Contacts of the helix formed by residues 367 - 372 (chain A) in PDB entry 1PJS
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 367 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 1.3 74.9 - - - +
368A TRP* 1.3 63.4 + - - +
369A GLU* 3.5 14.6 + - - +
370A ASN* 3.2 32.5 + - + +
371A LEU* 3.3 19.0 + - + +
397A PHE* 5.3 1.6 - - - -
373B ALA* 4.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 3.7 25.0 + - + +
366A LEU* 3.3 48.9 + - + +
367A ASP* 1.3 72.3 + - - +
369A GLU* 1.3 53.0 + - - +
371A LEU* 3.5 7.3 - - + +
372A ALA* 2.7 38.8 + - - +
380A PHE* 4.8 4.5 - + - -
386A GLN* 5.6 7.0 - - - -
389A THR* 4.3 6.5 - - - -
390A ILE* 3.7 49.4 - - + -
393A LYS* 3.5 37.8 - - + +
394A LEU* 4.2 16.1 - - + +
397A PHE* 3.5 33.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASP* 3.3 8.3 + - - +
368A TRP* 1.3 75.7 - - - +
370A ASN* 1.3 61.0 + - - +
372A ALA* 4.5 0.5 - - - +
373A ALA* 3.5 22.3 + - - +
397A PHE* 3.2 40.7 - - + +
370B ASN* 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ARG* 2.6 30.0 + - - +
367A ASP* 3.2 27.5 + - + +
369A GLU* 1.3 78.9 - - - +
371A LEU* 1.3 59.2 - - + +
373A ALA* 4.1 1.7 - - - +
376A GLN* 3.1 11.4 + - - -
354B ARG* 3.4 0.5 + - - -
369B GLU 4.4 2.7 + - - -
370B ASN* 2.3 93.9 + - - +
373B ALA* 4.0 10.5 - - - +
376B GLN* 4.3 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ARG* 4.6 12.3 - - - +
356A VAL* 3.9 19.5 - - + -
366A LEU* 4.1 31.0 - - + -
367A ASP* 3.3 20.5 + - + +
368A TRP* 3.2 11.8 + - + +
370A ASN* 1.3 78.3 - - - +
372A ALA* 1.3 57.7 + - - +
373A ALA 3.3 3.1 - - - +
376A GLN* 3.2 11.0 + - - +
378A LEU* 3.0 63.4 - - + +
380A PHE* 3.6 21.5 - - + -
394A LEU* 3.6 7.1 - - + +
399A MET* 4.7 0.9 - - - +
352B SER* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TRP 2.7 20.1 + - - +
369A GLU 4.7 0.9 - - - +
371A LEU* 1.3 70.7 - - - +
373A ALA* 1.3 65.6 - - - +
374A GLU* 3.8 2.1 + - - +
394A LEU* 3.5 38.8 - - + +
397A PHE* 3.9 20.2 - - + +
398A GLY 4.5 3.4 - - - +
399A MET* 3.7 26.9 + - + +
----------------------------------------------------------
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