Contacts of the helix formed by residues 339 - 350 (chain B) in PDB entry 2R8K
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 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B ASN* 1.3 71.9 - - - +
340B GLY* 1.3 55.7 + - - +
341B GLN 3.1 2.9 - - - -
342B LEU* 2.7 27.4 + - - +
343B LYS* 3.0 9.8 + - - -
371B ALA* 3.6 25.7 - - + +
372B GLU* 3.7 20.6 - - + +
375B PHE* 3.8 23.7 - - + -
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Residues in contact with GLY 340 (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 ASN* 3.2 16.7 + - - +
339B ALA* 1.3 79.2 - - - +
341B GLN* 1.3 59.7 + - - +
343B LYS* 3.2 14.8 + - - +
344B GLU* 3.2 28.8 + - - +
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Residues in contact with GLN 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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334B THR 5.3 0.2 - - - +
335B TRP* 3.3 26.0 + - + -
336B PRO* 3.2 17.0 - - - +
337B ASP* 2.8 37.3 + - + +
338B ASN* 2.7 45.4 + - - +
339B ALA 3.1 0.4 - - - -
340B GLY* 1.3 75.8 - - - +
342B LEU* 1.3 59.1 + - - +
344B GLU* 4.1 10.2 + - - +
345B PHE* 3.9 8.3 - - - +
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Residues in contact with LEU 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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320B LEU* 4.1 22.7 - - + -
331B ILE* 5.3 4.3 - - + -
335B TRP* 4.0 41.0 - - + -
338B ASN 4.3 0.6 + - - -
339B ALA* 2.7 15.6 + - - +
341B GLN* 1.3 77.2 - - - +
343B LYS* 1.3 67.9 + - - +
345B PHE* 3.4 10.5 - - + +
346B LEU* 3.5 14.1 + - + +
371B ALA* 3.3 36.1 - - + +
374B LEU* 3.7 27.8 - - + -
375B PHE* 4.5 6.5 - - + +
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Residues in contact with LYS 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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339B ALA 3.0 7.3 + - - +
340B GLY* 3.2 14.9 + - - +
342B LEU* 1.3 73.5 - - - +
344B GLU* 1.3 62.5 + - + +
345B PHE 2.6 17.8 + - - -
346B LEU* 3.2 13.5 + - - +
347B ASP* 3.2 26.9 + - - +
367B THR* 4.5 15.0 + - + +
368B ALA* 3.8 37.0 + - + +
371B ALA* 3.5 14.5 - - + +
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Residues in contact with GLU 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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340B GLY 3.2 14.9 + - - +
341B GLN* 4.1 8.3 - - - +
342B LEU 3.4 0.2 - - - -
343B LYS* 1.3 84.9 - - + +
345B PHE* 1.3 59.3 + - - +
347B ASP* 2.6 31.6 - - - +
348B ALA* 5.5 1.1 - - - +
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Residues in contact with PHE 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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319B VAL 4.3 3.4 - - - -
320B LEU* 3.4 45.8 - - + -
321B ASP* 4.4 14.8 - - - -
334B THR* 6.3 0.2 - - + -
335B TRP* 3.6 29.6 - + - +
341B GLN 3.9 9.9 - - - +
342B LEU* 3.4 11.0 - - + +
343B LYS 2.6 8.1 + - - -
344B GLU* 1.3 76.4 - - - +
346B LEU* 1.3 57.2 + - - +
347B ASP 3.0 4.0 - - - -
348B ALA* 3.6 5.1 + - - +
349B LYS* 3.0 42.2 + - + +
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Residues in contact with LEU 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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316B LEU* 5.5 3.4 - - + -
319B VAL* 3.9 22.7 - - + -
320B LEU* 3.8 30.3 - - + -
342B LEU* 3.5 19.3 + - + +
343B LYS 3.2 5.4 + - - +
345B PHE* 1.3 77.8 - - - +
347B ASP* 1.3 60.7 + - - +
349B LYS* 3.9 4.0 - - - -
350B VAL* 2.9 39.1 + - + +
362B ILE* 5.5 5.8 - - + -
367B THR* 3.5 29.3 - - - +
370B LEU* 3.6 36.1 - - + -
371B ALA* 4.8 4.5 - - + +
374B LEU* 5.1 1.6 - - + -
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Residues in contact with ASP 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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343B LYS* 3.2 19.0 - - - +
344B GLU* 2.6 37.8 - - - +
345B PHE 3.0 3.3 - - - +
346B LEU* 1.3 76.8 - - - +
348B ALA* 1.3 60.1 + - + +
350B VAL* 2.9 26.2 - - - +
351B LYS* 2.9 29.7 - - - +
364B PRO 5.3 0.3 - - - +
367B THR* 3.9 21.1 - - - +
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Residues in contact with ALA 348 (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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344B GLU 5.5 0.9 - - - +
345B PHE* 3.6 5.8 + - - +
347B ASP* 1.3 76.1 - - + +
349B LYS* 1.3 56.8 + - - +
350B VAL 3.0 5.6 - - - -
351B LYS* 2.8 33.7 + - + +
352B GLN* 3.6 12.1 + - - +
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Residues in contact with LYS 349 (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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318B ASP* 4.4 3.8 - - - -
319B VAL* 3.1 45.3 - - + +
320B LEU* 5.0 0.4 - - - +
321B ASP* 3.3 32.9 + - - -
345B PHE* 3.0 35.4 + - + +
346B LEU* 4.0 9.0 - - - -
348B ALA* 1.3 76.9 - - - +
350B VAL* 1.3 58.5 + - - +
351B LYS 3.4 0.2 - - - -
352B GLN* 3.4 44.6 + - - +
354B ASP* 5.8 0.5 - - - +
355B TYR* 4.6 5.4 + - - +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B VAL* 4.5 15.0 - - + -
346B LEU* 2.9 20.8 + - + +
347B ASP* 2.9 26.0 - - - +
349B LYS* 1.3 77.8 - - - +
351B LYS* 1.3 64.1 + - + +
352B GLN 3.3 6.9 + - - +
355B TYR* 3.3 49.2 - - + +
362B ILE* 5.1 8.5 - - + -
364B PRO* 4.1 26.4 - - + +
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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