Contacts of the helix formed by residues 336 - 357 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F PRO* 1.3 78.6 - - + +
337F THR* 1.3 74.2 + - + +
339F ILE* 3.2 25.3 + - + +
340F CYS* 3.3 17.4 + - - -
411F ALA* 4.0 28.3 - - + +
413F VAL* 5.1 11.7 - - + -
510F PHE* 3.9 28.5 - - + -
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Residues in contact with THR 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F PRO 4.3 4.7 - - - -
336F VAL* 1.3 82.0 - - + +
338F ASN* 1.3 63.6 + - - +
340F CYS* 3.2 5.0 + - - +
341F GLN* 2.8 36.5 + - - +
510F PHE* 3.5 33.0 - - + -
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Residues in contact with ASN 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F PRO* 3.3 38.3 + - + +
336F VAL 3.2 0.4 - - - -
337F THR* 1.3 86.5 + - - +
339F ILE* 1.3 56.8 + - - +
341F GLN* 3.7 18.8 - - - +
342F ALA* 3.0 27.7 + - - +
397F LEU* 3.9 7.2 - - + +
399F THR* 4.5 6.2 - - + +
401F LEU* 3.4 34.7 - - + +
403F VAL* 5.7 0.9 - - + -
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Residues in contact with ILE 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F PRO 3.5 17.5 - - - +
336F VAL* 3.2 17.8 + - + +
338F ASN* 1.3 77.0 - - - +
340F CYS* 1.3 61.8 + - - +
342F ALA* 3.3 7.3 + - - +
343F ALA* 2.8 29.1 + - + +
384F PHE* 6.1 5.4 - - + -
395F ILE* 6.0 3.1 - - + -
397F LEU* 4.4 21.8 - - + -
403F VAL* 4.8 14.4 - - + -
413F VAL* 5.4 12.1 - - + -
507F LEU* 5.6 7.6 - - + -
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Residues in contact with CYS 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336F VAL* 3.3 11.8 + - - +
337F THR 3.2 8.8 + - - +
339F ILE* 1.3 79.5 - - - +
341F GLN* 1.3 65.0 + - - +
343F ALA* 3.4 3.3 + - - +
344F ASP* 3.1 24.4 + - - +
507F LEU* 4.0 25.4 - - - -
510F PHE* 3.5 39.3 - - + -
519F ASP* 4.3 7.4 - - + +
522F LEU* 3.7 20.0 - - + +
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Residues in contact with GLN 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337F THR 2.8 20.2 + - - +
338F ASN* 3.7 20.4 - - - +
340F CYS* 1.3 74.8 - - - +
342F ALA* 1.3 61.7 + - - +
344F ASP* 3.3 5.6 + - - +
345F LYS* 3.3 20.4 + - - +
399F THR* 3.2 23.2 + - - +
519F ASP* 5.3 4.2 - - - +
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Residues in contact with ALA 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F ASN 3.0 18.5 + - - +
339F ILE* 3.5 6.1 - - + +
341F GLN* 1.3 75.0 - - - +
343F ALA* 1.3 63.1 + - - +
345F LYS* 3.5 6.0 + - - +
346F GLN* 3.1 29.5 + - + +
397F LEU* 4.0 30.7 - - + -
398F ALA* 4.5 3.1 - - + +
399F THR* 4.1 20.3 - - - +
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Residues in contact with ALA 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339F ILE* 2.8 22.3 + - + +
340F CYS* 3.6 6.3 - - - +
341F GLN 3.3 0.2 - - - -
342F ALA* 1.3 73.0 - - - +
344F ASP* 1.3 62.9 + - - +
346F GLN* 3.1 3.7 + - - +
347F LEU* 3.0 27.6 + - - +
376F TRP* 5.3 2.0 - - + -
380F LEU* 4.2 18.8 - - + +
507F LEU* 5.6 4.5 - - + -
522F LEU* 4.1 22.7 - - + -
