Contacts of the helix formed by residues 524 - 529 (chain P) in PDB entry 1ZD2
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 TRP 524 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P PHE 3.9 3.8 - - - -
266P PRO* 3.7 22.4 - - + -
267P GLU* 3.6 33.7 - - + -
332P HIS* 4.4 3.6 - + - -
406P LEU* 2.9 34.8 + - + -
407P PHE* 3.5 28.9 - + - -
408P ARG 3.5 31.1 + - - -
440P MET* 3.9 9.9 - - + -
522P GLY 3.4 0.8 - - - -
523P HIS* 1.3 104.0 - + + +
525P THR* 1.3 53.5 + - - +
526P GLN* 3.6 2.9 - - - -
527P MET* 3.3 19.1 + - + -
528P ASP* 2.8 36.7 + - - +
700P NC3 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 525 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332P HIS* 3.6 3.3 + - - -
356P LEU* 4.6 11.9 - - + -
357P ASN* 2.4 35.3 + - - +
490P VAL* 5.5 1.8 - - + -
492P ALA* 4.8 1.8 - - + -
518P ILE* 4.0 8.7 - - + -
521P CYS* 3.5 26.1 - - - -
522P GLY 4.1 1.9 + - - -
523P HIS 2.6 14.7 + - - -
524P TRP* 1.3 67.8 - - - +
526P GLN* 1.3 77.0 + - - +
527P MET 3.0 1.0 + - - -
528P ASP 3.1 9.0 + - - -
529P LYS 3.1 15.1 + - - -
533P VAL* 3.6 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 526 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263P HIS* 4.8 2.4 - - - +
267P GLU* 4.6 3.1 + - - +
271P SER* 2.9 34.0 + - - +
272P TRP* 3.3 48.6 - - + +
274P TYR* 3.7 6.0 - - - -
275P GLN* 3.0 25.1 - - - +
332P HIS* 3.4 40.7 + - - +
356P LEU* 4.4 6.3 - - + -
524P TRP* 3.6 1.1 - - - -
525P THR* 1.3 75.9 + - - +
527P MET* 1.3 60.9 + - + +
530P PRO* 3.4 26.0 - - - +
533P VAL* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 527 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226P LEU* 5.7 0.7 - - - +
267P GLU* 4.0 15.5 - - - +
271P SER* 4.5 5.4 - - - +
273P ARG* 3.2 29.6 - - - +
274P TYR* 4.4 11.2 - - + -
407P PHE* 3.8 30.7 - - + -
440P MET* 3.8 26.5 - - + +
441P VAL* 3.3 29.8 - - + -
449P TYR* 3.8 15.3 - - - +
524P TRP* 3.3 23.5 + - + +
525P THR 3.1 0.8 - - - -
526P GLN* 1.3 80.3 - - + +
528P ASP* 1.3 67.4 + - - +
530P PRO* 3.3 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 528 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226P LEU* 5.9 0.3 - - - +
409P ALA* 4.4 13.1 - - - +
410P SER* 4.4 1.7 + - - -
440P MET* 3.3 22.5 - - - +
520P ASP* 3.8 2.3 - - - +
521P CYS* 3.5 12.2 - - - -
522P GLY* 2.7 30.6 + - - -
524P TRP 2.8 24.6 + - - +
525P THR 3.9 1.6 - - - +
527P MET* 1.3 76.6 - - - +
529P LYS* 1.3 96.7 + - - +
530P PRO* 3.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 529 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518P ILE* 3.6 31.4 - - + -
519P GLU 4.2 6.1 - - - +
520P ASP* 3.1 27.1 + - - -
521P CYS* 4.4 7.4 - - - -
525P THR 3.1 8.2 + - - +
528P ASP* 1.3 107.5 + - - +
530P PRO* 1.3 65.9 - - + +
532P GLU* 3.0 34.4 - - + +
533P VAL* 3.1 22.9 + - - +
----------------------------------------------------------
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