Contacts of the strand formed by residues 526 - 531 (chain B) in PDB entry 5ZF6
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 ASP 526 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 4.5 5.0 - - + +
356B TYR* 4.6 1.0 + - - -
515B THR* 3.4 0.7 - - - -
516B LYS* 2.9 42.3 + - + +
524B ILE* 3.4 7.1 + - - +
525B GLU* 1.3 79.6 - - - +
527B TYR* 1.3 79.1 + - - +
528B ARG* 2.7 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 4.5 0.9 - - - -
513B LEU* 3.8 10.3 - - + -
514B VAL 3.3 7.6 - - - -
515B THR* 3.7 22.4 - - + -
524B ILE* 4.3 7.6 - - + -
526B ASP* 1.3 86.9 + - - +
528B ARG* 1.3 81.4 + - - +
529B LEU* 4.4 14.8 - - + -
569B LYS* 3.3 22.3 + - - -
570B ILE* 3.7 34.9 - - + +
573B GLU* 2.7 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B VAL* 3.2 38.9 + - + +
353B LEU* 2.7 45.9 + - + +
356B TYR* 3.1 36.5 + - - -
364B LEU* 3.7 24.0 - - + -
513B LEU* 3.3 8.2 - - - +
514B VAL* 2.8 35.6 + - + +
526B ASP* 2.7 35.5 + - - -
527B TYR* 1.3 92.5 + - - +
529B LEU* 1.3 61.6 + - - +
530B LEU* 3.8 6.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 3.2 20.4 - - - +
511B ILE* 4.1 5.2 - - + -
512B GLY 3.4 14.8 - - - +
513B LEU* 3.9 5.4 - - + -
527B TYR* 4.3 14.9 + - + -
528B ARG* 1.3 71.9 - - - +
530B LEU* 1.3 60.9 + - - +
543B MET* 3.6 21.3 - - + -
570B ILE* 3.9 17.3 - - + +
573B GLU* 3.6 40.2 - - + +
574B ALA* 3.8 13.7 - - + +
577B GLN* 3.1 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B VAL* 3.7 30.1 - - + -
358B ARG* 3.8 16.4 - - + +
364B LEU* 3.5 16.2 - - + -
511B ILE* 3.3 7.9 - - - +
512B GLY* 2.7 35.6 + - - +
513B LEU 4.5 4.0 - - - +
514B VAL* 3.7 22.9 - - + -
528B ARG* 4.1 11.0 - - + +
529B LEU* 1.3 77.2 - - - +
531B THR* 1.3 61.1 + - - +
532B ASP 3.7 0.2 + - - -
533B ILE* 3.6 18.9 - - + +
537B GLU* 3.6 32.8 - - + +
577B GLN* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ARG* 2.8 27.7 + - - +
362B ARG* 3.3 2.1 + - - -
364B LEU 2.6 16.3 + - - -
365B THR* 3.4 24.7 + - - +
366B SER 3.3 6.7 - - - +
367B LEU* 4.4 3.6 - - + +
509B VAL* 4.7 0.2 - - + -
511B ILE* 3.9 8.3 - - + +
530B LEU* 1.3 68.6 - - - +
532B ASP* 1.3 75.6 + - + +
577B GLN* 2.7 36.4 + - - +
581B ALA* 3.7 28.7 - - + -
----------------------------------------------------------
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