Contacts of the helix formed by residues 396 - 400 (chain A) in PDB entry 4ZPK
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 ILE 396 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A SER* 5.6 0.4 - - - +
367A HIS* 3.5 28.0 - - + +
371A GLY* 3.9 13.2 + - - +
373A PHE* 3.5 23.6 - - + -
395A ASN* 1.3 87.3 + - - +
397A VAL* 1.3 64.1 + - + +
398A GLU 3.1 2.7 - - - -
399A PHE* 2.9 26.6 + - - +
400A CYS 3.6 2.3 + - - -
408A LEU* 4.3 16.7 - - + +
412A PHE* 4.4 20.0 - - + -
427A PHE* 4.9 14.6 - - + -
429A PHE* 4.6 13.2 - - + -
441A THR* 6.4 1.6 - - + -
459A CYS* 6.2 0.4 - - + -
461A ASN* 5.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASN* 3.0 26.3 + - + +
396A ILE* 1.3 75.2 - - + +
398A GLU* 1.3 63.0 + - + +
399A PHE 2.9 5.8 - - - -
400A CYS 2.9 14.9 + - - -
405A GLN* 3.1 38.6 - - + +
408A LEU* 3.7 35.4 - - + -
409A ARG* 4.6 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 3.9 25.7 - - - +
395A ASN* 4.1 27.1 + - + +
397A VAL* 1.3 82.1 - - + +
399A PHE* 1.3 77.5 + - + +
400A CYS 4.4 1.1 - - - -
405A GLN* 4.6 5.2 - - - +
430A ARG* 3.2 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 5.3 3.4 - + - -
386A TYR* 3.8 29.8 - + - -
390A GLU 4.2 2.5 - - - -
391A LEU* 4.0 16.2 - - + -
394A LYS* 3.2 34.5 - - - -
395A ASN 4.2 9.0 - - - -
396A ILE* 2.9 16.1 + - - +
398A GLU* 1.3 99.1 - - + +
400A CYS* 1.3 63.6 + - - +
429A PHE* 3.2 45.0 - + + -
430A ARG* 2.9 43.1 + - + +
436A TRP* 3.7 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE 3.6 1.4 + - - -
397A VAL 2.9 12.1 + - - +
398A GLU 4.4 1.2 - - - -
399A PHE* 1.3 83.3 + - - +
401A HIS* 1.3 67.0 + - - +
402A PRO* 3.7 2.9 - - - +
404A ASP* 3.5 14.1 - - - -
405A GLN* 2.7 54.9 + - + -
408A LEU* 3.5 24.2 - - + -
427A PHE* 3.4 25.7 - - + -
428A ARG 3.1 6.7 - - - -
430A ARG* 4.6 1.9 + - - -
436A TRP* 3.7 4.8 - - - -
----------------------------------------------------------
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