Contacts of the helix formed by residues 286 - 298 (chain A) in PDB entry 1ZRZ
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 ASP 286 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU 3.6 16.1 - - - +
281A VAL* 3.8 28.8 - - + +
282A ASN 3.3 19.1 - - - +
283A ASP* 3.0 12.1 + - - +
285A GLU* 1.3 89.7 - - - +
287A ILE* 1.3 65.5 + - - +
288A ASP 3.1 1.8 - - - -
289A TRP* 3.3 19.0 + - + +
290A VAL* 3.3 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 5.1 5.2 - - - +
283A ASP 3.7 11.0 - - - +
284A ASP* 3.9 18.4 - - + +
286A ASP* 1.3 75.0 - - + +
288A ASP* 1.3 60.2 + - - +
290A VAL* 3.6 7.9 - - + +
291A GLN* 2.7 68.7 + - + +
569A GLU* 3.6 59.9 - - + +
570A PHE* 5.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP 2.7 24.8 - - - +
285A GLU* 3.7 13.2 - - + +
287A ILE* 1.3 82.0 - - - +
289A TRP* 1.3 60.6 + - + +
290A VAL 3.1 1.6 - - - -
291A GLN* 4.3 13.8 + - - +
292A THR* 2.5 38.9 + - - +
393A GLU* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 6.0 1.3 - - + -
285A GLU* 3.4 30.6 + - - -
286A ASP* 3.3 20.8 + - + +
287A ILE 3.3 0.2 - - - -
288A ASP* 1.3 78.3 - - - +
290A VAL* 1.3 58.1 + - + +
292A THR* 4.3 3.0 - - - -
293A GLU* 3.4 24.9 + - - +
389A GLY* 2.6 42.0 + - - -
390A MET* 4.1 18.8 - - + -
403A TPO 6.1 6.3 - - + -
405A CYS* 5.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 6.0 3.4 - - + -
281A VAL* 4.2 19.3 - - + -
286A ASP 3.3 15.6 + - - +
287A ILE* 3.6 10.3 - - + +
288A ASP 3.1 0.2 - - - -
289A TRP* 1.3 77.3 - - + +
291A GLN* 1.3 57.9 + - + +
292A THR 3.0 1.3 - - - -
293A GLU* 3.0 7.7 + - - +
294A LYS* 2.7 35.2 + - + +
319A LEU* 4.5 15.0 - - + -
321A PHE* 4.1 13.9 - - + -
573A PHE* 4.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ILE* 2.7 50.6 + - + +
288A ASP* 4.3 11.4 + - - +
290A VAL* 1.3 74.9 - - + +
292A THR* 1.3 52.8 + - - +
294A LYS* 3.4 14.8 - - + +
295A HIS* 2.6 44.2 + - + +
393A GLU* 4.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASP* 2.5 26.9 + - - +
289A TRP* 4.3 2.9 - - - -
291A GLN* 1.3 73.9 - - - +
293A GLU* 1.3 65.5 + - - +
294A LYS 3.0 1.1 - - - -
295A HIS* 3.7 0.3 - - - +
296A VAL* 2.9 37.0 + - + +
388A TYR 4.7 3.6 - - - +
390A MET 6.0 0.2 - - - +
391A CYS* 3.6 29.6 - - + +
393A GLU* 2.6 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 2.8 38.3 + - - +
289A TRP* 3.4 15.0 + - - +
290A VAL* 3.0 11.1 + - - +
292A THR* 1.3 78.8 - - - +
294A LYS* 1.3 58.3 + - - +
296A VAL* 3.8 1.2 - - - +
297A PHE* 2.9 57.9 + - + +
321A PHE* 4.4 14.3 - - + -
387A ASP* 4.3 1.6 - - - -
388A TYR* 3.2 44.0 + - + +
389A GLY* 3.7 5.9 + - - -
1000A BI1 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A VAL* 2.7 17.4 + - + +
291A GLN* 3.4 15.9 - - + +
293A GLU* 1.3 74.2 - - - +
295A HIS* 1.3 67.6 + - + +
297A PHE* 3.3 6.6 + - - +
298A GLU* 2.9 43.3 + - + +
309A LEU* 5.0 2.2 - - + -
312A CYS* 4.7 14.6 - - - -
321A PHE* 4.9 9.4 - - + -
572A GLY 2.5 34.1 + - - -
573A PHE* 3.3 28.7 + - + +
574A GLU 4.0 1.6 + - - -
575A TYR* 3.9 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN* 2.6 25.7 + - + +
292A THR 3.2 3.6 + - - +
294A LYS* 1.3 76.3 - - + +
296A VAL* 1.3 61.7 + - - +
298A GLU* 2.7 41.3 + - - +
299A GLN* 3.9 8.5 - - - +
365A ILE* 5.1 2.3 - - - +
393A GLU* 2.4 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 2.9 27.6 + - + +
293A GLU 3.8 0.7 - - - +
295A HIS* 1.3 74.6 - - + +
297A PHE* 1.3 53.5 + - - +
298A GLU 2.8 3.8 - - - -
299A GLN* 2.6 36.3 + - + +
300A ALA* 3.2 5.7 + - + +
360A LEU* 4.3 12.6 - - + -
365A ILE* 4.3 28.5 - - + -
388A TYR* 3.3 38.1 - - + -
391A CYS* 4.0 28.0 - - + -
392A LYS 5.9 0.4 - - - +
393A GLU* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 5.4 1.3 - - + -
293A GLU* 2.9 52.9 + - + +
294A LYS 3.3 2.0 + - - +
296A VAL* 1.3 75.4 - - - +
298A GLU* 1.3 55.4 + - - +
299A GLN 2.9 6.3 + - - -
300A ALA* 3.9 4.4 + - - +
301A SER* 3.9 9.0 + - - -
307A VAL* 3.4 37.2 - - + -
309A LEU* 3.3 42.3 + - + +
321A PHE* 4.3 12.1 - + + -
323A ILE* 3.6 42.8 - - + -
387A ASP 5.5 2.0 - - - -
388A TYR* 3.4 17.9 - + - -
577A ASN* 5.4 0.5 - - - +
1000A BI1 4.6 16.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS* 2.9 30.9 + - + +
295A HIS* 2.7 49.2 + - - +
296A VAL 2.7 1.2 + - - -
297A PHE* 1.3 74.8 - - - +
299A GLN* 1.3 73.1 + - - +
301A SER* 4.0 6.7 - - - -
302A ASN* 4.5 1.6 + - - -
309A LEU* 5.0 1.3 - - + -
575A TYR* 3.8 50.1 - - + +
577A ASN* 5.2 1.1 - - - -
----------------------------------------------------------
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