Contacts of the strand formed by residues 242 - 245 (chain F) in PDB entry 1SXG
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 ALA 242 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F LEU* 3.9 19.3 - - + -
177F HIS* 3.3 26.0 - - + +
179F ASN 3.4 3.2 + - - +
180F ILE* 3.2 22.3 - - + -
181F ALA 3.0 22.0 + - - -
240F PRO* 3.3 3.3 - - - +
241F THR* 1.3 80.8 - - - +
243F ILE* 1.3 66.3 + - - +
270F GLU* 3.5 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F LEU* 4.6 3.6 - - - +
180F ILE* 4.7 2.5 - - - -
181F ALA* 3.9 13.7 - - + -
183F VAL* 4.0 19.7 - - + -
230F VAL* 3.9 22.7 - - + -
233F LEU* 3.5 27.8 - - + -
234F LEU* 6.0 2.5 - - + -
240F PRO* 4.8 7.0 - - + -
242F ALA* 1.3 79.5 - - - +
244F PHE* 1.3 75.2 + - - +
245F VAL* 4.1 6.7 - - + -
254F VAL* 3.9 7.6 - - + -
269F LEU* 3.8 22.2 - - + -
270F GLU 3.2 6.1 + - - -
271F ILE* 3.2 13.1 - - + +
272F ILE* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F ALA* 3.9 36.3 - - + -
168F ALA* 3.5 20.4 - - + -
169F VAL* 5.0 6.3 - - + -
172F LEU* 5.1 3.4 - - + -
180F ILE* 4.8 8.1 - - + -
181F ALA 3.1 14.3 + - - +
182F PHE* 3.1 39.0 - + + -
183F VAL 2.8 25.3 + - - -
196F LYS* 4.9 2.2 - - + -
200F TYR* 4.7 11.2 - + + -
243F ILE* 1.3 75.9 - - - +
245F VAL* 1.3 77.5 + - - +
246F GLY* 5.1 0.9 - - - -
272F ILE* 3.4 17.3 - - + +
273F GLY 3.9 12.1 - - - -
274F PHE* 3.5 25.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F PHE* 4.5 0.9 - - - -
183F VAL* 3.4 15.0 - - + +
243F ILE* 4.1 12.6 - - + -
244F PHE* 1.3 84.5 - - - +
246F GLY* 1.3 64.0 + - - +
247F THR 3.2 20.3 + - - +
250F MET* 3.6 15.0 - - + -
251F ALA* 3.4 26.0 - - + +
254F VAL* 4.4 9.9 - - + -
271F ILE* 3.8 26.9 - - + -
272F ILE 2.8 17.2 + - - +
273F GLY 3.5 2.1 - - - -
274F PHE* 3.5 14.6 - - - +
----------------------------------------------------------
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