Contacts of the helix formed by residues 288 - 294 (chain D) in PDB entry 1ZQ1
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 288 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D PHE 4.1 1.4 + - - -
287D TYR* 1.3 71.5 - - - +
289D VAL* 1.3 52.3 + - - +
290D THR* 2.7 42.4 + - - -
291D ASP* 3.8 15.0 - - - +
310D LYS* 4.1 19.3 + - - +
311D VAL 4.0 2.9 - - - -
312D LEU* 4.3 8.7 - - + +
370D ARG* 4.0 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D TYR* 3.2 7.9 + - + -
288D ASP* 1.3 69.6 - - - +
290D THR* 1.3 67.0 + - - +
291D ASP 3.2 0.9 - - - -
292D ILE* 2.8 40.6 + - + +
293D PHE* 3.5 26.2 - - + -
311D VAL* 3.6 6.3 + - + +
313D ALA* 3.8 21.8 - - + -
367D VAL* 3.7 12.3 - - + -
370D ARG* 4.3 13.9 - - + +
371D LEU* 3.6 31.4 - - + -
381D LEU* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ASP* 2.7 25.4 + - - -
289D VAL* 1.3 74.3 - - - +
291D ASP* 1.3 59.6 + - - +
293D PHE* 2.7 35.9 + - - +
294D GLU* 3.5 2.6 + - - -
305D ILE* 4.7 13.8 - - + +
309D GLY 4.4 6.7 - - - +
310D LYS* 3.5 18.0 - - + +
311D VAL* 2.8 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ASP* 3.8 14.9 - - - +
289D VAL 3.0 1.6 + - - -
290D THR* 1.3 74.5 - - - +
292D ILE* 1.3 54.9 + - - +
293D PHE 2.7 6.7 + - - -
294D GLU* 2.6 37.6 + - + +
295D ASN 4.6 0.2 + - - -
370D ARG* 3.9 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D VAL* 2.8 37.0 + - + +
291D ASP* 1.3 71.2 - - - +
293D PHE* 1.3 59.3 + - + +
294D GLU 3.5 0.2 - - - -
295D ASN 4.9 3.3 + - - +
296D THR* 4.2 0.5 + - - -
363D GLU* 4.1 28.6 - - + +
366D LYS* 3.1 56.5 - - + +
367D VAL* 4.1 5.2 - - + -
370D ARG* 3.1 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D VAL* 3.5 35.7 - - + -
290D THR 2.7 10.9 + - - +
291D ASP 2.7 4.2 + - - -
292D ILE* 1.3 80.6 - - + +
294D GLU* 1.3 65.1 + - - +
295D ASN 2.8 5.3 + - - -
296D THR* 3.4 21.3 + - - +
301D ILE* 3.4 40.2 - - + -
302D ALA* 5.7 1.0 - - - +
305D ILE* 3.6 20.3 - - + +
311D VAL* 4.2 15.5 - - + -
354D LEU* 6.2 0.2 - - + -
359D ILE* 4.3 9.6 - - + -
363D GLU* 3.4 28.3 - - + -
367D VAL* 3.9 12.1 - - + -
381D LEU* 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D THR 3.5 2.0 + - - -
291D ASP* 2.6 29.3 + - + +
293D PHE* 1.3 70.8 - - - +
295D ASN* 1.3 72.4 + - - +
296D THR 4.0 0.9 + - - -
305D ILE* 4.4 15.0 - - - +
----------------------------------------------------------
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