Contacts of the strand formed by residues 286 - 291 (chain A) in PDB entry 2FO1
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 LEU 286 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 4.8 17.3 - - + -
249A TRP* 5.3 13.0 - - + +
253A LYS* 6.2 1.3 - - + -
284A THR 3.8 6.3 - - - +
285A GLU* 1.3 75.4 - - - +
287A VAL* 1.3 64.1 + - - +
288A ALA 3.8 0.3 + - - -
303A ASP 3.7 7.1 - - - +
304A PHE* 3.4 47.7 + - + +
305A SER* 4.8 0.7 + - - -
322A TYR* 4.2 24.5 - - + +
347A PHE* 5.3 13.0 - - + -
348A PHE 3.9 5.8 - - - +
349A TYR* 3.7 37.0 - - + +
355A ILE* 5.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 4.3 2.2 - - + +
286A LEU* 1.3 75.2 - - - +
288A ALA* 1.3 64.6 + - - +
289A TYR* 3.7 20.9 - - + -
301A GLN* 4.3 5.6 - - - +
302A LEU 5.8 0.2 - - - -
346A GLN 3.6 1.0 - - - +
347A PHE* 3.4 1.7 - - - +
348A PHE* 2.7 78.6 + - + +
350A GLY* 4.0 9.9 - - - +
103D TYR* 3.3 46.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU 3.8 2.2 + - - -
287A VAL* 1.3 79.9 - - - +
289A TYR* 1.3 63.7 + - - +
301A GLN* 3.5 6.1 - - - +
302A LEU* 2.9 38.9 + - + +
304A PHE* 3.6 29.6 - - + -
346A GLN 3.1 10.1 - - - +
347A PHE* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 3.7 22.0 - - + -
288A ALA* 1.3 75.4 - - - +
290A ILE* 1.3 59.8 + - - +
299A ARG* 3.3 36.8 - - + +
300A GLN 3.2 5.8 - - - +
301A GLN* 2.9 45.9 + - + -
302A LEU* 4.7 1.8 - - - -
344A ASN 3.5 4.2 - - - +
345A ALA* 3.6 0.8 - - - -
346A GLN* 3.0 33.4 + - + +
348A PHE* 4.5 3.1 - + - -
99D LEU* 3.6 37.9 - - + -
102D ARG* 3.2 34.4 + - - -
103D TYR* 3.4 21.5 + - - -
106D ASP* 5.1 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ILE* 5.6 2.9 - - + -
240A PRO* 5.4 1.3 - - + -
242A ILE* 4.8 11.9 - - + -
289A TYR* 1.3 74.6 - - - +
291A GLY* 1.3 62.2 - - - +
299A ARG* 3.3 3.9 - - - -
300A GLN* 2.9 34.2 + - + +
302A LEU* 3.5 20.1 - - + +
327A ALA* 3.4 31.0 - - + -
330A LEU* 3.9 15.2 - - + +
343A LEU* 4.2 23.3 - - + -
344A ASN 3.3 25.4 - - - +
345A ALA* 3.3 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 1.3 78.4 - - - +
292A ILE* 1.3 66.4 + - - -
294A SER* 4.8 1.6 - - - -
299A ARG* 4.2 19.7 - - - -
300A GLN* 6.1 0.2 - - - -
330A LEU* 4.4 6.7 - - - -
343A LEU* 3.4 6.4 - - - +
344A ASN* 2.7 42.6 + - - +
----------------------------------------------------------
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