Contacts of the helix formed by residues 448 - 454 (chain A) in PDB entry 1ZJA
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 ASN 448 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 4.2 2.9 - - - -
422A GLN* 3.2 13.2 - - + +
424A ASP* 3.5 37.5 - - - +
425A ASP* 4.1 10.9 + - - +
444A TYR 2.9 19.6 + - - +
445A THR 3.9 13.3 + - - -
446A GLU 4.0 2.2 + - - -
447A ILE* 1.3 77.1 - - - +
449A ALA* 1.3 66.4 + - - +
450A ALA* 3.5 2.1 + - - +
451A ARG* 3.1 37.6 + - - +
452A GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.3 14.1 - - + -
369A LEU* 3.8 17.6 - - + +
421A PHE* 4.0 19.1 - - + -
422A GLN 2.9 13.9 + - - +
423A TRP* 3.2 20.5 + - + +
448A ASN* 1.3 71.2 - - - +
450A ALA* 1.3 63.8 + - - +
452A GLU* 4.3 0.2 - - - -
453A ILE* 2.9 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A TRP 2.8 18.1 + - - +
424A ASP* 3.9 14.4 - - + -
448A ASN* 3.3 6.5 - - - +
449A ALA* 1.3 73.9 - - - +
451A ARG* 1.3 63.2 + - - +
453A ILE* 3.5 7.6 + - - +
454A GLY* 3.3 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU* 4.4 12.0 + - - -
445A THR 5.6 1.1 - - - -
446A GLU* 3.9 22.9 + - - +
448A ASN* 3.1 26.0 + - - +
450A ALA* 1.3 75.4 - - - +
452A GLU* 1.3 91.5 + - - +
454A GLY* 3.2 10.0 + - - -
455A ASP* 3.0 49.8 + - - +
458A SER* 3.7 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 5.3 3.5 + - - -
344A GLU* 4.7 5.4 - - - +
369A LEU* 3.8 33.2 - - + +
446A GLU 4.9 4.2 - - - +
447A ILE* 5.4 1.1 - - - -
448A ASN 3.0 27.0 + - - +
449A ALA 3.7 3.1 - - - +
451A ARG* 1.3 102.8 + - - +
453A ILE* 1.3 62.9 + - - +
455A ASP 3.3 8.8 + - - +
458A SER* 2.6 27.5 + - - -
459A VAL* 3.1 17.0 + - - +
460A TYR* 3.0 43.0 + - + +
461A SER* 3.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.8 28.0 - - + -
449A ALA* 2.9 26.5 + - + +
450A ALA* 4.0 6.5 - - - +
451A ARG 3.3 0.2 - - - -
452A GLU* 1.3 78.4 - - - +
454A GLY* 1.3 61.8 + - - +
455A ASP 3.2 3.9 + - - +
460A TYR* 3.9 38.0 - - + +
461A SER* 4.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ALA 3.3 8.3 + - - -
451A ARG 3.2 9.0 + - - -
453A ILE* 1.3 78.3 - - - +
455A ASP* 1.3 57.4 + - - +
456A PRO* 3.8 8.1 - - - +
----------------------------------------------------------
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