Contacts of the helix formed by residues 336 - 357 (chain B) in PDB entry 5I4V
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 VAL 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B PRO* 1.3 78.6 - - + +
337B THR* 1.3 80.6 + - + +
339B ILE* 3.2 24.4 + - + +
340B CYS* 3.3 16.2 + - - -
411B ALA* 4.0 28.5 - - + +
413B VAL* 5.3 4.0 - - + -
510B PHE* 3.3 40.5 - - + -
294E GLN* 4.1 20.9 - - + +
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Residues in contact with THR 337 (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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335B PRO 4.4 4.3 - - - -
336B VAL* 1.3 90.6 - - + +
338B ASN* 1.3 63.6 + - - +
340B CYS* 3.2 9.4 + - - +
341B GLN* 2.7 43.7 + - - +
517B PRO* 4.6 26.5 - - + +
518B ILE* 6.5 0.4 - - + -
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Residues in contact with ASN 338 (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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335B PRO* 3.3 37.5 + - + +
336B VAL 3.2 0.2 - - - -
337B THR* 1.3 87.6 + - - +
339B ILE* 1.3 56.4 + - - +
341B GLN* 3.7 18.7 - - - +
342B ALA* 3.0 27.2 + - - +
397B LEU* 3.9 7.3 - - + +
399B THR* 4.3 3.7 - - - +
401B LEU* 3.4 35.7 - - + +
403B VAL* 5.7 1.6 - - + -
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PRO 3.5 16.8 - - - +
336B VAL* 3.2 18.5 + - + +
338B ASN* 1.3 76.5 - - - +
340B CYS* 1.3 61.8 + - - +
342B ALA* 3.3 6.9 + - - +
343B ALA* 2.8 29.1 + - + +
384B PHE* 6.1 4.3 - - + -
395B ILE* 6.0 3.4 - - + -
397B LEU* 4.4 20.6 - - + -
403B VAL* 4.8 15.9 - - + -
413B VAL* 5.5 10.8 - - + -
507B LEU* 5.5 6.5 - - + -
510B PHE* 5.2 7.2 - - + -
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Residues in contact with CYS 340 (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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336B VAL 3.3 6.9 + - - +
337B THR* 3.2 11.3 + - - +
339B ILE* 1.3 78.4 - - - +
341B GLN* 1.3 65.2 + - - +
343B ALA* 3.4 3.6 + - - +
344B ASP* 3.1 24.1 + - - +
507B LEU* 4.0 18.8 - - - -
510B PHE* 3.6 32.5 - - - -
517B PRO 6.1 0.4 - - - +
518B ILE* 4.6 22.9 - - + -
519B ASP* 4.8 4.6 - - - +
522B LEU* 3.7 20.0 - - + +
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Residues in contact with GLN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B THR* 2.7 24.4 + - - +
338B ASN* 3.7 26.2 + - - +
340B CYS* 1.3 74.8 - - - +
342B ALA* 1.3 63.4 + - - +
344B ASP* 3.3 3.1 + - - +
345B LYS* 3.3 20.6 + - - +
399B THR* 4.2 10.3 - - + +
519B ASP* 4.1 22.9 + - - +
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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
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338B ASN 3.0 18.5 + - - +
339B ILE* 3.5 5.6 - - - +
341B GLN* 1.3 75.6 - - - +
343B ALA* 1.3 63.8 + - - +
345B LYS* 3.5 6.0 + - - +
346B GLN* 3.1 29.1 + - + +
397B LEU* 4.0 26.2 - - + -
398B ALA* 4.5 3.6 - - + +
399B THR* 3.4 25.1 - - + +
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Residues in contact with ALA 343 (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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339B ILE* 2.8 18.8 + - + +
340B CYS* 3.6 6.7 - - - +
341B GLN 3.3 0.2 - - - -
342B ALA* 1.3 77.6 - - - +
344B ASP* 1.3 63.9 + - - +
346B GLN* 3.1 3.8 + - - +
347B LEU* 3.0 28.2 + - - +
376B TRP* 5.3 2.2 - - + -
380B LEU* 4.2 17.9 - - + +
507B LEU* 5.6 4.7 - - + -
522B LEU* 4.1 22.2 - - + -
