Contacts of the helix formed by residues 330 - 336 (chain B) 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 ARG 330 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLY* 6.1 0.2 - - - -
328B ASN 3.8 0.2 + - - -
329B PRO* 1.3 69.6 - - - +
331B ALA* 1.3 66.4 + - - +
333B SER* 3.0 6.2 + - - +
334B HIS* 2.8 22.7 + - - +
364B PHE* 3.5 15.7 - - - -
365B GLN* 2.9 33.7 + - - +
366B GLY 3.6 2.0 - - - -
367B ASP* 2.9 31.3 + - - +
371B MET* 3.5 47.5 - - - +
372B THR* 3.4 30.2 + - - +
373B ASN* 3.0 16.2 + - - +
416B ASN* 3.6 21.3 + - - +
417B ALA* 3.6 22.2 + - - +
419B THR* 4.5 4.0 + - - -
421B PHE* 5.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 3.7 38.3 + - + +
324B GLY* 5.0 1.4 - - - -
329B PRO 3.5 2.8 + - - -
330B ARG* 1.3 70.2 - - - +
332B VAL* 1.3 57.9 + - - +
334B HIS* 4.6 0.9 - - - -
335B PHE* 2.8 32.5 + - - +
350B LEU* 3.4 14.9 - - + +
367B ASP* 3.8 29.3 + - + +
463B TYR* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG* 3.3 0.4 - - - +
331B ALA* 1.3 78.5 - - - +
333B SER* 1.3 62.9 + - - +
336B GLY* 3.0 32.0 + - - -
337B ASP 3.3 7.3 + - - +
338B ASP* 3.9 4.6 + - + -
343B ARG* 3.6 18.8 - - + +
346B SER* 3.2 26.0 - - - +
347B ALA* 3.8 18.6 - - + +
350B LEU* 3.8 7.4 - - - +
367B ASP* 5.1 1.0 + - - -
370B GLY* 4.0 8.5 - - - +
371B MET 3.4 24.2 + - - +
372B THR* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG 3.0 5.6 + - - -
332B VAL* 1.3 80.2 - - - +
334B HIS* 1.3 61.1 + - - +
336B GLY 4.0 6.8 - - - +
338B ASP* 2.6 34.3 + - - -
372B THR* 3.6 5.2 - - - -
373B ASN* 2.9 52.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 3.1 32.1 - - + +
285B TYR* 5.3 2.1 + - - -
286B ASP* 2.9 37.6 + - - +
287B ARG* 5.8 1.6 - - - -
294B THR* 6.3 0.2 - - + -
323B LEU 4.9 0.2 + - - -
329B PRO* 3.9 34.2 + - + +
330B ARG 2.8 18.6 + - - +
331B ALA 3.9 1.6 - - - +
333B SER* 1.3 80.8 - - - +
335B PHE* 1.3 91.8 + + + +
336B GLY 4.8 0.9 - - - +
373B ASN* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 4.0 14.8 - - + -
283B ILE* 4.0 9.2 - - + -
285B TYR* 3.5 36.1 - + - -
302B PHE* 3.5 32.3 - + + -
323B LEU* 3.3 51.6 - - + -
331B ALA 2.8 16.2 + - - +
334B HIS* 1.3 100.3 - + + +
336B GLY* 1.3 61.3 + - - +
350B LEU* 3.8 21.3 - - + +
509B PHE* 4.2 9.2 - - + -
549B TRP* 3.8 11.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ALA 3.6 2.4 + - - -
332B VAL 3.0 16.3 + - - +
333B SER 4.0 8.0 - - - +
334B HIS 4.8 1.0 - - - +
335B PHE* 1.3 82.5 - - - +
337B ASP* 1.3 60.6 + - - +
346B SER* 3.8 7.6 - - - -
350B LEU* 3.6 8.7 - - - +
549B TRP* 3.8 17.2 - - - -
----------------------------------------------------------
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