Contacts of the helix formed by residues 337 - 342 (chain f) in PDB entry 5T0J
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 337 (chain f).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326f LEU* 3.4 38.0 - - - +
327f GLY* 3.7 12.0 - - - -
330f TYR* 3.8 30.9 - - + -
336f GLU* 1.3 83.6 + - - +
338f VAL* 1.3 49.0 + - - +
339f LEU* 2.9 14.8 + - - +
340f THR* 2.5 32.1 + - - -
341f LEU* 2.8 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335f ARG* 5.1 11.9 - - + +
336f GLU 2.8 23.4 + - - +
337f ASP* 1.3 76.3 - - - +
339f LEU* 1.3 68.8 + - + +
341f LEU* 3.9 18.4 + - + +
342f LEU* 4.0 12.0 + - - +
363f CYS* 5.0 12.1 - - - -
367f ALA* 5.8 5.6 - - - -
370f SER* 5.0 6.5 - - - +
375f VAL* 4.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336f GLU* 5.9 3.1 - - - +
337f ASP* 2.9 9.8 + - - +
338f VAL* 1.3 87.1 - - + +
340f THR* 1.3 92.4 + - + +
341f LEU 3.2 1.5 + - - -
342f LEU* 3.7 8.1 + - - +
343f LEU* 4.0 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 340 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326f LEU* 4.9 6.0 - - - +
337f ASP* 2.5 27.9 + - - -
339f LEU* 1.3 95.8 - - + +
341f LEU* 1.3 62.1 + - - +
342f LEU 3.4 0.2 - - - -
343f LEU* 3.5 21.0 + - + +
344f PRO* 3.3 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323f ILE* 4.5 2.9 - - + +
326f LEU* 4.0 14.1 - - + -
327f GLY* 3.9 27.1 - - - +
336f GLU 5.1 2.9 - - - +
337f ASP* 2.8 36.2 + - - +
338f VAL* 3.9 15.7 - - + +
339f LEU 3.2 0.8 - - - -
340f THR* 1.3 78.0 - - - +
342f LEU* 1.3 58.0 + - - +
344f PRO* 3.4 4.9 - - - +
359f THR* 3.2 24.5 + - - +
362f ALA* 3.6 28.5 - - + +
363f CYS* 3.7 28.7 - - + +
366f ILE* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338f VAL 4.0 10.6 + - - +
339f LEU 3.7 5.3 + - - +
340f THR 3.4 0.2 - - - -
341f LEU* 1.3 77.6 - - - +
343f LEU* 1.3 64.0 + - - +
344f PRO 3.5 0.4 - - - -
345f VAL* 3.3 28.2 - - + +
346f MET* 3.8 26.7 + - + +
363f CYS* 4.0 28.5 - - + -
378f THR* 3.7 26.0 - - + +
379f ILE* 5.0 3.4 - - + -
382f THR* 3.5 34.3 - - + +
----------------------------------------------------------
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