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Residues in contact with ASP 344 (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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340B CYS 3.1 10.5 + - - +
341B GLN 3.3 4.5 + - - +
343B ALA* 1.3 80.3 - - - +
345B LYS* 1.3 64.2 + - - +
347B LEU* 3.5 17.5 + - - +
348B PHE* 3.2 27.5 - - - -
519B ASP* 3.5 34.3 - - + +
520B THR* 4.3 5.5 - - - +
521B PHE* 2.8 34.3 + - - +
522B LEU* 3.1 14.1 + - + +
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Residues in contact with LYS 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 GLN 3.3 9.6 + - - +
342B ALA* 3.5 10.5 - - - +
343B ALA 3.2 1.0 - - - -
344B ASP* 1.3 82.4 + - - +
346B GLN* 1.3 83.4 + - + +
348B PHE* 3.2 26.5 + - - +
349B THR* 3.7 8.8 + - - -
398B ALA* 4.1 13.8 + - + -
399B THR* 4.3 25.4 - - + +
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Residues in contact with GLN 346 (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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342B ALA* 3.1 13.2 + - + +
343B ALA* 3.1 5.2 + - - +
345B LYS* 1.3 88.9 - - + +
347B LEU* 1.3 60.2 + - - +
349B THR* 3.0 28.8 + - - +
350B LEU* 2.8 29.5 + - - +
380B LEU* 3.8 23.3 - - + +
383B SER* 4.7 5.9 + - - -
387B ARG* 3.6 21.3 - - - +
398B ALA* 3.2 36.0 - - + +
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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
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343B ALA 3.0 18.6 + - - +
344B ASP* 3.6 7.9 - - - +
345B LYS 3.2 0.4 - - - -
346B GLN* 1.3 77.7 - - - +
348B PHE* 1.3 61.2 + - - +
350B LEU* 3.3 17.2 + - + +
351B VAL* 3.3 18.7 + - - +
376B TRP* 3.9 30.3 - - + -
380B LEU* 4.4 7.6 - - + +
521B PHE* 3.5 22.1 - - + -
522B LEU* 3.7 43.3 - - + +
525B MET* 3.9 33.8 - - + +
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Residues in contact with PHE 348 (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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344B ASP* 3.2 40.4 - - - -
345B LYS* 3.2 13.8 + - - +
346B GLN 3.1 0.4 - - - -
347B LEU* 1.3 78.4 - - - +
349B THR* 1.3 63.2 + - - +
351B VAL* 3.3 13.9 + - - +
352B GLU* 3.6 16.4 + - - +
520B THR* 5.3 7.0 - - + -
521B PHE* 3.8 22.4 - + + -
537B ILE* 4.8 8.3 - - + -
541B LEU* 3.7 36.3 - - + +
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Residues in contact with THR 349 (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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311B VAL* 3.4 37.6 - - + +
345B LYS* 3.8 8.7 + - - -
346B GLN* 3.0 34.5 + - - +
348B PHE* 1.3 78.3 - - - +
350B LEU* 1.3 57.2 + - - +
352B GLU* 3.1 11.5 + - + +
353B TRP* 2.9 25.3 + - - +
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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
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346B GLN 2.8 15.7 + - - +
347B LEU* 3.4 19.3 - - + +
349B THR* 1.3 73.5 - - - +
351B VAL* 1.3 58.3 + - + +
353B TRP* 3.1 14.3 + - + +
354B ALA* 2.8 27.7 + - - +
372B LEU* 3.9 20.0 - - + -
376B TRP* 3.7 38.8 - - + +
379B LEU* 3.8 19.3 - - + -
380B LEU* 4.5 9.4 - - + -
442B ARG* 3.4 28.9 - - - +
525B MET* 5.7 1.3 - - + -
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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
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347B LEU 3.5 13.7 - - - +
348B PHE 3.3 6.7 + - - +
349B THR 3.3 0.4 - - - -
350B LEU* 1.3 76.7 - - + +
