Contacts of the helix formed by residues 298 - 304 (chain X) in PDB entry 2FSM
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 298 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202X GLN* 5.1 14.1 - - - +
203X THR* 4.4 10.1 - - + -
206X ILE* 4.0 6.1 - - - -
296X ARG 4.6 5.4 - - - +
297X ILE* 1.3 75.4 - - - +
299X ALA* 1.3 59.2 + - - +
300X ALA* 3.6 7.7 + - - +
301X GLN* 3.0 42.0 + - - +
302X ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135X LEU* 3.8 14.1 - - + +
138X LEU* 4.1 11.7 - - + -
139X LYS* 3.7 30.7 - - - +
142X HIS* 4.4 11.7 + - + +
206X ILE* 3.6 18.7 - - + +
298X THR* 1.3 73.4 - - - +
300X ALA* 1.3 57.9 + - - +
302X ALA* 3.2 2.8 + - - +
303X LEU* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139X LYS* 4.2 25.9 - - + +
298X THR* 3.3 7.2 + - - +
299X ALA* 1.3 75.4 - - - +
301X GLN* 1.3 67.8 + - + +
303X LEU* 3.5 21.9 + - - +
304X ALA* 3.8 7.1 + - - +
312X HIS* 5.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 301 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296X ARG 4.5 1.6 + - - -
297X ILE* 3.4 27.6 - - + +
298X THR* 3.0 42.4 + - - +
300X ALA* 1.3 77.8 - - + +
302X ALA* 1.3 63.9 + - - +
304X ALA* 3.1 17.2 + - - +
305X HIS* 3.5 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135X LEU* 3.6 26.7 - - + -
206X ILE* 5.3 0.2 - - + -
284X LEU* 4.3 10.3 - - + -
288X MET* 4.5 1.3 - - + -
297X ILE* 3.7 22.4 - - + -
298X THR 2.9 18.2 + - - +
299X ALA 3.2 5.6 + - - +
301X GLN* 1.3 74.4 - - - +
303X LEU* 1.3 66.5 + - - +
305X HIS* 3.0 16.4 + - - +
308X PHE* 3.2 18.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132X TYR* 3.5 36.6 - - + +
135X LEU* 3.7 32.1 - - + +
136X ARG* 3.8 9.2 - - + +
139X LYS* 3.9 27.1 - - + +
299X ALA 3.0 17.2 + - - +
300X ALA* 3.7 7.9 - - - +
302X ALA* 1.3 78.5 - - - +
304X ALA* 1.3 58.1 + - - +
305X HIS 3.3 0.7 + - - -
308X PHE* 3.9 12.5 - - - +
312X HIS* 3.3 25.7 - - + +
317X GLU* 3.6 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300X ALA 3.8 5.3 + - - +
301X GLN* 3.1 13.5 + - - +
303X LEU* 1.3 76.3 - - - +
305X HIS* 1.3 61.7 + - - +
306X ALA* 3.6 1.9 + - - -
312X HIS* 3.8 25.8 - - + +
----------------------------------------------------------
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