Contacts of the helix formed by residues 329 - 355 (chain B) in PDB entry 4XK8
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 329 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B THR 3.3 19.4 + - - -
326B ILE 3.0 16.6 + - - +
328B ASN* 1.3 76.6 - - - +
330B ILE* 1.3 63.0 + - - +
331B HIS 3.2 0.5 + - - -
332B PHE* 3.2 15.8 + - - +
333B GLN* 3.4 6.7 + - - +
393B PHE* 3.2 21.7 - - - +
397B ASP* 2.5 37.5 + - - -
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLU* 5.7 4.0 + - - +
42B LEU* 3.9 22.4 - - + -
43B TYR* 3.6 44.0 - - + +
46B ILE* 3.7 34.8 - - + -
328B ASN 3.7 3.3 + - - +
329B SER* 1.3 72.8 - - - +
331B HIS* 1.3 60.8 + - + +
333B GLN* 3.3 19.1 + - + +
334B LEU* 2.9 30.3 + - + +
397B ASP* 4.2 2.4 + - - -
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Residues in contact with HIS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 5.5 1.3 - - - -
32B GLU* 2.5 35.7 + - - -
329B SER* 3.1 6.0 + - - +
330B ILE* 1.3 78.2 - - + +
332B PHE* 1.3 59.8 + - - +
334B LEU* 3.3 4.8 + - + +
335B GLY* 2.9 23.4 + - - -
389B HIS* 2.9 59.8 + + - +
392B ILE* 3.4 31.7 - - + +
393B PHE* 3.9 10.1 - - - +
396B ARG* 3.9 7.5 + - - -
397B ASP* 3.7 15.7 - - - -
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Residues in contact with PHE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 5.4 5.2 - - + -
325B THR* 4.3 4.5 - - - -
326B ILE* 3.7 35.2 - - + -
329B SER* 3.2 22.4 + - - +
331B HIS* 1.3 76.9 - - - +
333B GLN* 1.3 58.1 + - - +
335B GLY* 3.1 2.8 + - - -
336B LEU* 2.9 61.3 + - + +
389B HIS 5.0 0.2 - - - -
390B GLY* 6.1 1.1 - - - -
393B PHE* 3.5 47.5 - + + +
408B LEU* 4.1 19.5 - - + -
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 4.6 8.5 + - - -
174B ARG* 5.0 12.4 + - - +
326B ILE* 2.9 30.6 + - + +
327B ASN* 3.3 29.0 + - - +
329B SER 3.4 14.1 + - - +
330B ILE* 3.4 21.9 - - + +
332B PHE* 1.3 77.4 - - - +
334B LEU* 1.3 56.4 + - - +
336B LEU* 3.4 10.4 + - - +
337B ALA* 2.9 29.9 + - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 2.9 19.0 + - + +
331B HIS* 3.8 7.9 - - - +
333B GLN* 1.3 74.5 - - - +
335B GLY* 1.3 59.3 + - - +
337B ALA* 3.9 9.4 - - + -
338B LEU* 2.9 57.4 + - + +
389B HIS* 3.4 37.5 - - + +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B HIS 2.9 15.0 + - - -
332B PHE* 3.1 3.8 + - - -
334B LEU* 1.3 76.4 - - - +
336B LEU* 1.3 59.4 + - - +
338B LEU 3.4 0.2 + - - -
339B ALA* 2.9 32.3 + - - +
386B ALA* 3.6 25.1 - - - +
389B HIS* 4.3 2.7 - - - +
390B GLY* 4.8 3.6 - - - -
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 4.5 18.2 - - + -
332B PHE* 2.9 50.8 + - + +
333B GLN* 3.8 7.0 - - - +
335B GLY* 1.3 74.2 - - - +
337B ALA* 1.3 63.4 + - - +
339B ALA* 3.3 6.4 + - + +
340B SER* 3.0 30.2 + - - +
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLN 2.9 18.9 + - - +
334B LEU* 3.7 14.6 - - + +
336B LEU* 1.3 77.2 - - - +
