Contacts of the strand formed by residues 248 - 257 (chain D) in PDB entry 4CFE
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 248 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D SER 5.0 0.7 - - - +
244D ILE* 3.9 6.9 - - - +
245D LYS 3.1 34.5 + - - +
246D ASP* 3.2 6.7 - - + +
247D GLY* 1.3 77.9 - - - +
249D MET* 1.3 70.6 + - - +
250D VAL* 4.0 7.9 + - + +
267D TYR* 4.4 21.3 - - + -
268D LYS 4.0 16.2 - - - +
269D PRO* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C ALA* 4.2 21.3 - - - +
547C ILE* 3.8 29.8 - - + -
548C THR* 3.9 20.9 - - - +
241D ALA* 5.6 0.7 - - + -
242D LEU 5.3 4.5 - - - +
244D ILE* 4.0 32.7 - - + +
247D GLY 4.1 1.4 + - - -
248D VAL* 1.3 72.8 - - - +
250D VAL* 1.3 63.5 + - - +
251D LEU* 3.8 32.3 + - + +
266D LEU 3.5 1.7 - - - +
268D LYS* 2.9 43.1 + - + +
270D ILE* 4.1 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C TRP* 3.5 24.1 - - + -
241D ALA* 3.5 5.5 - - - +
242D LEU* 3.2 48.7 + - + +
243D SER 6.0 1.5 - - - +
248D VAL* 4.3 11.4 - - + +
249D MET* 1.3 78.0 - - - +
251D LEU* 1.3 65.2 + - - +
265D LEU* 4.9 0.4 - - + -
266D LEU 3.4 7.0 - - - +
267D TYR* 3.5 55.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C TRP* 4.0 1.2 - - - -
540C PHE* 3.3 47.9 - - + +
543C CYS* 4.3 7.6 - - + -
544C ALA* 4.0 20.9 - - + +
547C ILE* 4.4 4.5 - - + -
239D LEU* 3.8 20.2 - - + -
240D TYR 3.6 2.0 - - - -
241D ALA* 3.7 23.8 - - + -
249D MET* 3.8 24.0 - - + +
250D VAL* 1.3 76.1 - - - +
252D SER* 1.3 62.7 + - - +
265D LEU* 3.4 2.4 - - - +
266D LEU* 2.8 37.8 + - + +
268D LYS* 6.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C TRP* 3.4 26.0 - - - -
540C PHE* 3.7 4.2 - - - -
215D LEU* 3.5 19.7 - - - +
239D LEU* 3.5 1.9 - - - +
240D TYR* 2.7 45.3 + - - +
251D LEU* 1.3 79.3 - - - +
253D ALA* 1.3 62.9 + - - +
263D THR* 3.7 9.0 - - - +
264D THR 2.8 20.4 + - - -
265D LEU* 3.7 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C PHE* 4.3 5.4 - - + -
540C PHE* 3.4 17.3 - - + -
237D ASN 4.7 2.0 - - - -
238D HIS 3.3 24.2 - - - +
240D TYR* 5.3 2.5 - - - -
252D SER* 1.3 77.2 + - - +
254D THR* 1.3 63.6 + - - +
255D HIS* 3.6 27.7 + - + +
262D VAL 3.7 1.6 - - - +
263D THR* 3.6 2.9 - - - -
264D THR* 3.3 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D ILE* 3.9 13.8 - - + +
231D PRO* 4.1 20.0 - - + -
235D MET* 4.8 11.6 + - - +
236D LEU* 3.4 30.2 - - + +
237D ASN 3.0 23.9 + - - +
238D HIS 4.3 3.6 + - - -
240D TYR* 5.9 1.7 - - - -
253D ALA* 1.3 73.6 - - - +
255D HIS* 1.3 64.9 + - - +
261D TYR* 4.3 5.4 - - + -
262D VAL 3.5 9.4 - - - +
263D THR* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C SER* 3.1 25.4 + - - -
473C ASP* 5.7 2.2 - - - -
535C HIS* 5.6 5.5 + + - -
536C THR* 3.8 40.6 + - + +
539C PHE* 4.3 9.6 - + - -
236D LEU* 4.9 2.5 - - - -
237D ASN* 3.1 30.1 + - - +
253D ALA* 3.6 30.9 + - + +
254D THR* 1.3 75.4 - - - +
256D ARG* 1.3 62.8 + - - +
257D TYR 4.2 0.2 + - - -
261D TYR* 3.5 4.0 - - - +
262D VAL* 2.9 37.2 + - + +
264D THR* 4.8 0.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ASP* 3.0 30.1 + - - +
236D LEU* 4.4 8.6 - - + +
237D ASN* 5.0 2.4 + - - -
255D HIS* 1.3 77.8 - - - +
257D TYR* 1.3 59.8 + - - +
258D LYS* 2.6 42.5 + - - +
259D LYS* 5.0 2.1 - - - +
260D LYS 3.3 17.9 - - - +
261D TYR* 3.6 30.7 - - + -
262D VAL* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D HIS 4.2 0.8 + - - -
256D ARG* 1.3 74.6 - - - +
258D LYS* 1.3 103.0 + - + +
260D LYS* 2.8 42.0 + - + +
261D TYR* 4.9 0.2 - - - +
262D VAL* 5.4 10.7 - - + +
----------------------------------------------------------
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