Contacts of the strand formed by residues 257 - 262 (chain D) in PDB entry 4JFQ
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 TYR 257 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D LEU* 3.8 17.9 - - + -
217D TRP* 3.9 9.2 - + + -
218D GLN 3.2 13.9 - - - -
219D ARG* 3.5 44.5 + - + -
224D GLN* 4.4 14.3 + - + -
247D VAL* 4.1 16.8 - - + -
248D VAL 4.9 1.6 + - - -
249D VAL* 3.3 41.2 - - + +
250D PRO* 4.4 7.4 - - - +
253D GLN* 3.3 36.0 + - + -
254D GLU 2.9 13.1 + - - +
255D GLN 4.4 2.3 - - - +
256D ARG* 1.3 81.9 - - + +
258D THR* 1.3 67.0 + - - +
272D LEU 4.5 0.3 - - - +
274D TRP* 3.6 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D TRP* 3.1 10.6 - - - -
218D GLN* 2.8 43.0 + - - +
221D GLY 5.4 0.9 + - - -
255D GLN 5.1 4.0 - - - +
256D ARG 4.8 5.5 + - - +
257D TYR* 1.3 81.2 - - - +
259D CYS* 1.3 60.0 + - - +
260D HIS* 2.7 28.7 + - - -
271D THR* 4.0 8.5 - - + -
272D LEU 3.3 14.4 - - - +
273D ARG* 4.2 20.6 - - + +
274D TRP 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D MET* 3.7 14.8 - - - -
203D CYS* 2.0 55.0 - - + -
215D LEU* 4.8 3.1 - - - -
216D THR 3.4 13.0 - - - -
217D TRP* 3.7 8.8 - - + -
258D THR* 1.3 74.1 - - - +
260D HIS* 1.3 67.1 + - - +
261D VAL* 4.1 9.4 - - - -
270D LEU 3.7 0.9 - - - +
271D THR* 3.3 4.0 - - - +
272D LEU* 2.7 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D THR 3.5 1.6 - - - +
215D LEU* 3.4 6.6 - - - -
216D THR* 2.8 46.6 + - - +
218D GLN* 3.1 41.1 + - + -
258D THR* 2.7 34.4 + - - -
259D CYS* 1.3 80.9 - - - +
261D VAL* 1.3 62.1 + - - +
262D GLN* 4.2 6.1 + - + +
269D PRO* 6.5 0.9 - - + -
270D LEU 3.3 4.9 - - - +
271D THR* 3.5 27.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D PRO* 4.2 0.7 - - + -
187D THR* 4.2 21.1 - - + -
203D CYS* 4.2 5.6 - - - -
204D TRP 5.3 1.1 - - - +
205D ALA* 4.7 3.6 - - + -
213D ILE* 3.9 26.0 - - + -
214D THR 3.5 4.7 - - - +
215D LEU* 5.1 5.2 - - + -
259D CYS* 4.1 17.0 - - - -
260D HIS* 1.3 77.2 - - - +
262D GLN* 1.3 65.3 + - - +
263D HIS 4.2 0.2 - - - -
266D LEU* 3.9 16.6 - - + +
269D PRO* 3.3 5.5 - - - +
270D LEU* 2.7 45.9 + - + +
272D LEU* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D ILE* 3.1 22.8 - - - +
214D THR* 3.1 45.5 + - - +
216D THR* 4.9 8.9 + - - +
260D HIS* 5.3 4.7 + - + +
261D VAL* 1.3 78.1 - - - +
263D HIS* 1.3 60.0 + - - +
269D PRO* 4.0 22.3 - - + +
----------------------------------------------------------
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