Contacts of the helix formed by residues 332 - 348 (chain B) in PDB entry 2FGY
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 ALA 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B LEU* 1.3 74.0 - - - +
333B PRO* 1.3 77.0 - - + +
334B ASP* 4.6 4.5 - - + +
335B GLU* 3.1 31.6 + - + +
336B ALA* 2.9 19.9 + - - +
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Residues in contact with PRO 333 (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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52B PRO* 4.1 27.1 - - + +
53B LEU* 3.9 23.9 - - + +
331B LEU 3.9 0.2 - - - -
332B ALA* 1.3 84.7 - - + -
334B ASP* 1.3 64.2 + - - +
336B ALA* 3.1 8.1 + - + +
337B ARG* 3.0 36.2 + - - +
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Residues in contact with ASP 334 (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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332B ALA* 3.3 3.9 - - + +
333B PRO* 1.3 78.1 - - - +
335B GLU* 1.3 68.0 + - + +
337B ARG* 3.3 18.5 + - - +
338B VAL* 3.2 27.5 + - + +
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 4.1 21.8 - - + +
332B ALA* 3.1 32.4 + - + +
334B ASP* 1.3 77.6 - - + +
336B ALA* 1.3 62.6 + - - +
338B VAL* 3.1 10.8 + - - +
339B ILE* 3.1 26.0 + - - +
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Residues in contact with ALA 336 (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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51B HIS* 4.5 2.2 - - + -
52B PRO* 5.1 1.3 - - + -
53B LEU* 3.9 17.7 - - + -
328B THR* 3.8 28.7 - - + +
331B LEU* 4.0 11.5 - - + +
332B ALA 2.9 12.8 + - - +
333B PRO* 3.3 12.8 - - + +
335B GLU* 1.3 77.2 - - - +
337B ARG* 1.3 60.8 + - - +
339B ILE* 3.4 4.5 + - - +
340B ILE* 3.2 28.8 + - - +
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Residues in contact with ARG 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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53B LEU* 3.8 27.7 - - + +
333B PRO* 3.0 22.1 + - - +
334B ASP* 3.6 20.9 + - - +
335B GLU 3.3 0.4 - - - -
336B ALA* 1.3 77.7 - - - +
338B VAL* 1.3 61.6 + - + +
340B ILE* 3.3 10.3 + - - +
341B HIS* 3.1 23.0 + - - +
370B GLN* 5.3 6.5 + - - +
373B ILE* 4.2 35.2 - - + +
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Residues in contact with VAL 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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334B ASP 3.2 15.8 + - - +
335B GLU* 3.1 11.5 + - - +
337B ARG* 1.3 72.9 - - + +
339B ILE* 1.3 61.6 + - + +
341B HIS* 3.3 9.1 + - + +
342B GLU* 2.9 56.1 + - + +
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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
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324B THR* 5.2 4.3 - - + -
327B GLN* 4.7 19.7 - - + +
328B THR* 3.6 18.4 - - + -
331B LEU* 3.6 23.1 - - + -
335B GLU* 3.1 15.4 + - + +
336B ALA 3.4 8.0 + - - +
338B VAL* 1.3 77.9 - - + +
340B ILE* 1.3 56.3 + - + +
342B GLU* 3.3 18.3 + - + +
343B ALA* 2.8 31.4 + - + +
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.3 5.8 - - + -
319B VAL* 6.2 0.2 - - + -
324B THR* 3.5 25.4 - - + -
328B THR* 4.7 2.7 - - + -
336B ALA 3.2 15.7 + - - +
337B ARG* 3.7 7.9 - - - +
338B VAL 3.2 0.2 - - - -
339B ILE* 1.3 72.9 - - - +
341B HIS* 1.3 66.1 + - - +
343B ALA* 3.1 15.6 + - - +
344B ILE* 3.1 16.1 + - - +
369B GLY* 4.0 21.8 - - - +
372B LEU* 4.0 27.1 - - + -
373B ILE* 3.6 29.4 - - + +