352B GLU* 1.3 64.3 + - - +
354B ALA* 3.3 6.6 + - - +
355B LYS* 3.0 29.4 + - + +
360B PHE* 5.4 0.4 - - + -
372B LEU* 4.5 8.5 - - + -
521B PHE* 4.5 2.7 - - + -
525B MET* 6.1 0.7 - - + -
538B LEU* 4.0 21.5 - - + -
541B LEU* 3.9 34.5 - - + +
542B LEU* 3.9 35.4 - - + -
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Residues in contact with GLU 352 (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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311B VAL* 5.0 7.0 - - + -
348B PHE 3.6 14.6 - - - +
349B THR* 3.1 11.4 + - - +
351B VAL* 1.3 78.0 - - - +
353B TRP* 1.3 63.4 + - - +
355B LYS* 3.4 32.6 + - - +
356B ARG* 3.3 35.8 + - - +
541B LEU* 4.7 8.5 - - - +
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Residues in contact with TRP 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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304B ILE 4.9 0.2 + - - -
307B ALA* 3.5 35.4 - - + +
308B GLU* 2.6 25.8 + - - +
311B VAL* 4.2 15.4 - - + +
349B THR 2.9 12.7 + - - +
350B LEU* 3.4 24.0 - - + +
352B GLU* 1.3 76.8 - - - +
354B ALA* 1.3 82.1 + - + +
356B ARG* 3.0 18.5 + - - +
357B ILE* 3.4 35.8 + - + +
379B LEU* 4.0 18.8 - - + -
439B GLY* 4.1 2.9 - - - -
442B ARG* 3.3 59.9 - - + +
443B ALA 3.9 4.0 - - - -
446B LEU* 3.8 21.3 - - + -
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Residues in contact with ALA 354 (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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350B LEU 2.8 18.8 + - - +
351B VAL 3.3 4.7 + - - +
353B TRP* 1.3 87.2 - - + +
355B LYS* 1.3 62.2 + - - +
357B ILE* 3.2 14.7 + - - +
360B PHE* 3.1 44.7 - - + +
372B LEU* 4.1 19.7 - - + -
446B LEU* 4.4 7.2 - - + -
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Residues in contact with LYS 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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303B ARG* 4.8 4.0 + - - -
351B VAL* 3.0 29.8 + - + +
352B GLU* 3.6 36.5 + - - +
354B ALA* 1.3 78.4 - - - +
356B ARG* 1.3 60.2 + - + +
357B ILE 3.4 6.6 + - - +
360B PHE* 4.2 11.7 - - + -
361B SER* 4.7 21.2 + - - -
368B GLN* 5.8 1.6 - - - +
541B LEU 3.4 20.4 + - - -
542B LEU* 4.4 15.8 - - + +
543B GLN 5.3 1.0 + - - +
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Residues in contact with ARG 356 (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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303B ARG* 3.7 25.7 + - - +
306B GLU* 4.9 2.5 - - + +
307B ALA* 3.6 21.3 - - + +
310B ALA* 3.6 35.4 + - - +
311B VAL* 5.6 2.5 - - - +
352B GLU* 3.3 23.5 + - - +
353B TRP* 3.0 10.3 + - - +
355B LYS* 1.3 77.7 - - + +
357B ILE* 1.3 61.6 + - - +
358B PRO* 3.6 7.6 - - - +
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Residues in contact with ILE 357 (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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299B MET* 4.8 3.1 - - - -
303B ARG* 4.5 1.1 + - - -
304B ILE* 4.3 20.6 - - + -
307B ALA* 4.2 10.1 - - + -
353B TRP* 3.4 56.3 - - + +
354B ALA* 3.2 12.7 + - - +
355B LYS 3.7 6.2 - - - +
356B ARG* 1.3 77.4 - - - +
358B PRO* 1.3 76.1 - - + +
359B HIS 3.4 0.5 + - - -
360B PHE* 3.2 16.3 + - + +
361B SER* 4.6 0.7 + - - -
443B ALA* 4.4 9.9 - - + -
446B LEU* 4.2 4.3 - - + -
447B PHE* 3.7 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
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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