338B LEU* 1.3 57.8 + - + +
340B SER* 3.4 4.0 + - - -
341B LEU* 2.9 33.0 + - - +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 2.9 48.6 + - + +
337B ALA* 1.3 74.3 - - + +
339B ALA* 1.3 60.6 + - - +
341B LEU* 4.2 11.0 - - + -
342B GLY* 2.9 25.1 + - - -
382B ILE* 3.1 39.4 - - + +
383B MET* 4.5 0.2 - - - +
385B GLY* 3.6 30.3 - - - +
386B ALA* 3.5 14.6 - - + +
389B HIS* 4.2 7.2 - - + -
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLY 2.9 18.6 + - - +
336B LEU* 3.6 7.0 - - + +
337B ALA 3.3 0.2 - - - -
338B LEU* 1.3 78.8 - - - +
340B SER* 1.3 64.3 + - - +
342B GLY* 3.2 1.0 + - - -
343B VAL* 3.0 29.4 + - + +
383B MET* 3.7 14.0 - - + +
386B ALA* 3.4 12.9 - - + +
387B PHE* 6.5 0.2 - - + -
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Residues in contact with SER 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 3.0 18.7 + - - +
337B ALA* 3.8 3.6 - - - -
339B ALA* 1.3 75.6 - - - +
341B LEU* 1.3 58.0 + - - +
343B VAL* 3.2 8.3 + - - +
344B ILE* 2.9 38.2 + - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ALA 2.9 19.4 + - - +
338B LEU* 3.8 13.7 - - + +
340B SER* 1.3 76.6 - - - +
342B GLY* 1.3 52.5 + - - +
344B ILE* 3.4 21.9 - - + +
345B THR* 2.5 41.4 + - - +
382B ILE* 3.9 26.7 - - + -
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Residues in contact with GLY 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU 2.9 17.2 + - - -
339B ALA 3.7 1.6 - - - -
341B LEU* 1.3 74.7 - - - +
343B VAL* 1.3 65.1 + - - +
345B THR* 3.1 6.9 + - - -
346B SER* 3.0 22.2 + - - -
379B ALA* 3.7 14.3 - - - +
382B ILE* 3.7 14.1 - - - +
383B MET* 4.2 12.8 - - - -
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ALA* 3.0 20.0 + - + +
340B SER* 3.5 9.6 - - - +
342B GLY* 1.3 76.3 - - - +
344B ILE* 1.3 63.7 + - + +
346B SER* 3.3 6.8 + - - -
347B LEU* 2.9 27.9 + - + +
383B MET* 4.3 12.0 - - + -
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B SER* 2.9 19.8 + - - +
341B LEU* 3.4 30.5 - - + +
343B VAL* 1.3 77.6 - - + +
345B THR* 1.3 60.2 + - - +
347B LEU* 3.4 21.9 - - + +
348B VAL* 2.9 36.9 + - + +
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B LEU* 2.5 33.8 + - - +
342B GLY* 3.1 6.3 + - - -
344B ILE* 1.3 77.0 - - - +
346B SER* 1.3 65.0 + - - +
348B VAL* 3.0 11.7 + - + +
349B ALA* 3.0 20.6 + - - +
375B HIS* 3.3 42.4 - - + +
378B ILE* 4.3 9.0 - - + -
379B ALA* 3.9 13.5 - - + +
382B ILE* 4.3 5.5 - - - +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLY 3.0 8.3 + - - -
343B VAL* 3.6 9.4 - - - -
345B THR* 1.3 76.8 - - - +
347B LEU* 1.3 57.7 + - - +
349B ALA* 3.1 4.1 + - - +
350B GLN* 2.9 38.3 + - - +
375B HIS 5.1 0.2 - - - -
376B GLN* 2.7 29.1 + - - -
379B ALA* 3.3 14.0 - - - +
383B MET* 6.2 0.2 - - - +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B VAL* 2.9 19.7 + - + +
344B ILE* 3.4 23.8 - - + +
346B SER* 1.3 76.5 - - - +
348B VAL* 1.3 57.6 + - - +
350B GLN* 3.4 4.9 + - + -
