Contacts of the strand formed by residues 242 - 247 (chain A) in PDB entry 5JSJ
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 VAL 242 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 4.0 24.5 - - + -
156A LEU* 4.7 0.7 - - + -
235A GLN* 3.8 1.2 - - - -
236A VAL* 3.1 38.5 + - + +
239A LYS* 2.9 29.6 + - + +
240A PRO 4.1 1.4 - - - +
241A SER* 1.3 87.5 - - - +
243A TYR* 1.3 67.8 + - - +
255A VAL* 3.5 30.1 - - + -
256A TYR 3.3 12.1 - - - +
257A ASP* 4.1 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A SER* 4.2 1.9 + - - -
213A LEU* 3.8 42.6 + - + +
214A VAL* 4.1 6.5 - - + -
232A VAL* 3.5 25.8 - - + -
234A HIS 3.2 19.7 - - - +
235A GLN* 2.9 40.3 + - + -
236A VAL 4.8 0.2 - - - +
240A PRO 3.5 15.1 + - - -
241A SER* 3.6 13.7 - - - -
242A VAL* 1.3 76.6 - - - +
244A PHE* 1.3 69.2 + - - +
245A ILE* 4.4 4.7 - - + +
254A TYR 3.5 0.3 - - - +
255A VAL* 3.4 5.2 - - - -
256A TYR 2.8 32.1 + - - +
258A LEU* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 5.2 7.2 - - + -
156A LEU* 3.7 20.9 - - + -
157A ALA* 6.3 0.4 - - + -
167A TYR* 4.1 19.7 - + - -
176A LEU* 3.9 26.5 - - + -
232A VAL* 3.5 4.0 - - - +
233A ILE* 3.0 38.3 + - + -
234A HIS* 2.9 40.6 + + + -
236A VAL* 3.7 25.6 - - + -
243A TYR* 1.3 78.7 - - - +
245A ILE* 1.3 66.7 + - - +
253A ILE* 3.6 19.7 - - + -
254A TYR 3.2 2.7 - - - -
255A VAL* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 4.5 12.8 - - + -
231A MET 3.4 12.3 - - - +
232A VAL* 4.1 20.0 - - + -
233A ILE* 4.8 1.1 - - - -
243A TYR* 4.4 5.6 - - + +
244A PHE* 1.3 81.0 - - - +
246A LYS* 1.3 65.3 + - - +
247A PHE* 3.8 34.0 + - + -
253A ILE* 3.9 4.7 - - - -
254A TYR* 2.7 43.4 + - + +
256A TYR* 3.5 34.8 - - + -
258A LEU* 4.6 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.8 33.9 - - + -
99A GLY 3.3 27.1 + - - -
100A LEU* 5.4 0.2 - - - +
230A GLY* 3.1 2.1 - - - -
231A MET* 2.8 39.3 + - + +
233A ILE* 4.1 16.7 - - + +
245A ILE* 1.3 71.0 - - - +
247A PHE* 1.3 72.5 + - - +
248A ASP* 4.7 6.8 + - - +
249A ASP 4.8 1.2 - - - +
250A ASP 2.9 29.1 + - - +
251A PHE* 4.2 1.1 - - - +
252A HIS 4.1 10.3 - - - +
253A ILE* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 5.1 3.6 - - + -
219A GLU* 5.2 0.9 - - - -
220A TYR* 3.9 25.1 - + + -
228A ARG* 3.8 40.4 - - + +
229A THR 3.3 22.2 - - - +
230A GLY* 4.0 3.6 - - - -
245A ILE* 3.8 23.3 + - + -
246A LYS* 1.3 83.2 + - - +
248A ASP* 1.3 67.2 + - - +
250A ASP* 2.9 35.1 + - + +
252A HIS 4.9 2.0 + - - -
254A TYR* 3.5 45.1 - + + -
256A TYR* 3.9 19.3 - + - -
----------------------------------------------------------
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