Contacts of the helix formed by residues 332 - 358 (chain B) in PDB entry 4FE1
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 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B THR 3.3 19.0 + - - -
329B TYR 3.4 1.5 + - - +
331B ASN* 1.3 79.0 - - - +
333B LEU* 1.3 59.9 + - - +
334B HIS* 3.9 0.5 - - - -
335B PHE* 3.1 11.3 + - - -
336B GLN* 3.1 28.7 + - - +
396B PHE* 3.0 30.3 - - - -
400B ASP* 2.9 28.3 + - - -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU* 5.3 9.2 - - - +
41B LEU* 3.7 26.0 - - + -
42B TYR* 3.2 54.3 - - + +
45B ILE* 4.7 16.6 - - + -
331B ASN 4.0 1.6 + - - +
332B SER* 1.3 72.7 - - - +
334B HIS* 1.3 61.1 + - + +
336B GLN* 3.6 18.7 + - + +
337B LEU* 2.9 30.1 + - - +
400B ASP* 3.9 4.2 + - - +
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Residues in contact with HIS 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 5.6 0.9 - - - -
31B GLU* 2.6 35.2 + - - -
332B SER* 3.2 1.9 + - - +
333B LEU* 1.3 78.4 - - + +
335B PHE* 1.3 59.1 - - - +
337B LEU* 4.4 4.2 - - - +
338B GLY* 2.9 23.7 + - - -
392B HIS* 3.0 57.3 + + - +
395B ILE* 3.3 33.3 - - + +
396B PHE* 3.8 12.8 - - + +
399B ARG* 4.1 8.4 + - + -
400B ASP* 3.5 20.2 - - - -
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Residues in contact with PHE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 6.0 6.7 - - + -
328B THR* 4.5 5.6 - - + +
329B TYR* 3.4 42.4 - + + +
332B SER* 3.1 24.8 + - - +
334B HIS* 1.3 75.6 - - - +
336B GLN* 1.3 58.8 + - - +
338B GLY* 3.4 0.9 + - - -
339B TRP* 2.9 70.9 + + - +
392B HIS 4.9 0.2 - - - -
393B GLY* 5.7 2.2 - - - -
396B PHE* 3.4 47.5 - + + +
411B LEU* 4.2 16.6 - - + -
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR* 4.4 7.4 + - - -
173B ARG* 4.3 18.1 + - - -
329B TYR* 2.9 44.4 + - + +
330B ASN* 3.0 29.0 + - - +
332B SER 3.1 18.9 + - - +
333B LEU* 3.8 19.1 - - + +
335B PHE* 1.3 76.7 - - - +
337B LEU* 1.3 62.5 + - - +
339B TRP* 4.5 3.6 - - - -
340B HIS* 3.0 44.4 + - + -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU 2.9 19.8 + - - +
334B HIS* 4.0 5.6 - - - +
335B PHE 3.3 0.2 - - - -
336B GLN* 1.3 75.5 - - - +
338B GLY* 1.3 59.1 + - - +
340B HIS* 3.8 7.0 - - + +
341B LEU* 2.9 55.4 + - + +
392B HIS* 3.4 37.7 - - + +
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Residues in contact with GLY 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B HIS 2.9 17.4 + - - -
335B PHE 3.9 0.4 - - - -
337B LEU* 1.3 76.8 - - - +
339B TRP* 1.3 63.6 + - - +
341B LEU* 3.1 1.6 + - - -
342B ALA* 3.0 18.7 + - - +
389B ALA* 3.1 35.8 - - - +
392B HIS* 3.9 8.0 - - - +
393B GLY* 4.6 3.4 - - - -
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Residues in contact with TRP 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B TYR* 4.2 23.4 - + + -
335B PHE* 2.9 55.8 + + - +
336B GLN 3.7 3.4 - - - +
338B GLY* 1.3 75.1 - - - +
340B HIS* 1.3 64.2 + + + +
342B ALA* 2.9 24.2 + - + +
343B CYS* 3.0 30.3 + - - -
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Residues in contact with HIS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 4.8 15.7 - - - -
