Contacts of the helix formed by residues 298 - 304 (chain D) in PDB entry 1PZY
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 LYS 298 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D PHE* 4.2 6.2 - - + -
240D LEU* 3.9 30.0 - - + +
244D ASP* 5.9 2.6 - - - +
245D TYR 3.7 15.3 + - - +
246D ASN* 2.7 23.2 + - + +
248D PHE* 3.9 24.0 - - + -
296D LEU 3.8 0.2 + - - -
297D SER* 1.3 72.4 - - - +
299D GLN* 1.3 67.9 + - + +
301D PHE* 3.4 1.9 + - - +
302D LEU* 3.0 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D SER* 3.2 7.0 + - - +
298D LYS* 1.3 86.9 - - + +
300D GLN* 1.3 66.1 + - + +
302D LEU* 3.8 22.6 - - - +
303D SER* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D CYS* 5.0 1.2 - - - +
267D PHE 3.0 27.7 + - - +
268D SER* 3.4 19.6 + - - +
269D GLN* 3.7 5.3 - - - +
270D PRO* 3.8 16.9 - - + +
296D LEU* 3.4 18.3 - - + +
297D SER* 2.9 44.1 + - - +
299D GLN* 1.3 76.7 - - + +
301D PHE* 1.3 61.6 + - - +
303D SER* 2.6 24.9 + - - -
304D ILE* 3.7 5.9 + - - +
330D MET* 3.7 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ASN* 3.2 24.5 - - - -
236D PHE* 3.4 55.9 - + + -
248D PHE* 5.4 1.6 - - + -
250D PHE* 3.7 22.0 - + - -
296D LEU* 3.9 14.5 - - + +
297D SER 3.0 16.7 + - - +
298D LYS 3.6 4.5 - - - +
300D GLN* 1.3 75.8 - - - +
302D LEU* 1.3 63.1 + - - +
304D ILE* 3.1 10.6 - - - +
306D GLY* 3.1 34.6 + - - -
307D PHE* 3.5 42.6 - + - -
375D LEU* 3.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D PHE* 3.4 25.6 - - + -
298D LYS* 3.0 50.8 + - + +
299D GLN* 3.8 23.6 - - - +
301D PHE* 1.3 76.5 - - - +
303D SER* 1.3 63.0 + - - +
305D ASN* 3.1 14.3 + - - +
306D GLY 4.8 1.3 - - - +
375D LEU* 3.5 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D GLN 3.0 13.8 + - - -
300D GLN* 2.6 21.5 + - - -
302D LEU* 1.3 77.8 - - - +
304D ILE* 1.3 55.8 + - - +
305D ASN 3.3 1.6 + - - -
328D ARG* 3.4 26.3 + - - -
330D MET* 2.9 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D LEU* 4.2 14.6 - - + -
300D GLN 3.9 2.9 - - - +
301D PHE 3.1 14.4 - - - +
303D SER* 1.3 77.2 - - - +
305D ASN* 1.3 67.7 + - - +
306D GLY 3.0 21.4 - - - +
307D PHE* 3.9 24.5 - - + -
321D ILE* 4.6 3.6 - - + -
324D ARG* 3.4 51.7 + - + +
325D LEU* 4.0 9.2 - - + -
328D ARG* 3.8 3.6 - - + -
330D MET* 3.6 28.9 - - + -
370D MET* 3.6 12.0 - - - +
----------------------------------------------------------
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