Contacts of the helix formed by residues 332 - 349 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A HIS 4.2 0.2 + - - -
331A LEU* 1.3 73.3 - - - +
333A PRO* 1.3 76.7 - - + +
334A ASP* 4.6 3.4 - - + +
335A GLU* 3.1 31.2 + - + +
336A ALA* 2.9 20.3 + - - +
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Residues in contact with PRO 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PRO* 4.0 27.1 - - + +
53A LEU* 3.8 24.4 - - + +
331A LEU 3.9 0.4 - - - -
332A ALA* 1.3 84.2 - - + +
334A ASP* 1.3 63.0 + - - +
336A ALA* 3.1 7.9 + - + +
337A ARG* 2.9 36.4 + - - +
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Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ALA* 3.4 4.3 - - + +
333A PRO* 1.3 76.1 - - - +
335A GLU* 1.3 67.6 + - + +
337A ARG* 3.3 20.2 + - - +
338A VAL* 3.2 26.2 + - + +
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A LEU* 4.1 21.8 - - + +
332A ALA* 3.1 32.7 + - + +
334A ASP* 1.3 73.8 - - + +
336A ALA* 1.3 65.6 + - - +
338A VAL* 3.0 19.1 + - - +
339A ILE* 3.1 17.8 + - + +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A HIS* 4.4 2.7 - - + -
52A PRO* 4.9 1.3 - - + -
53A LEU* 3.8 18.8 - - + -
328A THR* 3.7 37.4 - - - +
331A LEU* 4.1 3.5 - - + +
332A ALA 2.9 13.8 + - - +
333A PRO* 3.4 10.5 - - + +
335A GLU* 1.3 77.2 - - - +
337A ARG* 1.3 60.8 + - - +
339A ILE* 3.5 2.9 + - - +
340A ILE* 3.2 29.0 + - - +
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.7 27.6 - - + +
333A PRO* 2.9 20.0 + - - +
334A ASP* 3.7 21.7 + - - +
335A GLU 3.2 0.4 - - - -
336A ALA* 1.3 76.9 - - - +
338A VAL* 1.3 60.4 + - + +
340A ILE* 3.4 10.8 + - - +
341A HIS* 3.0 23.6 + - - +
370A GLN* 5.3 6.7 + - - +
373A ILE* 4.0 37.7 - - + +
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASP 3.2 16.3 + - - +
335A GLU* 3.0 10.6 + - - +
337A ARG* 1.3 72.3 - - + +
339A ILE* 1.3 62.6 + - + +
341A HIS* 3.1 11.7 + - + +
342A GLU* 2.8 54.2 + - + +
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A THR* 5.1 4.9 - - + -
327A GLN* 4.7 20.9 - - + +
328A THR* 3.6 22.7 - - + -
331A LEU* 3.5 24.5 - - + -
335A GLU* 3.1 14.4 + - + +
336A ALA 3.7 0.9 - - - +
338A VAL* 1.3 78.1 - - + +
340A ILE* 1.3 57.0 + - - +
342A GLU* 3.3 19.3 + - - +
343A ALA* 2.8 30.9 + - + +
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.2 5.8 - - + -
319A VAL* 6.0 0.2 - - + -
324A THR* 3.4 24.2 - - + -
328A THR* 4.5 3.6 - - + -
336A ALA 3.2 16.9 + - - +
337A ARG* 3.6 7.2 - - - +
339A ILE* 1.3 71.3 - - - +
341A HIS* 1.3 66.4 + - - +
343A ALA* 3.2 7.1 + - - +
344A ILE* 3.1 24.1 + - + +
369A GLY* 4.2 17.0 - - - +
372A LEU* 3.9 32.1 - - + -
373A ILE* 3.8 27.1 - - + +
376A LEU* 3.8 24.0 - - + -
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Residues in contact with HIS 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG 3.0 14.2 + - - +
338A VAL* 3.5 14.1 - - + +