329B TYR* 2.7 29.8 + - - -
336B GLN* 3.0 34.0 + - + +
337B LEU* 4.0 7.7 - - + +
339B TRP* 1.3 79.0 - + + +
341B LEU* 1.3 60.4 + - - +
343B CYS* 3.8 10.4 - - - +
344B LEU* 2.9 31.4 + - - +
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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 LEU* 2.9 41.4 + - + +
338B GLY 3.1 5.1 + - - +
340B HIS* 1.3 79.1 - - - +
342B ALA* 1.3 56.3 + - - +
344B LEU* 4.0 6.9 - - + -
345B GLY* 3.0 26.5 + - - -
385B LEU* 3.7 36.2 - - + +
388B GLY* 3.3 33.9 - - - +
389B ALA* 3.6 11.9 - - - +
392B HIS* 4.0 17.3 - - + -
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLY 3.0 6.6 + - - +
339B TRP* 2.9 12.7 + - + +
341B LEU* 1.3 78.1 - - - +
343B CYS* 1.3 63.7 + - - +
345B GLY* 3.4 1.0 + - - -
346B VAL* 3.0 31.1 + - + +
386B MET* 3.8 16.2 - - + +
389B ALA* 3.4 18.8 - - + +
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Residues in contact with CYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B TRP* 3.0 33.8 + - - -
340B HIS* 3.8 11.9 - - - +
341B LEU 3.3 0.2 - - - -
342B ALA* 1.3 78.7 - - - +
344B LEU* 1.3 62.0 + - - +
346B VAL* 3.2 6.6 + - - +
347B ILE* 3.0 32.0 + - + +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B HIS 2.9 18.0 + - - +
341B LEU* 4.1 6.7 - - + +
343B CYS* 1.3 77.2 - - - +
345B GLY* 1.3 53.5 + - - +
347B ILE* 3.4 22.6 + - + +
348B THR* 2.5 41.1 + - - +
385B LEU* 3.7 24.5 - - + -
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU 3.0 17.4 + - - -
342B ALA 3.8 1.1 - - - -
344B LEU* 1.3 78.3 - - - +
346B VAL* 1.3 60.8 + - - +
348B THR* 3.2 5.0 + - - -
349B SER* 3.0 20.1 + - - -
382B ALA* 3.6 11.7 - - - +
385B LEU* 3.7 22.8 - - - +
386B MET* 4.0 12.7 - - - +
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ALA* 3.0 22.9 + - + +
343B CYS* 3.7 7.2 - - - +
345B GLY* 1.3 75.7 - - - +
347B ILE* 1.3 64.8 + - + +
349B SER* 3.0 11.0 + - - -
350B LEU* 2.9 27.4 + - + +
386B MET* 4.1 17.0 - - + -
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Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B CYS* 3.0 18.6 + - + +
344B LEU* 3.4 28.7 - - + +
346B VAL* 1.3 81.8 - - + +
348B THR* 1.3 59.7 + - - +
350B LEU* 3.5 19.6 - - + +
351B VAL* 2.9 34.3 + - + +
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Residues in contact with THR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 2.5 29.4 + - - +
345B GLY* 3.4 8.1 - - - -
346B VAL 3.1 0.4 - - - -
347B ILE* 1.3 75.4 - - - +
349B SER* 1.3 66.6 + - - +
351B VAL* 3.3 9.3 + - - +
352B ALA* 3.0 20.4 + - - +
378B HIS* 3.2 39.5 - - + +
381B ILE* 4.0 13.2 - - + +
382B ALA* 4.0 11.2 - - - +
385B LEU* 3.8 8.7 - - - +
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLY 3.0 10.2 + - - -
346B VAL* 3.0 11.6 + - - -
348B THR* 1.3 76.6 - - - +
350B LEU* 1.3 64.3 + - - -
352B ALA* 3.0 4.0 + - - +
353B GLN* 2.9 30.5 + - - +
379B GLN* 3.0 27.1 + - - +
382B ALA* 3.6 10.7 - - - +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B VAL* 2.9 17.7 + - + +
347B ILE* 3.5 22.0 - - + +
