Contacts of the strand formed by residues 250 - 257 (chain A) in PDB entry 2FBW
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 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 4.6 0.9 - - + +
220A TYR* 4.0 27.1 - - + +
247A LEU 3.8 15.7 - - - +
248A GLU 3.4 5.9 + - - +
249A PHE* 1.3 75.9 - - - +
251A GLN* 1.3 66.0 + - - +
252A PHE* 3.4 17.9 - - + -
363A VAL* 4.0 31.2 - - + -
365A TYR 3.9 7.4 - - - +
366A ASN* 4.2 15.9 - - - +
367A MET* 3.7 2.9 - - - +
484A ARG* 4.2 12.1 + - - +
535A THR* 4.0 12.1 - - + -
548A ALA* 3.5 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL* 1.3 72.1 - - - +
252A PHE* 1.3 72.6 + - - +
253A HIS 4.2 2.0 - - - +
297A ARG* 3.0 37.8 + - + +
298A ASP 6.2 0.2 - - - +
363A VAL* 3.8 1.7 - - - -
364A HIS* 2.9 31.3 + - + -
365A TYR* 2.8 27.1 + - + +
367A MET* 3.4 17.0 - - + +
407A ASN* 3.6 17.5 - - - +
408A ARG* 3.0 50.5 + - - +
548A ALA* 4.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 4.6 4.5 - + - -
250A VAL* 3.4 19.5 + - + -
251A GLN* 1.3 77.4 - - - +
253A HIS* 1.3 59.2 + - - +
254A PRO* 3.7 3.5 - - - +
297A ARG* 4.1 6.4 - - - +
298A ASP* 5.5 0.5 - - - -
301A SER* 2.8 29.0 + - - +
361A PRO* 4.4 2.2 - - + -
362A THR* 3.5 13.7 - - - +
363A VAL* 3.2 39.3 - - + -
477A GLN* 5.0 7.0 - - - -
480A ALA 3.8 8.3 - - - -
481A ALA* 3.6 37.9 - - + -
482A VAL* 3.6 32.5 - - + -
484A ARG* 4.3 8.7 - - - -
548A ALA* 5.1 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A THR* 4.9 3.6 - - + -
251A GLN* 4.8 3.1 - - - -
252A PHE* 1.3 69.7 - - - +
254A PRO* 1.3 70.1 - - + +
255A THR* 3.0 45.1 + - - -
256A GLY 4.4 0.5 + - - -
263A LEU* 3.2 33.2 - - + +
264A ILE 3.7 4.7 - - - -
266A GLU 4.0 8.3 + - - -
269A ARG* 4.0 15.3 - - - -
297A ARG* 3.5 39.7 + - - +
301A SER* 3.7 0.2 - - - -
360A LEU 4.1 0.2 - - - +
361A PRO* 3.0 1.7 - - - +
362A THR 2.8 33.9 + - - +
364A HIS* 3.5 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PHE 3.7 5.2 - - - +
253A HIS* 1.3 96.8 - - + +
255A THR* 1.3 60.4 + - + +
256A GLY 3.9 0.4 - - - -
269A ARG* 3.8 18.2 - - - +
297A ARG* 3.9 24.0 - - + +
300A VAL* 3.6 26.7 - - + -
301A SER* 3.5 14.1 - - - +
304A MET* 2.9 42.9 - - - +
360A LEU 3.2 12.8 - - - -
361A PRO* 3.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A HIS* 3.0 18.2 + - - -
254A PRO* 1.3 87.6 - - + +
256A GLY* 1.3 60.2 + - - +
263A LEU* 4.0 1.3 - - - -
264A ILE* 2.7 53.8 + - - +
265A THR 4.5 1.9 + - - -
269A ARG* 4.2 12.3 + - - +
275A LEU* 3.9 19.3 - - + -
323A LEU* 4.5 8.5 - - + +
359A VAL* 3.8 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A THR* 4.7 3.3 - - - +
253A HIS* 4.4 1.0 + - - -
255A THR* 1.3 75.4 - - - +
257A ILE* 1.3 67.1 + - - -
261A GLY 4.0 7.6 - - - -
262A CYS 3.4 9.6 - - - -
263A LEU* 4.3 2.5 - - - -
359A VAL* 3.3 4.4 - - - -
360A LEU* 3.0 31.9 + - - +
362A THR* 3.6 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A THR 4.0 0.8 + - - -
256A GLY* 1.3 72.5 - - - -
258A TYR* 1.3 67.2 + - - +
259A GLY 3.3 0.7 + - - -
260A ALA* 3.7 17.7 - - + -
261A GLY* 2.9 39.3 + - - +
262A CYS* 2.7 26.1 + - + +
264A ILE* 4.2 17.2 - - + +
343A THR* 4.5 2.2 - - + +
344A ALA* 4.2 13.2 - - - -
347A PHE* 4.3 12.8 - - + +
348A ALA* 3.8 28.7 - - + -
357A ILE* 3.9 18.4 - - + -
358A PRO* 3.5 12.6 - - + +
359A VAL* 4.5 2.2 - - - +
360A LEU* 4.5 2.5 - - - +
----------------------------------------------------------
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