Contacts of the helix formed by residues 347 - 357 (chain A) in PDB entry 4IQJ
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 GLU 347 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 4.5 8.6 - - + +
319A LEU* 4.7 14.2 - - + +
328A GLU* 3.2 36.0 - - + +
346A ASP* 1.3 88.1 - - - +
348A ARG* 1.3 63.6 + - + +
350A LEU* 3.4 18.8 + - - +
351A ALA* 3.6 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 4.7 6.0 - - - +
316A LEU* 4.1 34.8 - - + +
346A ASP* 3.3 15.5 + - - +
347A GLU* 1.3 80.4 - - + +
349A ALA* 1.3 60.1 + - - +
351A ALA* 3.5 1.8 + - - +
352A GLU* 3.0 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ASP* 3.4 27.8 + - + +
347A GLU 3.3 0.4 - - - -
348A ARG* 1.3 78.7 - - - +
350A LEU* 1.3 60.1 + - + +
352A GLU* 3.7 10.8 + - - +
353A ALA* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLU* 3.5 33.2 - - + +
331A TYR* 3.6 26.7 - - + -
332A ARG* 3.5 40.2 - - + +
335A LEU* 4.0 16.2 - - + +
346A ASP 2.9 31.9 - - - +
347A GLU* 3.7 10.1 - - - +
348A ARG 3.2 0.4 - - - -
349A ALA* 1.3 79.2 - - + +
351A ALA* 1.3 59.8 + - - +
353A ALA* 3.2 3.6 + - - +
354A LEU* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 3.9 7.6 - - + +
315A PHE* 4.0 27.2 - - + +
316A LEU* 3.6 39.7 - - + +
319A LEU* 5.7 0.4 - - + -
331A TYR* 5.1 3.3 - - + -
347A GLU 3.6 4.4 + - - +
348A ARG 3.5 4.4 + - - +
349A ALA 3.5 0.2 - - - -
350A LEU* 1.3 74.8 - - - +
352A GLU* 1.3 65.4 + - - +
354A LEU* 3.2 6.5 + - - +
355A ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 3.3 23.6 + - - +
308A GLN* 5.2 1.5 + - - +
312A GLU* 3.3 26.5 + - - +
348A ARG* 3.0 24.0 + - + +
349A ALA* 3.8 10.3 - - - +
351A ALA* 1.3 77.0 - - - +
353A ALA* 1.3 61.1 + - - +
355A ALA* 3.5 10.9 + - - +
356A ARG* 2.7 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 4.0 21.2 - - + +
349A ALA 3.1 18.8 + - - +
350A LEU 3.5 4.7 - - - +
352A GLU* 1.3 76.3 - - - +
354A LEU* 1.3 64.4 + - - +
356A ARG* 3.1 31.0 + - - +
357A VAL* 3.8 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG* 4.6 0.9 - - - -
315A PHE* 3.6 31.2 - - + -
331A TYR* 3.4 51.4 - - + -
334A VAL* 4.1 14.1 - - + -
335A LEU* 3.5 24.5 - - + -
338A LEU* 5.9 0.2 - - + -
350A LEU 2.9 20.4 + - - +
351A ALA* 3.2 1.8 + - - +
353A ALA* 1.3 77.0 - - - +
355A ALA* 1.3 62.7 + - - +
357A VAL* 3.2 23.9 + - + +
362A TRP* 3.7 31.6 + - + -
384A LEU* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN* 3.3 46.8 - - + +
311A ARG* 3.9 23.0 + - - -
312A GLU* 3.6 22.2 - - + +
315A PHE* 4.0 0.6 - - - -
351A ALA 3.0 5.5 + - - +
352A GLU 3.5 12.1 - - - +
353A ALA 3.2 0.4 - - - -
354A LEU* 1.3 78.0 - - - +
356A ARG* 1.3 60.4 + - - +
357A VAL 3.3 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLY 5.1 5.3 + - - -
304A ARG* 4.4 4.4 - - - +
308A GLN* 4.0 27.5 - - - +
352A GLU* 2.7 53.4 + - - +
353A ALA* 3.1 17.4 + - - +
355A ALA* 1.3 76.4 - - - +
357A VAL* 1.3 64.4 + - - +
358A GLU* 3.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG* 4.1 10.9 + - - -
335A LEU* 4.6 9.6 - - + -
338A LEU* 4.0 20.6 - - + -
353A ALA 3.8 10.5 - - - +
354A LEU* 3.2 22.5 + - + +
355A ALA 4.1 5.5 - - - +
356A ARG* 1.3 77.9 - - + +
358A GLU* 1.3 68.2 + - - +
361A ALA* 3.8 16.4 - - + -
362A TRP* 3.3 42.6 + - + +
----------------------------------------------------------
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