348B THR 3.2 0.2 - - - -
349B SER* 1.3 76.9 - - - +
351B VAL* 1.3 56.7 + - + +
353B GLN* 3.2 6.4 + - + +
354B HIS* 2.9 72.3 + - + +
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ILE* 2.9 23.9 + - + +
348B THR* 3.4 12.8 - - - +
349B SER 3.2 0.2 - - - -
350B LEU* 1.3 76.7 - - + +
352B ALA* 1.3 63.1 + - - +
354B HIS* 3.9 2.6 - - - -
355B MET* 3.0 57.4 + - + +
378B HIS* 4.4 24.2 - - + +
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B THR 3.0 11.2 + - - +
349B SER 3.0 7.8 + - - +
351B VAL* 1.3 81.5 - - - +
353B GLN* 1.3 62.7 + - - +
355B MET* 3.6 6.8 + - - +
356B TYR* 3.5 8.3 + - - -
375B TYR* 3.2 40.6 - - + +
378B HIS* 4.2 15.7 - - + -
379B GLN* 3.8 21.5 - - + +
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Residues in contact with GLN 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B SER* 2.9 22.8 + - - +
350B LEU* 3.7 6.5 - - + +
352B ALA* 1.3 77.1 - - - +
354B HIS* 1.3 68.1 + - + +
356B TYR* 3.0 39.8 + - + -
357B SER* 3.1 9.9 + - - -
375B TYR* 3.3 24.9 + - - -
379B GLN* 4.2 8.8 - - - +
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Residues in contact with HIS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 2.9 55.6 + - + +
351B VAL* 4.3 3.4 - - - +
353B GLN* 1.3 85.5 - - + +
355B MET* 1.3 63.2 + - + +
356B TYR 3.5 0.2 - - - -
357B SER* 3.9 5.2 - - - -
358B LEU* 3.1 38.6 + - + +
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Residues in contact with MET 355 (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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351B VAL* 3.0 48.2 + - + +
352B ALA* 3.6 3.1 + - - +
353B GLN 3.4 0.2 - - - -
354B HIS* 1.3 79.7 - - + +
356B TYR* 1.3 63.1 + - - +
358B LEU 4.8 2.7 - - - -
359B PRO* 3.7 19.4 - - - +
360B PRO* 4.2 24.6 - - + +
361B TYR* 5.0 16.8 - - - +
371B MET* 4.0 8.8 - - - +
374B LEU* 5.8 12.3 - - + -
378B HIS* 5.4 7.9 - - - -
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Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA 3.5 15.0 + - - +
353B GLN* 3.0 47.8 + - + -
354B HIS 3.5 0.2 - - - -
355B MET* 1.3 79.1 - - - +
357B SER* 1.3 68.8 + - - +
359B PRO* 3.9 4.0 - - - +
371B MET* 3.4 31.0 - - + +
375B TYR* 4.1 22.4 - + + -
513B SER* 3.6 37.6 + - - -
515B PHE* 5.9 0.9 + - - -
516B LEU* 4.4 15.3 + - + +
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PHE* 3.6 11.4 - - - -
353B GLN 3.1 17.3 + - - -
354B HIS* 3.7 6.8 + - - -
356B TYR* 1.3 90.0 - - - +
358B LEU* 1.3 69.1 + - - +
359B PRO* 3.3 12.2 - - - +
513B SER* 3.3 25.6 + - - -
514B LEU* 3.8 19.4 + - - +
515B PHE 4.8 2.0 - - - -
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLY* 6.1 2.2 - - - -
260B PHE* 3.4 28.9 - - + -
267B LEU* 3.8 21.4 - - + +
354B HIS* 3.1 28.5 + - + +
355B MET 4.1 0.9 - - - -
357B SER* 1.3 83.6 + - - +
359B PRO* 1.4 65.8 - - - +
360B PRO* 3.4 5.4 - - - +
503B TRP* 4.2 23.6 - - + -
514B LEU* 3.6 27.1 - - + -
515B PHE* 6.3 0.2 - - + -
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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