Contacts of the helix formed by residues 375 - 395 (chain A) in PDB entry 4FYT
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 SER 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A PHE* 3.7 6.6 - - - -
373A SER 3.9 0.4 + - - -
374A SER* 1.3 75.3 - - - +
376A SER* 1.3 59.7 + - - +
377A SER* 3.4 3.9 + - - -
378A ASN* 2.9 27.5 + - - +
379A LYS 3.0 21.7 + - - -
790A PRO* 3.6 21.4 - - - +
791A ASN* 3.5 17.5 - - - -
827A LYS* 4.4 1.5 - - - +
1017A SO4 2.6 29.6 + - - -
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PHE* 5.9 0.2 - - - -
375A SER* 1.3 71.9 - - - +
377A SER* 1.3 58.1 + - - +
379A LYS* 3.2 11.2 + - - +
380A GLU* 2.9 28.8 + - - +
429A TRP* 5.2 1.6 - - - -
743A ILE* 4.8 3.5 - - - +
747A LEU* 3.7 18.1 - - - +
750A GLN* 2.6 32.0 + - - -
751A TYR* 3.7 5.9 + - - -
791A ASN* 2.9 17.8 + - - -
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Residues in contact with SER 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A SER* 3.2 4.9 - - - -
376A SER* 1.3 79.7 - - - +
378A ASN* 1.3 62.5 + - - +
380A GLU* 3.3 5.5 + - - +
381A ARG* 3.0 21.7 + - - +
751A TYR* 3.4 26.9 + - - -
791A ASN* 5.4 0.6 - - - -
1017A SO4 3.1 29.9 + - - -
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Residues in contact with ASN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASN 5.2 1.1 - - - +
369A PHE* 4.5 1.3 - - + -
374A SER* 3.5 4.9 - - - -
375A SER* 2.9 35.4 + - - +
377A SER* 1.3 74.4 - - - +
379A LYS* 1.3 62.7 + - - +
381A ARG* 3.1 12.9 + - - +
382A VAL* 3.0 27.7 + - + +
823A ASN* 3.4 38.3 - - - +
827A LYS* 2.8 28.5 + - - +
1017A SO4 3.8 14.5 + - - -
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Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A TYR* 3.5 43.4 - - + -
369A PHE* 3.4 42.1 - - + -
375A SER 3.0 8.4 + - - +
376A SER* 3.2 13.0 + - - +
378A ASN* 1.3 72.8 - - - +
380A GLU* 1.3 64.9 + - - +
382A VAL* 3.2 5.7 + - - +
383A VAL* 3.1 22.7 + - - +
426A GLU* 4.5 1.8 + - - -
429A TRP* 3.8 25.4 - - + -
1005A NAG 4.1 11.5 + - - -
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A SER 2.9 7.7 + - - +
377A SER* 3.5 7.2 + - - +
379A LYS* 1.3 76.5 - - - +
381A ARG* 1.3 53.8 + - - +
383A VAL* 3.5 0.5 + - - +
384A THR* 2.7 50.2 + - + +
419A TYR* 5.7 2.6 - - - -
429A TRP* 3.8 16.3 - - + -
431A LEU* 3.9 22.3 - - + +
434A LEU* 3.5 23.0 - - - +
438A ASN* 4.5 8.8 + - - -
747A LEU* 4.5 0.8 - - + +
751A TYR* 2.5 50.0 + - - +
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Residues in contact with ARG 381 (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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352A GLY* 3.9 6.5 - - - -
365A ASN* 3.6 22.6 + - - +
366A SER* 2.7 28.4 + - - +
377A SER 3.0 12.7 + - - +
378A ASN* 3.1 16.6 + - - +
380A GLU* 1.3 76.6 - - - +
382A VAL* 1.3 58.1 + - - +
384A THR* 3.5 5.4 - - - -
385A VAL* 2.9 51.5 + - + +
2B VAL* 4.2 12.5 - - - +
4B ASP* 2.5 41.1 + - - +
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Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A TYR* 3.8 22.7 - - + -
317A ALA* 4.9 1.3 - - - -
365A ASN 4.5 5.6 - - - +
366A SER 3.6 21.6 - - - +
367A LEU 3.6 17.7 - - - +
368A LEU 3.6 24.2 - - - +
369A PHE* 4.4 8.1 - - + -
378A ASN* 3.0 15.0 + - + +
379A LYS 3.2 7.4 + - - +
381A ARG* 1.3 76.0 - - - +
383A VAL* 1.3 64.2 + - - +
386A ILE* 3.0 41.2 + - + +
823A ASN* 6.0 0.7 - - - +
