Contacts of the helix formed by residues 338 - 350 (chain A) in PDB entry 2R8J
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 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A TRP* 4.4 0.5 - - - +
337A ASP* 1.3 82.4 - - - +
339A ALA* 1.3 62.7 + - - +
340A GLY* 3.5 9.8 + - - +
341A GLN* 2.9 45.4 + - - +
342A LEU 4.0 1.0 + - - -
375A PHE* 3.7 21.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASN* 1.3 74.2 - - - +
340A GLY* 1.3 63.0 + - - +
341A GLN 3.2 0.5 + - - -
342A LEU* 3.2 4.7 + - - +
343A LYS* 2.8 27.0 + - - +
368A ALA 5.3 0.9 - - - +
371A ALA* 3.7 5.9 - - + +
372A GLU* 3.6 40.4 - - + +
375A PHE* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASN* 3.0 13.9 + - - +
339A ALA* 1.3 78.4 - - - +
341A GLN* 1.3 65.8 + - - +
343A LYS* 3.1 24.0 + - - +
344A GLU* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A TRP* 3.4 28.5 + - + -
337A ASP* 2.9 44.9 + - + +
338A ASN* 2.9 35.4 + - - +
340A GLY* 1.3 77.8 - - - +
342A LEU* 1.3 62.3 + - - +
344A GLU* 3.7 5.9 + - - +
345A PHE* 3.5 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.4 7.6 - - + -
331A ILE* 3.8 19.3 - - + +
335A TRP* 3.2 52.5 - - + +
338A ASN 4.0 0.8 + - - +
339A ALA* 3.2 8.7 + - - +
341A GLN* 1.3 76.5 - - - +
343A LYS* 1.3 66.1 + - - +
345A PHE* 3.2 3.2 + - - +
346A LEU* 3.2 43.5 + - + +
371A ALA* 3.7 21.1 - - + +
374A LEU* 4.4 20.2 - - + -
375A PHE* 5.1 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ALA* 2.8 15.6 + - - +
340A GLY* 3.1 19.5 + - - +
342A LEU* 1.3 76.0 - - - +
344A GLU* 1.3 64.7 + - + +
346A LEU* 2.9 21.2 + - - +
347A ASP* 2.9 28.5 + - - +
367A THR* 4.2 4.4 + - + +
368A ALA* 3.6 45.3 + - + +
371A ALA* 3.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLY* 3.1 18.1 + - - +
341A GLN* 4.3 5.2 + - - +
343A LYS* 1.3 85.5 - - + +
345A PHE* 1.3 57.4 + - - +
346A LEU 3.3 0.2 - - - -
347A ASP* 3.8 14.3 - - + +
348A ALA* 3.2 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A VAL 4.8 4.0 - - - -
320A LEU* 4.0 37.0 - - + -
321A ASP* 5.6 5.6 - - + -
334A THR* 6.2 0.9 - - + -
335A TRP* 3.6 35.4 - + - +
341A GLN 3.5 13.2 + - - +
342A LEU 3.2 11.2 + - - +
343A LYS 3.0 1.0 - - - -
344A GLU* 1.3 76.8 - - - +
346A LEU* 1.3 61.6 + - + +
348A ALA* 3.5 5.2 + - + +
349A LYS* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 5.4 1.3 - - + -
319A VAL* 4.4 15.5 - - + -
320A LEU* 3.4 30.7 - - + -
342A LEU* 3.2 31.2 + - + +
343A LYS 2.9 4.1 + - - +
345A PHE* 1.3 77.3 - - + +
347A ASP* 1.3 59.7 + - - +
348A ALA 3.0 1.6 - - - -
349A LYS* 2.9 4.1 + - + -
350A VAL* 2.8 41.5 + - + +
362A ILE* 5.2 6.3 - - + -
367A THR* 3.2 31.9 - - - +
370A LEU* 3.4 33.7 - - + -
371A ALA* 4.7 0.2 - - + -
374A LEU* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LYS* 2.9 43.0 + - - +
344A GLU* 3.8 11.6 - - + +
346A LEU* 1.3 75.5 - - - +
348A ALA* 1.3 57.5 + - - +
350A VAL* 3.1 11.0 - - - +
351A LYS* 2.9 46.5 + - - +
364A PRO 4.7 0.5 - - - +
367A THR* 2.9 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU 3.2 19.5 + - - +
345A PHE* 3.9 6.7 - - + +
346A LEU 3.0 0.6 - - - -
347A ASP* 1.3 75.3 - - - +
349A LYS* 1.3 60.1 - - - +
350A VAL 3.2 2.6 + - - -
351A LYS* 3.7 15.0 + - - +
352A GLN* 3.0 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASP 5.0 2.2 + - - -
319A VAL* 3.5 44.9 - - + +
321A ASP* 3.6 16.1 + - - -
345A PHE* 3.0 30.3 + - + +
346A LEU* 2.9 9.7 + - + +
348A ALA* 1.3 77.1 - - - +
350A VAL* 1.3 60.1 + - + +
351A LYS 3.5 0.2 - - - -
352A GLN* 3.2 27.9 + - - +
354A ASP* 3.1 30.6 + - + +
355A TYR* 3.9 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 2.8 24.3 + - + +
347A ASP* 3.1 28.3 - - - +
349A LYS* 1.3 81.8 - - + +
351A LYS* 1.3 67.3 + - + +
352A GLN 3.4 6.9 + - - +
355A TYR* 3.0 40.4 + - + +
362A ILE* 5.4 13.9 - - + -
364A PRO* 5.0 20.0 - - + -
367A THR* 5.5 3.6 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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