Contacts of the helix formed by residues 316 - 327 (chain B) 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 GLY 316 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B TYR* 3.7 9.6 - - - -
315B GLY* 1.3 71.2 - - - -
317B GLU* 1.3 63.1 + - - +
318B ASP* 3.1 3.6 - - - -
319B ASP* 2.8 19.4 + - - +
320B ASP* 3.1 9.2 + - - +
359B ARG* 4.2 2.2 - - - -
363B ILE* 3.6 10.3 - - - +
405B NAG 3.0 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 2.8 46.5 + - + +
229B ALA* 3.9 29.6 - - + +
308B PRO* 4.5 0.9 - - + +
311B TYR* 3.4 40.4 - - + +
314B ALA* 5.6 0.2 - - - -
315B GLY* 3.4 18.4 + - - +
316B GLY* 1.3 69.5 - - - +
318B ASP* 1.3 75.1 + - - +
320B ASP* 3.2 4.6 + - - +
321B ILE* 3.0 33.8 + - + +
405B NAG 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 4.4 4.9 - - - +
286B TYR* 4.1 1.4 + - - -
289B TYR* 3.6 16.3 - - - -
290B PHE* 4.0 12.1 + - - +
291B GLY* 3.7 21.8 + - - +
316B GLY 3.6 4.2 - - - -
317B GLU* 1.3 92.6 - - - +
319B ASP* 1.3 61.5 + - - +
321B ILE* 3.6 10.9 + - + +
322B TYR* 3.1 24.8 + - - +
405B NAG 2.6 49.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 4.3 19.0 - - + +
286B TYR* 2.5 33.8 + - - -
288B GLN* 4.4 5.2 - - - +
289B TYR* 5.1 0.5 - - - -
290B PHE 5.4 0.3 + - - -
316B GLY* 2.8 12.6 + - - +
318B ASP* 1.3 74.1 - - - +
320B ASP* 1.3 55.5 + - - +
322B TYR* 3.2 9.8 + - + +
323B ASN* 2.8 40.9 + - - +
363B ILE* 4.0 13.0 - - + -
405B NAG 2.7 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PRO* 3.7 5.5 - - + +
311B TYR* 2.9 42.8 + - + +
316B GLY 3.1 4.5 + - - +
317B GLU 3.3 9.2 - - - +
319B ASP* 1.3 75.7 - - - +
321B ILE* 1.3 59.5 + - - +
323B ASN* 2.9 6.6 + - - +
324B ARG* 2.7 66.7 + - - +
362B ARG 4.2 1.0 - - - +
363B ILE* 4.2 1.9 - - + +
366B THR* 2.8 32.9 + - - +
369B THR* 4.4 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 5.3 2.7 - - - +
229B ALA* 4.9 2.0 - - + -
232B LEU* 5.1 4.5 - - + -
290B PHE* 3.9 25.1 - - + -
296B LEU* 5.4 0.2 - - + -
304B ILE* 4.6 5.4 - - + -
307B PHE* 3.4 60.3 - - + -
308B PRO* 3.9 11.9 - - + -
317B GLU* 3.0 22.9 + - + +
318B ASP* 3.7 14.6 - - - +
320B ASP* 1.3 75.0 - - - +
322B TYR* 1.3 63.1 + - - +
324B ARG* 3.1 20.6 + - - +
325B LEU* 3.1 15.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 5.8 2.0 - - - -
114A LYS* 4.6 12.1 + - - -
287B VAL* 4.5 5.4 + - - +
288B GLN* 3.4 59.4 - - + +
289B TYR 5.1 0.2 - - - -
290B PHE* 4.1 13.7 - + + -
318B ASP 3.1 15.3 + - - +
319B ASP* 3.2 11.0 - - + +
320B ASP 3.1 0.2 - - - -
321B ILE* 1.3 78.0 - - - +
323B ASN* 1.3 75.7 + - - +
325B LEU* 3.2 20.8 + - + +
326B ALA* 3.3 17.0 + - + +
332B VAL* 4.1 28.7 - - + -
334B ARG* 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 5.7 5.2 - - - +
319B ASP* 2.8 20.0 + - - +
320B ASP* 2.9 7.8 + - - +
322B TYR* 1.3 88.2 - - - +
324B ARG* 1.3 61.9 + - - +
326B ALA* 3.1 9.9 + - - +
327B PHE* 3.1 36.7 + - + -
363B ILE* 2.8 38.6 + - - +
366B THR* 3.4 18.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ILE* 3.3 40.7 + - + +
305B ASN 3.7 3.8 + - - -
306B GLY 2.9 28.5 + - - -
307B PHE* 3.7 4.4 - - - +
308B PRO* 3.2 30.6 - - - +
320B ASP* 2.7 34.6 + - - +
321B ILE* 3.1 14.3 + - - +
323B ASN* 1.3 77.4 - - - +
325B LEU* 1.3 62.5 + - - +
327B PHE* 3.4 8.5 + - - +
328B ARG* 3.5 10.2 - - - +
366B THR* 3.4 10.8 - - + -
369B THR* 4.7 1.6 + - - -
370B MET* 3.6 39.1 + - + +
373B ASP* 2.7 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B PRO* 3.8 35.7 - - + -
290B PHE* 3.8 23.1 - - + -
296B LEU* 4.0 9.9 - - + -
304B ILE* 3.9 31.4 - - + -
321B ILE* 3.1 14.0 + - + +
322B TYR* 3.2 13.0 + - - +
324B ARG* 1.3 76.2 - - - +
326B ALA* 1.3 63.8 + - - +
328B ARG* 3.1 12.5 + - - +
330B MET* 3.1 36.2 + - + +
331B SER 4.9 0.7 - - - +
332B VAL* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B TYR* 3.3 14.3 + - + +
323B ASN* 3.1 12.4 + - - +
325B LEU* 1.3 74.8 - - - +
327B PHE* 1.3 60.4 - - + +
328B ARG 2.6 16.8 + - - -
329B GLY* 3.0 13.2 + - - -
330B MET 3.9 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASN* 3.1 30.2 + - + +
324B ARG 3.9 4.9 - - - +
325B LEU 3.3 0.6 - - - -
326B ALA* 1.3 78.3 - - + +
328B ARG* 1.3 80.4 + - - +
329B GLY 3.8 0.4 - - - -
366B THR* 4.1 10.5 - - - -
367B LYS* 3.3 71.4 + - + +
370B MET* 4.2 14.6 - - - -
----------------------------------------------------------
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