Contacts of the helix formed by residues 334 - 347 (chain B) in PDB entry 2EHQ
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 334 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL* 3.4 28.5 - - + +
298B ASP 3.6 20.6 - - - +
299B GLU* 4.0 0.4 - - - +
303B PHE* 4.2 13.5 - - + -
330B LEU* 4.4 2.5 - - + -
331B THR* 2.9 10.9 + - - +
333B GLY* 1.3 76.5 - - - +
335B TYR* 1.3 65.7 + - - +
336B GLU 3.6 0.7 - - - -
337B PRO* 3.4 1.7 - - - +
338B VAL* 3.0 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 3.6 22.2 - - + +
331B THR 3.0 10.5 + - - +
332B GLN 3.3 14.5 + - - +
333B GLY 3.4 0.2 - - - -
334B ALA* 1.3 76.8 - - - +
336B GLU* 1.3 77.2 + - + +
339B LEU* 2.9 62.2 + - + +
405B THR* 3.6 17.7 - - - -
406B GLU* 3.6 18.4 + - - -
425B VAL* 3.9 19.3 - - + -
427B ARG* 3.2 64.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLN 4.7 2.1 + - - +
335B TYR* 1.3 102.5 - - + +
337B PRO* 1.4 74.5 - - + +
339B LEU* 4.1 5.4 - - - +
340B GLU* 2.9 31.8 + - - +
427B ARG* 3.8 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 3.5 32.5 - - + -
332B GLN 5.5 0.2 - - - +
333B GLY 3.7 16.8 - - - +
334B ALA 3.4 12.1 - - - +
336B GLU* 1.4 94.5 - - + +
338B VAL* 1.3 59.5 + - - +
340B GLU* 3.2 15.9 - - + +
341B ARG* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL* 3.8 25.6 - - + -
303B PHE* 3.4 35.4 - - + +
306B ALA* 4.8 8.3 - - + -
307B ALA 5.0 3.6 - - - +
310B VAL* 5.3 0.4 - - + -
328B LEU* 4.4 4.3 - - + -
330B LEU* 3.7 23.1 - - + -
334B ALA* 3.0 20.9 + - + +
337B PRO* 1.3 73.9 - - - +
339B LEU* 1.3 63.0 + - - +
341B ARG* 3.2 7.1 + - - +
342B VAL* 2.8 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 5.4 1.1 - - + -
330B LEU* 4.1 8.9 - - + +
335B TYR* 2.9 53.8 + - + +
336B GLU* 4.1 7.2 - - - +
338B VAL* 1.3 78.8 - - - +
340B GLU* 1.3 57.0 + - - +
342B VAL* 3.3 8.6 + - + +
343B LEU* 2.9 57.2 + - + +
386B VAL* 6.1 0.4 - - + -
403B VAL* 4.4 5.2 - - + -
405B THR* 3.7 25.8 - - + -
425B VAL* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLU* 2.9 23.4 + - + +
337B PRO* 3.2 15.1 - - - +
339B LEU* 1.3 77.4 - - - +
341B ARG* 1.3 76.9 + - + +
343B LEU* 3.9 7.6 - - - +
344B LYS* 3.1 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 3.7 33.0 - - - +
304B ASP* 2.9 34.3 + - - +
307B ALA* 3.5 17.0 - - + -
337B PRO* 2.9 37.0 + - - +
338B VAL* 3.2 3.6 + - - +
340B GLU* 1.3 96.9 + - + +
342B VAL* 1.3 64.4 + - - +
344B LYS* 3.4 9.5 + - + +
345B ARG* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA* 3.9 24.0 - - - +
310B VAL* 4.0 16.2 - - + -
311B VAL* 4.0 14.4 - - + +
315B TYR* 5.5 1.3 - - + -
328B LEU* 4.1 7.6 - - + -
338B VAL* 2.8 31.7 + - + +
339B LEU* 3.8 10.8 - - + +
341B ARG* 1.3 75.9 - - - +
343B LEU* 1.3 57.7 + - + +
345B ARG* 3.8 1.2 - - - +
346B ALA* 2.8 33.8 + - + +
403B VAL* 5.0 8.7 - - + -
423B LEU* 4.2 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 2.9 42.3 + - + +
340B GLU* 3.9 6.1 - - - +
342B VAL* 1.3 76.0 - - + +
344B LYS* 1.3 56.8 + - + +
346B ALA* 4.1 2.4 - - - +
347B GLU* 3.0 40.3 + - - +
386B VAL* 3.9 34.5 - - + +
387B LEU* 4.0 16.0 - - + +
403B VAL* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLU* 3.1 45.7 + - + +
341B ARG* 3.8 9.4 - - + +
343B LEU* 1.3 74.8 - - - +
345B ARG* 1.3 63.7 + - + +
347B GLU* 3.3 30.2 - - - +
348B ARG* 3.4 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ASP* 3.5 30.3 + - - +
307B ALA* 3.7 18.1 - - - +
308B GLU* 3.5 50.2 - - - +
311B VAL* 3.8 14.8 - - + -
341B ARG* 3.0 17.8 + - - +
342B VAL 3.8 2.9 - - - +
344B LYS* 1.3 76.1 - - + +
346B ALA* 1.3 64.3 + - - +
348B ARG* 3.1 43.8 + - - +
349B LEU* 3.7 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B VAL* 4.5 3.1 - - + -
315B TYR* 4.0 27.8 - - + +
342B VAL* 2.8 24.2 + - + +
343B LEU* 4.6 0.2 - - - -
345B ARG* 1.3 73.2 - - - +
347B GLU* 1.3 62.2 + - - +
349B LEU* 3.1 32.6 + - + +
387B LEU* 3.6 21.9 - - + +
401B PRO* 4.2 9.3 - - + +
403B VAL* 5.0 0.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
343B LEU* 3.0 21.1 + - - +
344B LYS* 3.3 31.3 - - - +
346B ALA* 1.3 77.7 - - - +
348B ARG* 1.3 64.2 + - + +
349B LEU 3.4 4.0 + - - +
387B LEU* 4.0 25.8 - - + +
----------------------------------------------------------
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