Contacts of the strand formed by residues 244 - 253 (chain A) in PDB entry 5JKC
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 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY* 4.9 1.6 - - - -
165A CYS* 4.0 14.7 - - - -
182A CYS* 4.5 6.5 - - - -
184A LEU* 4.0 1.8 - - + -
186A TRP* 3.4 11.1 - - - -
187A HIS* 2.9 33.9 + - + +
233A CYS 3.6 0.7 - - - +
234A GLU* 3.4 5.4 - - - -
235A LEU* 3.0 37.1 + - - +
242A PRO* 3.5 1.1 - - - +
243A ALA* 1.3 82.8 + - - +
245A ILE* 1.3 67.4 + - - +
246A ILE* 3.8 31.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
163A TYR* 4.0 46.7 + - + +
164A ASP* 4.8 10.2 - - - +
165A CYS* 3.2 30.3 + - - +
166A GLY 4.1 0.9 + - - -
232A ARG* 3.9 29.2 - - + -
233A CYS 3.2 3.4 - - - -
234A GLU* 4.2 11.9 - - + +
242A PRO* 3.9 29.8 - - + +
244A THR* 1.3 79.3 - - - +
246A ILE* 1.3 62.3 + - - +
247A ASN* 4.0 9.6 - - - +
42B LYS* 4.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A CYS* 3.8 11.4 - - + -
166A GLY 3.7 15.9 - - - +
168A ARG* 3.9 28.0 - - + +
181A ASP 4.6 2.2 - - - +
182A CYS* 3.5 41.7 - - - +
184A LEU* 4.3 7.6 - - + -
232A ARG* 3.5 2.4 - - - +
233A CYS* 2.8 35.5 + - + +
244A THR* 3.8 13.7 - - + +
245A ILE* 1.3 79.5 - - - +
247A ASN* 1.3 69.2 + - - +
248A PHE* 3.8 24.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 5.4 2.8 - - - +
166A GLY 3.8 6.3 + - - +
167A GLU* 3.2 23.7 - - + +
168A ARG* 2.6 32.3 + - - -
201A VAL* 5.4 4.8 - - - +
230A SER* 5.6 3.0 - - - -
231A TYR 3.5 12.3 + - - -
232A ARG* 3.8 30.0 - - - +
245A ILE* 4.0 8.3 - - - +
246A ILE* 1.3 77.6 - - - +
248A PHE* 1.3 55.6 + - - +
249A HIS* 4.7 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 3.4 29.8 - - + +
170A VAL* 4.4 7.9 - - + -
180A LEU* 3.8 43.7 - - + -
181A ASP 3.6 34.1 - - - -
182A CYS* 4.3 4.5 - - - -
198A PHE* 4.3 7.4 - + - -
229A GLY 3.8 0.7 - - - +
230A SER* 3.6 3.8 - - - -
231A TYR* 2.9 49.7 + - + +
232A ARG 5.0 0.2 - - - -
233A CYS* 3.9 16.4 - - + -
246A ILE* 3.8 28.3 - - + -
247A ASN* 1.3 76.3 - - - +
249A HIS* 1.3 63.4 + - - +
250A VAL* 4.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 3.7 43.8 + - + +
168A ARG 2.8 13.6 + - - +
169A ASN* 3.7 8.8 - - - +
170A VAL 2.8 28.4 + - - +
229A GLY 3.6 3.9 + - - +
230A SER* 3.0 30.8 + - - -
247A ASN* 4.7 11.4 - - + +
248A PHE* 1.3 75.5 + - - +
250A VAL* 1.3 62.0 + - - +
251A THR* 3.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 3.3 18.2 - - + +
172A VAL* 4.7 9.4 - - + -
178A MET* 3.9 22.0 - - - -
180A LEU* 4.5 7.0 - - + -
223A VAL* 5.7 0.9 - - + -
227A ASP* 3.8 15.7 - - + +
228A ALA* 3.3 8.0 - - - +
229A GLY* 2.8 39.0 + - - +
231A TYR* 3.7 29.4 - - + -
248A PHE* 4.8 2.5 - - + -
249A HIS* 1.3 76.0 - - - +
251A THR* 1.3 71.9 + - - +
252A VAL* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 4.2 8.0 + - - -
170A VAL 2.9 6.4 + - - +
171A GLU* 3.2 26.9 - - + +
172A VAL 2.9 24.9 + - - -
228A ALA* 4.6 1.6 - - - -
249A HIS 4.9 1.0 + - - -
250A VAL* 1.3 75.3 - - - +
252A VAL* 1.3 70.3 + - - +
253A LEU* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.4 10.8 - - + +
174A GLN* 3.8 33.7 + - - +
223A VAL* 4.1 13.2 - - + -
224A GLY 3.5 29.8 - - - +
225A PRO* 4.1 8.1 - - + +
227A ASP 4.2 1.1 - - - -
228A ALA* 3.7 30.0 - - + +
250A VAL* 4.2 8.5 - - + -
251A THR* 1.3 80.9 - - - +
253A LEU* 1.3 60.7 + - - +
254A PRO* 3.3 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 3.9 37.7 - - + +
172A VAL 2.9 14.2 + - - +
173A PRO* 3.9 20.4 - - + +
174A GLN* 3.0 22.0 + - - +
251A THR* 4.4 15.0 - - + -
252A VAL* 1.3 69.4 - - - +
254A PRO* 1.4 75.3 - - + +
----------------------------------------------------------
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