351B HIS* 2.9 73.0 + - + +
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 2.9 30.3 + - + +
345B THR* 3.0 13.2 + - + +
347B LEU* 1.3 75.9 - - + +
349B ALA* 1.3 57.9 + - - +
351B HIS* 5.0 2.0 - - - -
352B MET* 2.9 61.0 + - + +
375B HIS* 4.4 22.9 - - + +
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B THR 3.0 11.3 + - - +
346B SER 3.1 7.2 + - - +
348B VAL* 1.3 78.8 - - - +
350B GLN* 1.3 56.7 + - - +
352B MET* 3.9 2.7 - - - +
353B TYR* 3.0 31.0 + - - -
371B LEU 6.1 0.2 - - - -
372B TYR* 3.5 31.8 - - + +
375B HIS* 4.0 17.9 - - + +
376B GLN* 3.9 19.7 - - + +
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B SER* 2.9 24.2 + - - +
347B LEU* 3.9 6.5 - - + +
349B ALA* 1.3 75.8 - - - +
351B HIS* 1.3 70.9 + - + +
353B TYR* 3.0 36.2 + - + -
354B SER* 2.8 18.4 + - - -
372B TYR* 3.2 24.0 + - - +
376B GLN* 3.9 10.8 - - - +
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Residues in contact with HIS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 2.9 54.8 + - + +
348B VAL* 4.3 2.5 - - - +
350B GLN* 1.3 89.8 - - + +
352B MET* 1.3 62.3 + - + +
353B TYR 3.3 0.7 - - - -
354B SER* 3.8 4.3 - - - -
355B LEU* 2.8 44.7 + - + +
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Residues in contact with MET 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B VAL* 2.9 42.0 + - + +
349B ALA* 4.1 3.1 - - - +
351B HIS* 1.3 78.9 - - + +
353B TYR* 1.3 62.6 + - - +
355B LEU 4.3 5.2 - - - +
356B PRO* 3.8 19.7 - - + +
357B ALA* 5.9 5.4 - - + +
358B TYR* 4.1 31.2 - - + -
361B ILE* 5.6 1.8 - - + -
368B GLN* 4.0 12.6 + - - +
371B LEU* 4.3 25.4 - - + -
375B HIS* 5.1 9.2 - - + -
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ALA 3.0 17.9 + - - +
350B GLN* 3.0 51.2 + - + -
352B MET* 1.3 80.1 - - - +
354B SER* 1.3 66.6 + - - +
356B PRO* 4.2 4.0 - - - +
362B ALA* 5.7 0.2 - - - +
368B GLN* 3.9 23.4 + - + +
372B TYR* 3.7 24.2 - + + -
507B SER* 3.5 41.6 + - - -
509B PHE* 5.7 1.6 + - - -
510B LEU* 4.3 17.4 + - + +
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Residues in contact with SER 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE* 3.4 14.0 - - - -
350B GLN 2.8 23.4 + - - -
351B HIS* 3.6 6.6 + - - -
353B TYR* 1.3 91.6 - - - +
355B LEU* 1.3 69.4 + - - +
356B PRO* 3.4 8.9 - - - +
506B ASN* 5.7 0.2 - - - +
507B SER* 3.3 26.6 + - - -
508B LEU* 3.9 18.5 + - - +
509B PHE 4.9 1.8 - - - -
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Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLY* 6.3 1.8 - - - +
261B PHE* 3.5 24.7 - - + -
268B LEU* 3.9 27.0 - - + +
351B HIS* 2.8 32.3 + - + +
352B MET* 4.2 2.5 - - - +
354B SER* 1.3 84.9 + - - +
356B PRO* 1.3 67.1 - - - +
357B ALA* 3.6 2.3 + - - +
497B TRP* 4.2 18.4 - - + -
508B LEU* 3.6 26.2 - - + -
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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