.3 69.4 + - + +
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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