340A ILE* 1.3 75.8 - - - +
342A GLU* 1.3 69.6 + - + +
344A ILE* 3.5 11.4 + - - +
345A LEU* 3.3 37.0 + - + +
362A GLU* 5.1 7.0 - - - -
365A ARG* 3.6 29.7 + - - +
369A GLY* 6.2 0.2 - - - -
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A VAL* 2.8 35.6 + - + +
339A ILE* 3.6 23.9 - - - +
341A HIS* 1.3 82.0 - - + +
343A ALA* 1.3 59.3 + - - +
345A LEU* 3.3 7.1 + - + +
346A ASN* 2.8 43.8 + - - +
349A ARG* 5.8 2.7 - - - +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 3.6 29.3 - - + +
324A THR* 5.2 4.9 - - + +
327A GLN* 5.9 2.7 - - - +
339A ILE* 2.8 23.9 + - + +
340A ILE* 3.2 8.7 + - - +
342A GLU* 1.3 71.8 - - - +
344A ILE* 1.3 62.0 + - - +
346A ASN* 3.4 8.2 + - - +
347A ALA* 3.1 18.7 + - - +
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ILE* 4.0 19.1 - - + +
319A VAL* 3.9 10.8 - - + -
340A ILE* 3.1 19.1 + - + +
341A HIS* 3.8 10.8 - - - +
343A ALA* 1.3 75.6 - - - +
345A LEU* 1.3 59.7 + - - +
347A ALA* 3.5 15.0 + - - +
348A ASN* 3.6 10.7 + - - +
365A ARG* 3.6 40.2 - - + +
368A ILE* 4.0 10.1 - - + -
369A GLY* 3.5 37.7 - - - +
372A LEU* 4.0 17.0 - - + -
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A HIS* 3.3 34.7 + - + +
342A GLU* 3.7 8.3 - - + +
344A ILE* 1.3 76.2 - - - +
346A ASN* 1.3 65.8 + - - +
348A ASN* 3.1 16.3 + - - +
349A ARG* 3.2 42.4 + - - +
359A VAL* 3.9 27.6 - - + -
365A ARG* 3.7 33.9 - - - +
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Residues in contact with ASN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A GLU* 2.8 34.2 + - - +
343A ALA* 3.8 7.4 - - - +
345A LEU* 1.3 71.5 - - - +
347A ALA* 1.3 63.1 + - - +
349A ARG* 3.2 40.0 + - - +
350A SER* 3.8 8.8 + - - -
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ILE* 3.8 24.0 - - + -
317A ARG* 3.2 22.2 - - + +
318A TYR 4.5 10.3 - - - +
319A VAL* 4.4 5.8 - - + -
343A ALA 3.1 13.5 + - - +
344A ILE 3.5 11.0 - - - +
345A LEU 3.2 0.4 - - - -
346A ASN* 1.3 74.2 - - - +
348A ASN* 1.3 56.0 + - - +
350A SER* 3.0 27.8 + - - -
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ILE* 3.3 21.6 - - - +
307A PRO 2.9 26.3 + - - -
308A ASP* 4.0 1.4 - - - +
317A ARG* 4.1 11.2 - - - +
344A ILE 3.6 6.7 + - - +
345A LEU* 3.1 11.8 + - - +
347A ALA* 1.3 75.2 - - - +
349A ARG* 1.3 58.9 + - - +
350A SER 3.1 9.1 + - - +
356A GLY* 5.5 5.4 + - - +
358A GLY* 3.8 20.0 + - - +
359A VAL* 3.4 30.1 - - + +
360A ALA 3.2 15.6 + - - +
365A ARG* 3.9 8.5 - - - -
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Residues in contact with ARG 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A GLU* 5.1 3.0 + - - +
345A LEU* 3.5 47.2 + - - +
346A ASN* 3.2 30.3 + - - +
348A ASN* 1.3 77.5 - - - +
350A SER* 1.3 61.9 + - - +
351A ASP* 3.7 3.3 + - - +
359A VAL* 4.9 8.5 - - + +
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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