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Residues in contact with ASP 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F CYS 3.1 14.1 + - - +
341F GLN* 3.3 5.1 + - - +
343F ALA* 1.3 79.5 - - - +
345F LYS* 1.3 62.4 + - - +
347F LEU* 3.5 17.4 + - - +
348F PHE* 3.2 32.2 - - - -
519F ASP* 4.0 17.0 - - + -
520F THR* 3.6 10.4 + - - +
521F PHE* 2.8 33.7 + - - +
522F LEU* 3.1 12.3 + - + +
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Residues in contact with LYS 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F GLN 3.3 9.7 + - - +
342F ALA* 3.9 8.5 - - - +
343F ALA 3.2 0.4 - - - -
344F ASP* 1.3 81.7 + - - +
346F GLN* 1.3 79.7 + - - +
348F PHE* 3.2 26.4 + - - +
349F THR* 3.7 7.7 + - - +
398F ALA* 3.6 18.9 + - - -
399F THR* 4.3 23.7 - - - +
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Residues in contact with GLN 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F VAL 5.9 0.6 + - - -
342F ALA* 3.1 18.6 + - + +
343F ALA* 3.1 3.6 + - - +
345F LYS* 1.3 88.0 - - - +
347F LEU* 1.3 60.6 + - - +
349F THR* 3.0 28.6 + - - +
350F LEU* 2.8 29.6 + - - +
380F LEU* 3.8 24.8 - - + +
383F SER* 4.7 5.7 + - - -
387F ARG* 3.6 21.1 - - - +
398F ALA* 3.1 36.4 - - + +
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Residues in contact with LEU 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F ALA 3.0 19.0 + - - +
344F ASP* 3.6 8.5 - - - +
345F LYS 3.2 0.4 - - - -
346F GLN* 1.3 77.5 - - - +
348F PHE* 1.3 61.8 + - - +
350F LEU* 3.3 18.0 + - + +
351F VAL* 3.4 18.2 + - - +
376F TRP* 3.9 40.2 - - + -
380F LEU* 4.3 7.4 - - + +
521F PHE* 3.5 22.9 - - + -
522F LEU* 3.7 43.5 - - + +
525F MET* 4.0 18.8 - - + -
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Residues in contact with PHE 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344F ASP* 3.2 40.6 - - - -
345F LYS* 3.2 13.6 + - - +
346F GLN 3.1 0.4 - - - -
347F LEU* 1.3 78.6 - - - +
349F THR* 1.3 62.8 + - - +
351F VAL* 3.3 15.6 + - - +
352F GLU* 3.6 16.2 + - - +
520F THR* 5.4 7.0 - - + -
521F PHE* 3.9 22.4 - + + -
537F ILE* 4.7 7.0 - - + -
540F ARG* 4.9 8.5 - - - -
541F LEU* 3.9 34.8 - - + +
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Residues in contact with THR 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F VAL* 3.4 37.4 - - + +
345F LYS* 3.8 7.4 + - - +
346F GLN* 3.0 34.6 + - - +
348F PHE* 1.3 77.8 - - - +
350F LEU* 1.3 64.2 + - - +
352F GLU* 3.1 17.3 + - - +
353F TRP* 2.9 20.1 + - + +
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Residues in contact with LEU 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346F GLN 2.8 16.1 + - - +
347F LEU* 3.4 19.7 - - + +
348F PHE 3.2 0.4 - - - -
349F THR* 1.3 73.6 - - - +
351F VAL* 1.3 56.6 + - + +
353F TRP* 3.1 14.8 + - + +
354F ALA* 2.8 28.6 + - - +
372F LEU* 3.9 20.4 - - + -
376F TRP* 3.7 38.1 - - + +
379F LEU* 3.8 20.2 - - + -
380F LEU* 4.5 9.9 - - + -
442F ARG* 3.4 28.7 - - - +
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Residues in contact with VAL 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F LEU 3.4 14.1 + - - +
