Contacts of the helix formed by residues 332 - 349 (chain B) in PDB entry 2FYU
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
----------------------------------------------------------
303B VAL* 4.5 11.6 - - - +
305B GLN* 3.1 33.3 + - - +
328B SER* 3.9 5.2 - - - -
329B GLN* 3.0 20.2 + - - +
331B ALA* 1.3 76.0 - - - +
333B ALA* 1.3 63.8 + - - +
334B GLY 3.4 2.8 + - - -
335B ASP* 3.4 12.5 + - - +
336B VAL* 3.0 34.5 + - - +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL* 3.8 15.3 - - + -
326B THR* 6.1 0.2 - - - -
328B SER* 3.3 17.3 - - - +
329B GLN 3.2 3.2 + - - +
330B ALA 3.3 15.0 + - - +
331B ALA 3.4 0.6 - - - -
332B SER* 1.3 75.9 - - - +
334B GLY* 1.3 57.3 + - - +
336B VAL* 3.3 2.3 + - - +
337B ILE* 3.0 40.6 + - + +
432B HIS 4.1 2.0 - - - +
433B THR* 3.3 28.3 - - - +
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Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ALA 4.8 1.8 + - - -
332B SER 3.4 0.6 - - - -
333B ALA* 1.3 74.9 - - - +
335B ASP* 1.3 57.0 + - - +
337B ILE* 3.4 1.9 + - - +
338B LYS* 3.0 44.6 + - - +
432B HIS 3.1 21.9 + - - -
434B PRO* 3.7 16.6 - - - -
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Residues in contact with ASP 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLY 5.5 1.6 - - - +
303B VAL* 4.0 20.3 - - + +
331B ALA 4.6 8.8 - - - +
332B SER* 3.4 12.3 + - - +
334B GLY* 1.3 73.9 - - - +
336B VAL* 1.3 56.8 + - - +
338B LYS* 3.5 5.6 + - - +
339B ALA* 2.9 33.6 + - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B VAL* 3.5 37.4 - - + +
303B VAL* 3.9 20.4 - - + -
307B PHE* 4.5 3.4 - - + -
308B ASP 4.5 7.9 - - - +
309B VAL* 5.0 0.7 - - + -
326B THR* 3.8 29.4 - - + -
327B ILE 4.8 0.9 - - - +
328B SER* 3.8 22.2 - - - +
332B SER 3.0 21.3 + - - +
333B ALA 3.7 3.8 - - - +
335B ASP* 1.3 72.4 - - - +
337B ILE* 1.3 59.8 + - - +
340B ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ALA* 4.0 13.5 - - + -
257B LEU* 4.7 8.5 - - + -
324B PHE* 3.5 23.9 - - + -
326B THR* 3.7 20.0 - - + +
333B ALA* 3.0 30.3 + - + +
334B GLY 4.0 3.4 - - - +
336B VAL* 1.3 72.6 - - - +
338B LYS* 1.3 52.4 + - - +
340B ALA* 3.3 3.8 + - - +
341B TYR* 2.8 36.3 + - - +
424B MET* 3.9 26.9 - - + -
433B THR* 4.0 6.1 - - + -
434B PRO* 4.0 14.4 - - + -
439B LEU* 3.6 26.7 - - + -
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLY* 3.0 25.6 + - - +
335B ASP* 4.0 5.6 - - - +
337B ILE* 1.3 72.5 - - - +
339B ALA* 1.4 58.7 + - - +
341B TYR* 3.3 6.5 + - - -
342B ASN* 2.9 45.1 + - - +
434B PRO* 4.2 21.0 - - + +
438B GLU* 3.5 26.2 + - - +
439B LEU* 4.3 19.3 - - + +
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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
----------------------------------------------------------
298B ALA* 4.0 24.8 - - - +
299B VAL* 4.0 14.4 - - + +
302B GLY* 6.6 0.4 - - - -
303B VAL* 5.8 1.8 - - + -
335B ASP 2.9 19.6 + - - +
336B VAL* 3.9 3.8 - - - +
338B LYS* 1.4 74.1 - - - +
340B ALA* 1.3 60.4 - - - +
342B ASN* 3.4 7.0 + - - +
343B GLN* 3.1 23.3 + - - +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.3 35.1 - - + +
299B VAL* 3.9 14.2 - - + +
309B VAL* 4.2 6.7 - - + -
324B PHE* 3.7 23.3 - - + -
326B THR* 4.7 0.2 - - + -
336B VAL 3.0 19.6 + - - +
337B ILE 3.5 3.6 - - - +
339B ALA* 1.3 75.2 - - - +
341B TYR* 1.3 61.1 + - - +
343B GLN* 3.4 2.6 + - - -
344B VAL* 3.4 15.9 + - - +
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Residues in contact with TYR 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 4.4 4.7 - - + -
324B PHE* 3.6 13.3 - + + -
