Contacts of the helix formed by residues 321 - 329 (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 ASN 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ILE 2.8 24.3 + - - +
319B VAL 3.7 2.0 + - - -
320B ASP* 1.3 69.6 + - - +
322B THR* 1.3 55.5 + - - +
323B VAL 3.3 0.2 - - - -
324B THR* 3.4 19.8 + - - +
325B TYR* 2.8 32.9 + - - +
372B LEU* 3.0 46.4 + - + +
375B ASN* 2.9 31.4 + - - +
376B LEU* 3.5 19.5 - - - +
379B ILE* 3.9 5.4 - - + +
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Residues in contact with THR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PRO* 2.7 63.5 - - + +
40B ALA* 3.6 13.2 - - - +
296B ASP* 5.7 0.5 + - - -
299B THR* 4.7 1.7 + - - -
301B ALA* 3.3 23.5 - - - +
320B ASP* 3.2 14.1 + - - +
321B ASN* 1.3 78.1 - - - +
323B VAL* 1.3 65.1 + - + +
325B TYR* 3.6 2.6 + - - +
326B ALA* 3.3 18.2 + - - +
379B ILE* 4.4 1.5 - - - +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PRO 5.4 0.4 - - - -
319B VAL* 5.4 1.8 - - + -
320B ASP* 3.0 44.6 + - + +
322B THR* 1.3 77.4 - - + +
324B THR* 1.3 63.2 + - - +
326B ALA* 3.3 5.5 + - - +
327B GLN* 3.0 45.4 + - + +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B VAL* 3.4 20.7 - - + +
320B ASP 3.0 13.4 + - - -
321B ASN* 3.4 21.5 + - - +
323B VAL* 1.3 79.4 - - - +
325B TYR* 1.3 58.1 + - - +
327B GLN* 3.9 6.9 - - - +
328B THR* 2.8 42.4 + - + +
339B ILE* 5.2 3.1 - - + -
340B ILE* 3.5 39.5 - - + -
343B ALA* 5.2 4.0 - - + +
372B LEU* 5.6 0.7 - - + -
376B LEU* 4.7 1.8 - - + -
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Residues in contact with TYR 325 (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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40B ALA* 3.4 33.4 - - + -
41B CYS* 4.5 2.7 - - + +
49B CYS* 3.2 26.9 - - + +
51B HIS* 3.5 28.4 + + + -
321B ASN 2.8 21.9 + - - +
322B THR 3.7 4.9 - - - +
324B THR* 1.3 73.7 - - - +
326B ALA* 1.3 61.2 + - - +
328B THR* 4.0 1.3 - - - -
329B LEU* 3.1 37.5 + - + +
376B LEU* 3.8 25.8 - - + +
379B ILE* 3.8 32.3 - - + -
380B ASP* 2.3 32.7 + - - -
383B VAL* 5.1 2.3 - - + +
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Residues in contact with ALA 326 (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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39B PRO 4.9 2.5 - - - +
40B ALA* 3.6 22.0 - - - +
42B ILE* 3.9 26.3 - - + +
322B THR 3.3 12.1 + - - +
323B VAL* 4.0 5.6 - - - +
324B THR 3.3 0.2 - - - -
325B TYR* 1.3 81.9 - - - +
327B GLN* 1.3 63.1 + - + +
328B THR 3.4 0.9 + - - -
329B LEU* 3.7 14.2 + - - +
330B HIS* 4.9 7.3 + - - -
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Residues in contact with GLN 327 (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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323B VAL* 3.0 31.6 + - + +
324B THR* 4.1 6.5 - - - +
325B TYR 3.4 0.2 - - - -
326B ALA* 1.3 77.9 - - + +
328B THR* 1.3 61.3 + - + +
329B LEU 3.6 0.4 - - - -
330B HIS 5.4 0.4 + - - -
331B LEU* 3.9 14.0 - - - +
339B ILE* 4.7 14.6 - - + +
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Residues in contact with THR 328 (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* 2.6 34.9 + - - -
52B PRO* 4.0 3.6 - - - +
324B THR* 2.8 28.1 + - + +
325B TYR* 4.0 0.2 - - - -
327B GLN* 1.3 76.6 - - - +
329B LEU* 1.3 67.5 + - - +
330B HIS 3.2 2.9 - - - -
331B LEU* 3.1 23.3 + - + +
336B ALA* 3.8 24.6 - - - +
339B ILE* 3.6 38.6 - - + -
340B ILE* 4.7 1.1 - - + -
376B LEU* 4.9 1.9 - - - +
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Residues in contact with LEU 329 (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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40B ALA 5.2 2.9 - - - +
42B ILE* 5.9 4.9 - - + +
43B THR* 6.4 1.1 - - + -
49B CYS* 3.6 41.1 - - + -
50B ARG 3.7 22.4 - - - +
51B HIS* 3.8 17.3 - - + -
52B PRO* 3.3 21.0 - - - +
325B TYR* 3.1 29.7 + - + +
326B ALA* 3.7 10.9 + - - +
327B GLN 3.6 1.2 - - - -
328B THR* 1.3 77.2 - - - +
330B HIS* 1.3 83.7 + - + +
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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
------------------------------------------------------------
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