Contacts of the helix formed by residues 328 - 335 (chain M) in PDB entry 6FF7
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 328 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326M ASP* 2.7 11.0 + - + +
327M LEU* 1.3 79.5 - - - +
329M LEU* 1.3 51.8 + - - +
330M ARG 3.6 0.4 - - - -
331M LEU* 5.0 2.7 - - - -
332M ALA* 2.6 45.7 + - + +
349M LEU* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293M THR* 4.1 28.3 - - - -
296M PHE* 4.5 3.0 - - + +
326M ASP* 4.8 14.0 - - + +
327M LEU* 3.5 2.4 - - - +
328M GLU* 1.3 77.1 - - - +
330M ARG* 1.3 62.0 + - - +
332M ALA* 3.8 2.7 - - - +
333M ARG* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292M PHE 5.1 1.1 - - - +
296M PHE* 3.9 14.8 - - + +
314M ALA* 3.8 8.5 - - - +
317M LEU* 3.4 22.7 - - + +
318M GLY* 3.4 32.5 - - - +
327M LEU 4.8 3.5 + - - +
329M LEU* 1.3 76.4 - - - +
331M LEU* 1.3 60.9 + - - +
333M ARG* 3.3 2.3 + - - +
334M PHE* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314M ALA 5.6 0.4 - - - -
318M GLY* 4.9 5.6 - - - -
327M LEU 4.3 9.6 + - - +
328M GLU* 4.1 3.5 + - - +
329M LEU 3.4 0.2 - - - -
330M ARG* 1.3 78.5 - - - +
332M ALA* 1.3 57.9 + - - +
334M PHE* 3.3 3.7 + - - +
335M GLU* 2.9 32.6 + - - +
345M LEU* 3.6 28.9 - - + +
348M VAL* 5.8 1.1 - - + -
349M LEU* 4.1 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328M GLU* 2.6 27.1 + - + +
329M LEU* 3.9 3.8 - - - +
331M LEU* 1.3 77.3 - - - +
333M ARG* 1.3 49.9 + - - +
335M GLU* 3.8 4.6 - - - +
336M GLN* 2.5 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296M PHE* 4.6 13.5 - - + +
297M ASP* 4.9 3.1 - - + +
300M ALA* 4.3 26.1 - - + +
329M LEU 2.9 19.0 + - - +
330M ARG* 3.7 6.3 - - - +
331M LEU 3.2 0.2 - - - -
332M ALA* 1.3 76.1 - - - +
334M PHE* 1.3 58.7 + - - +
336M GLN* 2.7 23.6 + - - -
337M LEU* 2.9 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300M ALA* 6.4 0.2 - - - +
314M ALA* 3.8 27.3 - - + +
330M ARG 2.9 17.1 + - - +
331M LEU* 3.8 6.7 - - - +
333M ARG* 1.3 76.7 - - - +
335M GLU* 1.3 61.3 + - - +
336M GLN 3.5 0.2 + - - -
337M LEU* 3.7 14.4 + - - +
342M PRO* 4.5 15.6 - - + +
344M LEU* 6.4 1.1 - - + -
345M LEU* 5.2 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 335 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331M LEU 2.9 17.2 + - - +
332M ALA* 3.8 4.3 - - - +
334M PHE* 1.3 75.7 - - - +
336M GLN* 1.3 58.1 + - - +
337M LEU* 3.4 1.6 + - - -
338M ILE 4.1 8.0 - - - +
339M SER* 4.4 10.0 - - - -
340M ARG 5.1 1.6 + - - -
341M ARG* 5.9 1.1 - - - +
342M PRO* 4.2 24.1 - - + +
345M LEU* 5.2 2.9 - - + -
----------------------------------------------------------
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