Contacts of the helix formed by residues 320 - 330 (chain B) in PDB entry 2FQ6
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 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B LYS 3.5 2.6 + - - +
319B LEU* 1.3 75.5 - - - +
321B ASN* 1.3 64.7 + - - +
322B GLU* 3.2 11.6 + - - +
323B GLU* 2.8 47.9 + - - +
324B LEU* 3.0 21.6 + - - +
351B GLN* 5.1 0.7 - - - -
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Residues in contact with ASN 321 (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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320B ASN* 1.3 75.2 - - - +
322B GLU* 1.3 59.0 + - - +
324B LEU* 3.3 17.9 + - - +
325B ALA* 3.0 28.2 + - - +
351B GLN* 5.8 0.7 + - - -
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Residues in contact with GLU 322 (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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320B ASN* 3.2 10.4 + - - +
321B ASN* 1.3 76.4 - - - +
323B GLU* 1.3 64.1 + - + +
325B ALA* 3.6 6.3 + - + +
326B ASN* 3.0 31.2 + - - +
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Residues in contact with GLU 323 (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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317B LYS* 3.3 28.0 + - - +
318B LYS 4.3 1.4 - - - +
319B LEU* 3.3 25.6 - - + +
320B ASN* 2.8 54.1 + - - +
322B GLU* 1.3 79.9 - - + +
324B LEU* 1.3 58.9 + - - +
326B ASN* 3.4 5.7 + - - +
327B TYR* 3.0 30.3 + - - +
393B ARG 6.0 0.4 - - - +
394B ILE* 3.5 15.8 - - + +
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Residues in contact with LEU 324 (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 LEU* 4.0 23.1 - - + -
320B ASN 3.0 11.4 + - - +
321B ASN* 3.3 24.5 - - - +
323B GLU* 1.3 75.3 - - - +
325B ALA* 1.3 58.7 + - - +
327B TYR* 3.4 1.1 + - + +
328B LEU* 2.9 49.2 + - + +
349B ALA* 3.8 27.6 - - + -
351B GLN* 3.9 25.6 - - + +
354B HIS* 6.2 0.7 - - + -
369B THR* 4.2 10.1 - - + -
371B ILE* 5.4 1.1 - - + -
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Residues in contact with ALA 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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321B ASN 3.0 15.6 + - - +
322B GLU* 4.0 7.0 - - + +
324B LEU* 1.3 74.9 - - - +
326B ASN* 1.3 58.5 + - - +
328B LEU* 5.1 0.7 - - - -
329B ASP* 2.8 59.5 + - - +
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Residues in contact with ASN 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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322B GLU* 3.0 24.1 + - - +
323B GLU* 3.5 8.5 - - - +
325B ALA* 1.3 76.5 - - - +
327B TYR* 1.3 59.0 + - - +
330B ASN* 2.8 33.6 + - - +
393B ARG* 2.7 54.2 + - - +
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Residues in contact with TYR 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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313B PHE* 3.5 25.9 - + - -
315B LEU* 5.0 2.5 - - + -
319B LEU* 4.4 9.2 - - + -
323B GLU 3.0 16.5 + - - +
324B LEU* 3.7 3.6 - - + +
325B ALA 3.2 0.2 - - - -
326B ASN* 1.3 77.1 - - - +
328B LEU* 1.3 77.6 + - + +
329B ASP 3.5 0.2 + - - -
330B ASN 3.6 0.2 + - - -
331B PHE* 3.0 33.3 - + - -
347B ILE* 4.0 7.2 - - + +
371B ILE* 3.8 27.8 - - + -
387B LEU* 4.5 6.4 + - - +
390B GLY* 3.4 32.1 - - - -
391B PHE* 4.2 9.2 - + - -
393B ARG* 2.8 31.7 + - - +
394B ILE* 3.7 28.9 - - + +
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Residues in contact with LEU 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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324B LEU* 2.9 29.4 + - + +
325B ALA* 5.1 0.7 - - - -
327B TYR* 1.3 98.2 - - + +
329B ASP* 1.3 68.3 + - - +
330B ASN 3.3 0.7 + - - -
331B PHE* 3.8 14.6 + - - +
336B MET* 3.7 37.2 - - + +
347B ILE* 3.8 33.9 - - + +
348B LEU 4.9 0.2 - - - -
349B ALA* 3.7 35.7 - - + +
371B ILE* 4.9 0.4 - - + -
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Residues in contact with ASP 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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325B ALA* 2.8 46.4 + - - +
328B LEU* 1.3 76.0 - - - +
330B ASN* 1.3 71.8 + - - +
331B PHE 3.6 3.6 + - - +
336B MET* 4.0 15.3 - - - +
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Residues in contact with ASN 330 (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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326B ASN* 2.8 39.2 + - - +
327B TYR 3.6 1.6 + - - -
328B LEU 3.2 1.0 - - - -
329B ASP* 1.3 90.5 - - - +
331B PHE* 1.3 63.6 + - - +
332B SER* 3.8 5.4 + - - -
386B ASP* 4.9 0.9 - - - +
393B ARG* 3.3 38.6 + - - +
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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