Contacts of the strand formed by residues 296 - 301 (chain D) in PDB entry 1FBA
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 ALA 296 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 3.8 44.6 - - + +
265D THR 3.7 6.9 + - - +
267D VAL* 3.0 27.6 + - - +
295D TRP* 1.3 75.5 - - - +
297D LEU* 1.3 62.1 + - - +
298D THR* 3.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D VAL* 4.8 2.5 - - + -
256D LEU* 3.9 16.4 - - + -
267D VAL* 3.6 13.9 - - + -
269D PHE* 3.7 32.3 - - + -
283D LEU* 3.7 4.0 - - - +
286D ILE* 4.0 13.2 - - + -
287D ASN* 2.9 39.7 + - - +
293D ARG* 3.6 44.2 - - + +
295D TRP* 3.5 16.3 + - + +
296D ALA* 1.3 75.1 - - - +
298D THR* 1.3 62.8 + - - +
338D ALA* 3.7 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE 5.1 0.2 - - - +
23D VAL* 3.9 20.9 - - + -
27D LYS 2.8 29.3 + - - +
28D GLY* 3.6 2.4 - - - -
267D VAL 2.8 17.3 + - - +
268D THR* 3.8 18.4 - - + -
269D PHE* 2.8 37.5 + - - +
283D LEU* 3.9 6.4 - - - +
296D ALA* 5.1 1.8 - - + -
297D LEU* 1.3 78.5 - - - +
299D PHE* 1.3 77.2 + - - +
338D ALA* 3.5 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS 4.1 2.5 - - - -
28D GLY* 3.4 39.4 - - - -
29D ILE* 2.8 40.6 + - - +
72D ASN 3.6 11.0 - - - -
73D ILE* 3.8 15.3 - - + -
268D THR* 4.0 7.5 - - - -
269D PHE 3.9 3.6 - - - -
283D LEU* 3.9 7.0 - - + -
298D THR* 1.3 91.5 + - - +
300D SER* 1.3 59.0 + - - +
301D TYR* 3.6 33.9 - + + -
305D LEU* 3.9 11.9 - - + -
331D ALA* 4.3 4.9 - - - -
334D ASN* 3.4 48.5 - - + -
335D GLY* 3.8 3.4 - - - -
338D ALA* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 3.4 29.5 - - - +
31D ALA* 4.5 1.0 - - - +
77D ILE* 3.7 4.9 - - - +
229D LYS* 2.7 45.6 + - - +
268D THR* 3.7 24.5 - - - -
269D PHE 3.0 14.9 + - - +
270D LEU* 4.1 3.3 - - - -
271D SER 4.9 0.2 + - - -
299D PHE* 1.3 75.4 - - - +
301D TYR* 1.3 61.7 + - - +
302D GLY 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE 3.0 7.5 + - - -
30D LEU* 3.5 8.5 - - - +
31D ALA* 2.9 23.4 + - - -
232D MET* 3.4 15.8 - - - +
269D PHE* 3.2 28.2 - - + +
270D LEU 4.1 1.3 - - - -
271D SER* 3.8 22.4 - - - -
279D ALA* 2.8 37.8 + - + -
283D LEU* 3.8 8.5 - - + +
299D PHE* 3.6 20.9 - + + -
300D SER* 1.3 76.9 - - - +
302D GLY* 1.3 60.8 + - - +
304D ALA* 3.9 19.5 - - + -
305D LEU* 3.5 20.9 - - + +
334D ASN* 3.3 37.2 - - - -
----------------------------------------------------------
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