337B ILE 2.8 21.7 + - - +
338B LYS* 3.7 6.5 - - - +
340B ALA* 1.3 72.2 - - - +
342B ASN* 1.3 58.7 + - - +
344B VAL* 3.4 4.1 + - - +
345B LYS* 3.1 52.8 + - + +
417B PHE* 3.5 35.7 - + - -
418B VAL* 3.3 18.3 + - + +
422B LYS* 3.1 35.0 + - + +
439B LEU* 3.8 44.9 - - + -
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Residues in contact with ASN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LYS* 2.9 30.1 + - - +
339B ALA* 3.8 6.3 - - - +
341B TYR* 1.3 73.2 - - - +
343B GLN* 1.3 59.7 + - - +
344B VAL 3.4 0.2 - - - -
345B LYS* 3.4 32.2 + - + +
346B THR* 2.9 31.3 + - - -
439B LEU 5.3 2.6 + - - -
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Residues in contact with GLN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 4.3 5.6 - - + -
294B SER* 2.8 49.3 + - - +
295B LEU* 4.1 6.7 - - + +
298B ALA* 3.6 26.6 - - + +
339B ALA 3.1 7.4 + - - +
340B ALA* 3.7 9.4 - - - +
341B TYR 3.4 0.4 - - - -
342B ASN* 1.3 73.4 - - - +
344B VAL* 1.3 63.9 + - - +
346B THR* 3.5 15.1 + - - +
347B ILE* 3.4 30.3 + - - +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 5.2 0.7 - - + -
279B LEU* 3.8 37.9 - - + -
295B LEU* 4.1 5.4 - - + -
322B PHE* 5.1 4.0 - - + -
324B PHE* 4.3 14.6 - - + -
340B ALA 3.4 17.3 + - - +
341B TYR 3.7 5.8 - - - +
342B ASN 3.4 0.2 - - - -
343B GLN* 1.3 73.7 - - - +
345B LYS* 1.3 51.7 + - - +
347B ILE* 2.9 8.9 + - - +
348B ALA* 2.9 30.7 + - - +
414B ALA* 4.2 21.1 - - + +
417B PHE* 3.6 31.2 - - + -
418B VAL* 4.4 2.5 - - + -
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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
----------------------------------------------------------
341B TYR* 3.1 47.6 + - + +
342B ASN* 3.4 31.2 - - - +
343B GLN 3.4 0.2 - - - -
344B VAL* 1.3 72.0 - - - +
346B THR* 1.4 51.3 + - - +
348B ALA* 3.2 3.4 + - - +
349B GLN* 2.9 56.8 + - - +
418B VAL* 3.8 32.7 - - + +
439B LEU* 4.1 9.5 + - - -
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ASN 2.9 16.5 + - - -
343B GLN* 3.6 21.7 + - - +
344B VAL 3.3 0.4 - - - -
345B LYS* 1.4 73.0 - - - +
347B ILE* 1.3 59.4 + - - +
349B GLN* 3.6 11.3 + - - +
350B GLY 3.5 3.3 + - - -
351B ASN* 3.1 55.6 + - + +
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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
----------------------------------------------------------
275B LEU* 3.9 13.0 - - + -
278B VAL* 4.0 15.9 - - + -
279B LEU* 3.7 22.2 - - + -
294B SER* 4.3 2.7 - - - +
343B GLN* 3.4 36.2 + - - +
344B VAL* 2.9 8.9 + - - +
346B THR* 1.3 73.7 - - - +
348B ALA* 1.3 60.9 + - - +
350B GLY* 3.1 18.9 + - - -
351B ASN 3.7 17.9 + - - +
352B LEU* 4.4 29.3 - - + +
410B VAL 4.6 3.4 - - - +
411B ILE* 3.6 12.7 - - - +
414B ALA* 3.9 17.7 - - + -
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL 2.9 10.4 + - - +
345B LYS* 3.2 8.7 + - - +
347B ILE* 1.3 75.7 - - - +
349B GLN* 1.3 57.4 + - + +
350B GLY 3.2 3.2 + - - -
411B ILE* 3.7 9.9 - - - +
414B ALA* 3.8 29.3 - - - +
415B LYS* 3.4 31.7 - - + +
418B VAL* 3.8 18.2 - - + -
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Residues in contact with GLN 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LYS* 2.9 38.4 + - - +
346B THR* 3.7 14.8 + - - +
347B ILE 3.3 0.2 - - - -
348B ALA* 1.3 74.5 - - + +
350B GLY* 1.3 57.1 + - - +
351B ASN* 3.6 12.9 + - - +
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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
------------------------------------------------------------
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