Contacts of the helix formed by residues 346 - 357 (chain B) in PDB entry 3E0D
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 ASP 346 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU* 5.3 0.2 - - - -
332B ARG* 4.1 20.1 + - - +
347B GLU* 1.3 75.3 + - - +
348B ARG* 3.6 17.5 + - - +
349B ALA* 3.4 33.6 + - + +
350B LEU* 3.4 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 4.6 15.8 - - + +
319B LEU* 3.5 40.3 - - + +
320B ARG* 5.2 5.9 - - - +
328B GLU* 3.4 26.7 - - + +
331B TYR* 5.6 0.3 - - - -
346B ASP* 1.3 78.5 + - - +
348B ARG* 1.3 65.7 + - - +
350B LEU* 3.3 26.2 + - - +
351B ALA* 3.7 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG* 6.1 1.1 - - - +
312B GLU* 5.3 4.6 + - - +
316B LEU* 3.7 40.3 - - + +
346B ASP* 3.6 13.6 + - - +
347B GLU* 1.3 81.1 + - + +
349B ALA* 1.3 58.1 + - - +
351B ALA* 3.2 4.3 + - - +
352B GLU* 3.0 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASP* 3.4 27.9 + - + +
347B GLU 3.3 1.0 - - - -
348B ARG* 1.3 79.5 - - - +
350B LEU* 1.3 59.7 + - + +
352B GLU* 3.7 10.6 - - - +
353B ALA* 3.2 26.0 + - - +
356B ARG* 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 5.7 0.2 - - + -
328B GLU* 4.0 34.8 - - + +
331B TYR* 4.3 16.4 - - + -
332B ARG* 3.8 38.6 - - + +
335B LEU* 3.7 26.0 - - + +
346B ASP 3.4 17.7 - - - +
347B GLU 3.3 8.5 + - - +
348B ARG 3.2 0.4 - - - -
349B ALA* 1.3 76.3 - - + +
351B ALA* 1.3 54.6 + - - +
353B ALA* 3.3 7.3 + - - +
354B LEU* 2.8 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLU* 3.9 9.1 - - + +
315B PHE* 3.9 22.3 - - + -
316B LEU* 3.8 32.5 - - + +
331B TYR* 5.6 2.8 - - + -
347B GLU 3.7 3.1 + - - +
348B ARG 3.2 8.2 + - - +
350B LEU* 1.3 76.1 - - - +
352B GLU* 1.3 65.0 + - - +
354B LEU* 3.1 12.4 + - - +
355B ALA* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG* 3.4 30.7 + - - +
308B GLN* 5.3 1.2 + - - -
312B GLU* 3.6 20.5 + - - +
348B ARG* 3.0 29.6 + - + +
349B ALA* 3.7 11.1 - - - +
351B ALA* 1.3 76.2 - - - +
353B ALA* 1.3 60.0 + - - +
355B ALA* 3.7 11.6 - - - +
356B ARG* 3.2 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 4.3 17.7 - - + +
349B ALA 3.2 15.9 + - - +
350B LEU* 3.4 7.0 - - - +
351B ALA 3.1 0.6 - - - -
352B GLU* 1.3 76.0 - - - +
354B LEU* 1.3 63.2 + - - +
355B ALA 3.1 2.0 - - - -
356B ARG* 3.1 31.2 + - - +
357B VAL* 3.7 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 5.0 0.5 - - - -
315B PHE* 3.8 27.1 - - + -
331B TYR* 3.4 43.7 - - + +
334B VAL* 4.4 14.6 - - + -
335B LEU* 3.7 24.9 - - + -
350B LEU 2.8 28.4 + - - +
351B ALA* 3.1 10.1 + - - +
353B ALA* 1.3 72.9 - - - +
355B ALA* 1.3 62.2 + - - +
357B VAL* 3.3 25.1 + - + +
362B TRP* 4.1 29.4 + - + -
384B LEU* 5.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLN* 3.5 41.2 - - + +
311B ARG* 3.7 19.5 + - + +
312B GLU* 3.8 15.5 - - + +
315B PHE* 3.9 9.6 - - - -
351B ALA 2.9 15.3 + - - +
352B GLU 3.7 8.7 - - - +
353B ALA 3.1 0.2 - - - -
354B LEU* 1.3 78.5 - - - +
356B ARG* 1.3 59.7 + - - +
357B VAL 3.6 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLY 5.8 1.0 + - - -
304B ARG* 3.6 10.7 - - - +
308B GLN* 3.3 28.0 + - - +
349B ALA 5.4 0.2 + - - -
352B GLU* 3.2 56.1 + - - +
353B ALA* 3.1 18.1 + - - +
355B ALA* 1.3 76.5 - - - +
357B VAL* 1.3 66.5 + - - +
358B GLU* 3.1 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 4.3 9.4 + - - -
335B LEU* 4.8 9.6 - - + -
338B LEU* 3.7 28.5 - - + -
353B ALA 3.8 10.8 - - - +
354B LEU* 3.3 22.3 + - + +
355B ALA 3.9 6.4 - - - +
356B ARG* 1.3 76.4 - - - +
358B GLU* 1.3 67.2 + - - +
361B ALA* 4.1 7.2 - - + -
362B TRP* 3.4 46.9 + - + +
----------------------------------------------------------
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