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A TYR* 3.5 22.7 - - + +
320A VAL* 4.2 8.5 - - + -
324A ILE* 3.9 21.4 - - + +
379A LYS 3.1 11.5 + - - +
380A GLU* 3.5 10.1 - - - +
382A VAL* 1.3 79.3 - - - +
384A THR* 1.3 62.3 + - + +
386A ILE* 3.9 4.3 - - - +
387A ALA* 2.9 27.7 + - - +
422A ALA* 4.2 18.4 - - + +
425A ALA* 4.0 16.8 - - + -
426A GLU* 4.5 2.5 - - + -
429A TRP* 3.7 24.5 - - + -
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Residues in contact with THR 384 (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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380A GLU* 2.7 42.2 + - + +
381A ARG* 3.2 12.6 + - - -
383A VAL* 1.3 75.0 - - + +
385A VAL* 1.3 62.3 + - - +
387A ALA* 3.4 2.6 + - - +
388A HIS* 2.8 29.8 + - - +
418A GLU* 3.7 24.6 - - + +
419A TYR* 5.6 7.2 - - + -
422A ALA* 3.9 22.0 - - + -
431A LEU* 4.2 8.7 - - + -
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Residues in contact with VAL 385 (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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352A GLY 4.8 0.4 - - - +
353A ALA* 3.6 30.1 - - + -
362A TYR* 3.9 11.2 - - + -
366A SER* 4.1 10.5 - - - +
381A ARG* 2.9 53.3 + - + +
382A VAL 4.2 1.8 - - - +
384A THR* 1.3 75.7 - - - +
386A ILE* 1.3 67.7 + - - +
388A HIS* 3.2 6.3 + - - +
389A GLU* 3.0 27.4 + - - +
2B VAL* 4.4 17.3 - - + -
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Residues in contact with ILE 386 (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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317A ALA* 3.8 24.2 - - + -
320A VAL* 3.9 12.8 - - + -
321A THR* 3.6 24.9 - - + +
324A ILE* 4.6 6.5 - - + -
362A TYR* 3.6 32.0 + - + +
366A SER 4.7 0.7 - - - +
367A LEU* 4.1 4.7 - - + -
382A VAL* 3.0 40.2 + - + +
383A VAL* 3.9 3.8 - - - +
385A VAL* 1.3 76.5 - - - +
387A ALA* 1.3 63.0 + - - +
389A GLU* 3.3 1.4 + - - +
390A LEU* 2.9 41.7 + - + +
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Residues in contact with ALA 387 (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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324A ILE* 4.1 18.4 - - + -
328A PHE* 3.3 8.9 - - + -
383A VAL 2.9 20.4 + - - +
384A THR 3.7 3.1 - - - +
386A ILE* 1.3 75.5 - - - +
388A HIS* 1.3 57.0 + - - +
391A ALA* 2.9 27.0 + - - +
418A GLU* 3.3 28.9 - - - +
421A GLY* 4.2 5.2 - - - -
422A ALA* 3.7 13.5 - - + +
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Residues in contact with HIS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A THR 2.8 21.1 + - - +
385A VAL* 3.2 8.7 + - - +
387A ALA* 1.3 74.2 - - - +
389A GLU* 1.3 73.4 + - - +
391A ALA* 3.1 13.6 + - - +
392A HIS* 3.2 11.2 + - - -
411A GLU* 3.7 3.8 - - - -
414A ALA* 3.4 23.3 + - + +
415A SER* 3.6 19.3 - - - -
418A GLU* 2.8 30.4 + - - +
477A TYR* 3.9 5.8 - + - -
1012A ZN 2.0 37.1 - - - -
1B L2O 3.0 13.7 + - - -
2B VAL* 3.9 11.0 - - + +
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Residues in contact with GLU 389 (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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353A ALA* 3.4 28.6 - - + +
354A MET 3.9 3.1 - - - -
355A GLU* 3.3 9.9 + - + +
360A VAL* 3.6 28.3 - - + -
362A TYR* 4.3 4.0 - - + +
385A VAL* 3.0 18.2 + - + +
386A ILE 4.1 2.0 - - - +
388A HIS* 1.3 80.7 - - - +
390A LEU* 1.3 61.9 + - + +
392A HIS* 3.3 18.0 + - - +
393A GLN* 2.9 23.2 + - - -
1B L2O 2.6 33.9 + - - +