348F PHE 3.3 7.5 + - - +
349F THR 3.2 0.4 - - - -
350F LEU* 1.3 76.3 - - + +
352F GLU* 1.3 64.0 + - + +
354F ALA* 3.3 7.1 + - - +
355F LYS* 3.0 29.6 + - + +
372F LEU* 4.5 8.1 - - + -
521F PHE* 4.5 2.5 - - + -
538F LEU* 4.0 23.3 - - + -
541F LEU* 4.1 39.3 - - + +
542F LEU* 4.0 25.8 - - + -
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Residues in contact with GLU 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F VAL* 5.0 6.3 - - + +
348F PHE 3.6 8.5 + - - +
349F THR* 3.1 24.6 + - - +
351F VAL* 1.3 75.2 - - + +
353F TRP* 1.3 65.0 + - - +
355F LYS* 3.4 17.0 + - + +
356F ARG* 3.3 36.0 + - - +
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Residues in contact with TRP 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304F ILE 4.8 0.2 + - - -
307F ALA* 3.4 35.5 - - + +
308F GLU* 2.6 24.1 + - - +
311F VAL* 4.2 16.7 - - + +
349F THR 2.9 12.4 + - - +
350F LEU* 3.1 24.7 + - + +
352F GLU* 1.3 76.3 - - - +
354F ALA* 1.3 78.1 + - + +
356F ARG* 3.0 18.3 + - - +
357F ILE* 3.3 34.4 + - + +
379F LEU* 4.0 18.8 - - + -
439F GLY* 4.1 6.5 - - - -
442F ARG* 3.3 58.8 - - + +
443F ALA 3.9 1.6 - - - -
446F LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F LEU 2.8 18.2 + - - +
351F VAL 3.3 4.7 + - - +
353F TRP* 1.3 88.2 - - + +
355F LYS* 1.3 62.5 + - - +
357F ILE* 3.2 14.5 + - - +
360F PHE* 3.1 45.0 - - + +
372F LEU* 4.1 19.3 - - + -
446F LEU* 4.4 7.0 - - + -
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Residues in contact with LYS 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303F ARG* 4.9 4.3 + - - -
351F VAL* 3.0 25.3 + - + +
352F GLU* 3.6 20.1 - - + +
353F TRP 3.2 0.2 - - - -
354F ALA* 1.3 78.0 - - - +
356F ARG* 1.3 60.1 + - + +
357F ILE 3.4 6.1 + - - +
360F PHE* 4.0 7.4 - - + -
361F SER* 3.5 27.5 + - - +
368F GLN* 5.9 1.1 - - - +
541F LEU 3.4 17.2 + - - -
542F LEU* 4.2 14.4 - - + +
543F GLN 3.9 7.1 + - - +
544F ASP* 3.1 37.4 + - - +
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Residues in contact with ARG 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303F ARG* 3.7 25.3 + - - +
306F GLU* 4.9 2.5 - - - +
307F ALA* 3.5 20.9 - - + +
310F ALA* 3.6 34.0 + - - +
311F VAL* 5.6 1.7 - - - +
352F GLU* 3.3 22.1 + - - +
353F TRP* 3.0 10.7 + - - +
355F LYS* 1.3 75.6 - - + +
357F ILE* 1.3 63.0 + - - +
358F PRO* 3.5 7.4 - - - +
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Residues in contact with ILE 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F MET* 4.8 2.2 - - - -
303F ARG* 4.6 1.3 + - - -
304F ILE* 4.3 19.7 - - + -
307F ALA* 4.2 9.4 - - + -
353F TRP* 3.4 56.5 - - + +
354F ALA* 3.2 13.1 + - - +
355F LYS 3.7 5.9 - - - +
356F ARG* 1.3 78.1 - - - +
358F PRO* 1.3 74.9 - - + +
359F HIS 3.3 0.7 + - - -
360F PHE* 3.2 17.1 + - + +
361F SER 4.6 0.2 + - - -
443F ALA* 4.4 9.9 - - + -
446F LEU* 4.1 5.2 - - + -
447F PHE* 3.7 33.9 - - + -
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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