Contacts of the strand formed by residues 558 - 562 (chain B) in PDB entry 5FLZ
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 PHE 558 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 4.2 28.5 - - + -
500B LEU* 4.8 14.6 - - + -
512B LEU* 4.4 33.9 - - + -
516B LEU* 5.6 1.1 - - + -
543B ALA* 4.3 13.9 - - + -
544B ARG 4.1 5.4 - - - -
545B VAL* 5.5 0.9 - - - +
546B LEU 5.0 0.3 - - - +
554B GLY 3.5 8.2 + - - +
555B TRP 3.3 14.5 + - - +
556B ASP 3.2 7.6 - - - +
557B VAL* 1.4 77.4 - - - +
559B THR* 1.3 79.8 + - - +
560B LEU* 3.7 32.1 - - + -
587B PHE* 6.1 1.5 - + - -
588B ASN* 4.8 10.7 + - - -
591B TRP* 3.9 30.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ARG* 2.7 50.0 + - + +
546B LEU* 3.6 38.4 - - + +
558B PHE* 1.3 91.0 - - - +
560B LEU* 1.4 74.5 + - - +
584B LEU* 4.4 19.9 - - - +
587B PHE* 5.9 5.9 - - - -
588B ASN* 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B ILE* 5.3 15.5 - - + -
488B PHE* 6.0 4.7 - - + -
492B LEU* 6.2 2.5 - - + -
516B LEU* 4.1 25.8 - - + -
541B LEU* 5.3 10.1 - - + -
542B ASP 4.2 4.0 - - - +
543B ALA* 4.4 11.7 - - + -
544B ARG* 4.3 3.7 - - - +
558B PHE* 3.7 32.3 - - + -
559B THR* 1.4 87.5 + - - +
561B ASP* 1.4 58.0 + - - +
562B TYR 4.4 0.2 + - - -
584B LEU* 4.6 11.6 - - + +
587B PHE* 3.8 37.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B GLY 3.6 0.3 - - - +
541B LEU* 3.4 9.8 - - - +
542B ASP* 2.8 49.7 + - + +
544B ARG* 3.8 32.2 + - + +
560B LEU* 1.4 72.5 - - - +
562B TYR* 1.3 73.9 + - - +
563B ILE* 4.2 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B VAL* 4.2 10.7 - - + +
477B LEU* 5.8 9.6 - - + -
536B SER* 3.3 44.1 + - - -
540B GLY* 3.4 18.2 - - - -
541B LEU* 3.9 14.8 - - + -
560B LEU 4.4 0.2 + - - -
561B ASP* 1.3 82.5 + - - +
563B ILE* 1.4 76.6 + - - +
564B LEU 4.1 0.7 + - - -
565B TYR* 4.5 28.9 - + + -
568B LEU* 6.2 2.2 - - + -
----------------------------------------------------------
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