376B LEU* 4.0 21.1 - - + -
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Residues in contact with HIS 341 (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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337B ARG 3.1 15.7 + - - +
338B VAL* 3.7 9.0 - - + +
340B ILE* 1.3 76.9 - - - +
342B GLU* 1.3 71.5 + - + +
344B ILE* 3.6 10.7 + - - +
345B LEU* 3.3 38.0 + - + +
362B GLU* 5.2 5.4 - - - -
365B ARG* 3.7 28.5 + - - +
369B GLY* 6.3 0.4 - - - -
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Residues in contact with GLU 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 VAL* 2.9 37.1 + - + +
339B ILE* 3.6 20.6 - - - +
341B HIS* 1.3 83.4 - - + +
343B ALA* 1.3 59.7 + - - +
345B LEU* 3.3 6.9 + - + +
346B ASN* 2.8 42.9 + - - +
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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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319B VAL* 3.5 30.1 - - + +
324B THR* 5.2 4.7 - - + +
327B GLN* 6.0 2.0 - - - +
339B ILE* 2.8 24.6 + - + +
340B ILE* 3.1 8.9 + - - +
342B GLU* 1.3 69.8 - - - +
344B ILE* 1.3 63.5 + - - +
346B ASN* 3.5 8.4 + - - +
347B ALA* 3.2 17.3 + - - +
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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
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306B ILE* 4.0 18.0 - - + +
319B VAL* 3.8 12.1 - - + -
340B ILE* 3.1 19.2 + - + +
341B HIS* 3.8 8.5 - - - +
343B ALA* 1.3 75.6 - - - +
345B LEU* 1.3 65.4 + - - +
347B ALA* 3.3 13.1 + - - +
348B ASN* 3.5 13.0 + - - +
365B ARG* 3.7 41.5 - - + +
368B ILE* 4.1 9.0 - - + -
369B GLY* 3.6 36.6 - - - +
372B LEU* 3.9 18.8 - - + -
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Residues in contact with LEU 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 HIS* 3.3 38.3 + - + +
342B GLU* 3.8 9.4 - - + +
344B ILE* 1.3 79.8 - - - +
346B ASN* 1.3 64.1 + - - +
348B ASN* 3.1 16.2 + - - +
349B ARG* 3.2 15.8 + - - +
359B VAL* 4.0 24.0 - - + +
365B ARG* 3.8 36.6 - - - +
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Residues in contact with ASN 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 GLU* 2.8 31.4 + - - +
343B ALA* 3.9 8.0 - - - +
344B ILE 3.3 0.2 - - - -
345B LEU* 1.3 77.7 - - - +
347B ALA* 1.3 62.2 + - - +
349B ARG* 2.8 55.8 + - - +
350B SER* 3.9 5.4 + - - -
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Residues in contact with ALA 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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306B ILE* 3.8 24.0 - - + -
317B ARG* 3.3 20.4 - - + +
318B TYR 4.4 15.0 - - - +
319B VAL* 4.5 1.6 - - + -
343B ALA 3.2 13.1 + - - +
344B ILE 3.6 9.0 - - - +
345B LEU 3.2 0.4 - - - -
346B ASN* 1.3 75.5 - - - +
348B ASN* 1.3 57.6 + - - +
350B SER* 2.9 28.9 + - - -
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Residues in contact with ASN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ILE* 3.3 22.3 - - - +
307B PRO 3.0 24.9 + - - -
308B ASP* 4.1 0.4 - - - +
317B ARG* 4.0 13.0 - - - +
344B ILE 3.5 6.1 + - - +
345B LEU* 3.1 11.8 + - - +
347B ALA* 1.3 72.8 - - - +
349B ARG* 1.3 57.0 + - - +
350B SER 3.1 9.5 + - - +
356B GLY* 5.6 3.8 + - - +
358B GLY* 3.7 18.8 + - - +
359B VAL* 3.5 34.1 - - + +
360B ALA* 3.2 14.7 + - - +
365B ARG* 4.0 6.8 - - - -
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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