Contacts of the helix formed by residues 334 - 345 (chain D) in PDB entry 3REO
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 THR 334 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 5.8 1.9 - - - +
302D ILE* 4.0 1.6 - - - -
303D LEU* 3.9 34.3 - - + +
304D PRO 5.1 4.3 - - - +
305D PRO* 6.3 0.7 - - + -
333D ARG* 1.3 77.5 - - - +
335D GLU* 1.3 63.6 + - - +
336D LYS* 3.5 7.9 + - - +
337D GLU* 2.9 43.1 + - - +
338D PHE* 3.2 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ILE* 3.6 27.1 - - + +
334D THR* 1.3 74.3 - - - +
336D LYS* 1.3 65.5 + - + +
338D PHE* 3.2 10.0 + - - +
339D GLN* 2.9 26.4 + - - +
350D PHE* 3.7 24.3 - - + -
352D VAL* 3.6 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 5.9 8.3 - - + -
334D THR* 3.2 7.1 + - - +
335D GLU* 1.3 82.8 + - + +
337D GLU* 1.3 56.3 + - + +
339D GLN* 3.4 27.8 + - + +
340D ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 3.7 35.4 + - - +
276D ASP* 5.2 3.4 - - - +
303D LEU* 4.8 2.8 - - - +
331D LYS* 4.3 18.7 + - - -
332D GLU 4.4 2.0 - - - +
333D ARG* 3.4 23.1 - - + -
334D THR* 2.9 46.5 + - - +
336D LYS* 1.3 73.8 - - + +
338D PHE* 1.3 59.3 + - - +
340D ALA* 3.3 7.0 + - - +
341D LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D CYS* 4.1 16.8 - - + -
272D HIS* 5.9 1.8 - - + -
298D VAL* 4.4 2.7 - - + -
300D GLU* 3.7 33.9 - - + -
301D TYR 3.6 14.4 - - - -
302D ILE* 4.3 3.1 - - + -
332D GLU* 5.9 0.9 - - - -
333D ARG* 3.6 43.5 - - + -
334D THR 3.2 25.4 + - - -
335D GLU* 3.6 7.4 - - - +
337D GLU* 1.3 72.4 - - - +
339D GLN* 1.3 67.7 + - - +
341D LEU* 3.3 9.2 + - + +
342D ALA* 2.9 24.3 + - - +
350D PHE* 3.7 15.0 - - + -
362D MET* 3.6 27.1 - - + -
364D PHE* 3.6 19.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D GLU* 2.9 18.8 + - - +
336D LYS* 3.6 36.3 - - + +
338D PHE* 1.3 76.6 - - - +
340D ALA* 1.3 56.6 + - - +
342D ALA* 3.3 3.6 + - - +
343D MET* 3.0 57.6 + - + +
350D PHE* 3.5 48.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 6.5 1.3 - - - -
336D LYS 2.9 17.7 + - - +
337D GLU* 3.8 8.1 - - - +
338D PHE 3.2 0.2 - - - -
339D GLN* 1.3 76.4 - - - +
341D LEU* 1.3 56.6 + - - +
343D MET* 4.1 11.0 - - + +
344D ALA* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D CYS* 5.1 2.0 - - - -
276D ASP* 4.0 30.3 - - + +
279D CYS* 4.0 22.0 - - + -
280D LEU* 4.0 22.5 - - + +
283D LEU* 3.9 16.7 - - + +
333D ARG* 3.7 32.8 - - - +
337D GLU* 2.9 15.3 + - + +
338D PHE* 3.8 17.3 - - + +
340D ALA* 1.3 71.8 - - - +
342D ALA* 1.3 65.9 + - - +
344D ALA* 3.4 3.3 + - + +
345D SER* 2.9 26.8 + - - -
364D PHE* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D PHE 2.9 13.6 + - - +
339D GLN 3.4 10.1 - - - +
341D LEU* 1.3 75.6 - - - +
343D MET* 1.3 64.7 + - + +
345D SER* 3.1 19.2 + - - -
347D PHE* 3.1 28.8 + - + +
349D GLY 4.9 0.7 - - - +
350D PHE* 4.2 14.4 - - + -
364D PHE* 3.9 33.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D GLN* 3.0 58.4 + - + +
340D ALA* 4.1 9.2 - - + +
342D ALA* 1.3 80.3 - - + +
344D ALA* 1.3 62.7 + - - +
346D GLY* 3.1 14.7 + - - -
347D PHE 3.8 16.3 - - - +
348D ARG* 5.8 3.1 - - - -
350D PHE* 6.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 3.6 26.4 - - + +
284D LYS* 3.9 15.8 + - - -
340D ALA 3.0 19.7 + - - +
341D LEU* 3.9 0.7 - - + +
343D MET* 1.3 76.4 - - - +
345D SER* 1.3 57.9 + - - +
346D GLY 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 4.3 6.3 - - - -
283D LEU* 3.4 26.2 - - - +
284D LYS* 3.9 27.3 - - - +
287D TYR* 3.7 23.0 - - - +
341D LEU 2.9 17.0 + - - -
342D ALA* 3.1 7.8 + - - -
343D MET 3.1 0.6 - - - -
344D ALA* 1.3 78.2 - - - +
346D GLY* 1.3 59.2 + - - +
347D PHE* 3.2 15.5 - - - -
----------------------------------------------------------
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