2B VAL* 3.3 21.1 + - - +
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Residues in contact with LEU 390 (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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321A THR* 3.4 29.8 - - + +
324A ILE* 3.9 15.5 - - + -
325A LEU* 3.9 26.2 - - + +
328A PHE* 3.9 13.2 - - + -
341A SER* 4.2 17.3 - - - +
343A GLN* 4.3 15.9 - - - +
360A VAL* 4.9 4.0 - - + -
362A TYR* 5.3 0.2 - - - +
386A ILE* 2.9 37.4 + - + +
387A ALA 3.8 3.6 - - - +
389A GLU* 1.3 75.0 - - - +
391A ALA* 1.3 65.5 + - - +
393A GLN* 2.9 25.5 + - + +
394A TRP* 3.2 11.6 - - - -
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Residues in contact with ALA 391 (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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328A PHE* 3.5 10.9 - - + -
387A ALA 2.9 15.8 + - - +
388A HIS 3.1 11.0 + - - +
390A LEU* 1.3 75.8 - - - +
392A HIS* 1.3 58.3 + - - +
394A TRP* 3.1 11.6 + - - +
395A PHE* 3.0 27.4 + - + -
414A ALA* 3.9 16.2 - - - +
417A VAL* 3.7 34.1 - - + -
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Residues in contact with HIS 392 (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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355A GLU* 3.4 27.9 + - + -
388A HIS* 3.2 14.1 + + - -
389A GLU* 3.3 21.5 + - - +
390A LEU 3.1 0.6 - - - -
391A ALA* 1.3 74.1 - - - +
393A GLN* 1.3 65.4 + - - +
394A TRP 3.0 3.2 + - - -
395A PHE 2.9 23.4 + - - -
396A GLY* 3.4 4.1 + - - -
397A ASN* 2.9 25.5 + - - +
410A ASN* 3.2 30.7 + - + +
411A GLU* 3.4 14.3 + - - -
414A ALA* 3.4 5.3 - - + +
1012A ZN 2.1 36.0 - - - -
1B L2O 2.8 10.6 + - - -
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Residues in contact with GLN 393 (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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325A LEU* 4.5 0.4 - - + -
336A TYR* 3.8 27.1 + - + -
337A PRO* 6.0 0.9 - - - +
341A SER* 5.1 2.0 + - - +
355A GLU* 3.3 21.8 + - - +
357A TRP* 3.2 34.8 + - - +
358A GLY 4.0 3.5 + - - -
360A VAL* 4.0 14.2 - - - +
389A GLU 2.9 23.0 + - - -
390A LEU* 2.9 32.5 + - + +
392A HIS* 1.3 75.9 - - - +
394A TRP* 1.3 72.0 + - + +
397A ASN* 3.2 11.5 + - - +
398A LEU* 3.1 26.5 + - - +
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Residues in contact with TRP 394 (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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325A LEU* 3.5 40.4 - - + -
328A PHE* 3.6 24.8 + + + -
329A ALA* 3.5 26.8 - - + +
332A TYR* 4.7 6.7 - + + +
334A THR* 2.8 46.1 + - + +
335A PRO 4.2 3.0 + - - -
336A TYR* 4.1 16.4 - - + -
390A LEU 3.2 23.8 - - - -
391A ALA* 3.1 6.7 + - - +
392A HIS 3.0 0.2 - - - -
393A GLN* 1.3 87.9 - - + +
395A PHE* 1.3 73.3 + - + +
396A GLY 3.2 6.6 + - - -
398A LEU* 3.8 8.7 - - + +
399A VAL* 3.2 22.3 + - - +
504A LEU* 3.8 26.0 - - + +
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A TYR* 4.0 37.7 - + - -
391A ALA* 3.0 21.3 + - + +
392A HIS* 2.9 28.1 + - - -
394A TRP* 1.3 79.0 - - + +
396A GLY* 1.3 57.1 + - - +
399A VAL* 4.3 2.0 - - - -
409A LEU 4.0 6.1 - - - +
410A ASN* 3.6 11.2 - - - +
413A PHE* 3.6 52.7 - + + -
414A ALA 5.0 0.9 - - - +
417A VAL* 4.2 14.1 - - + -
500A LEU* 4.1 14.1 - - + -
503A TYR* 4.3 14.8 - + - -
504A LEU* 3.9 34.3 - - + -
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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