Contacts of the helix formed by residues 290 - 304 (chain A) in PDB entry 1DZI
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 ALA 290 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASN* 1.3 80.2 - - - +
291A LEU* 1.3 59.0 + - - +
292A ASP 3.3 0.7 - - - -
293A THR* 3.4 4.4 + - - -
294A LYS* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASN* 3.9 5.7 - - + +
290A ALA* 1.3 78.2 - - - +
292A ASP* 1.3 62.6 + - - +
294A LYS* 4.3 7.2 - - + -
295A ASN* 2.6 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 4.4 12.6 - - + +
289A ASN* 2.7 40.8 + - + +
290A ALA 3.3 0.4 - - - -
291A LEU* 1.3 84.5 - - - +
293A THR* 1.3 60.7 + - - +
295A ASN* 3.8 5.6 + - - +
296A LEU* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.8 10.5 - - + -
288A ARG* 3.6 16.1 + - - +
289A ASN 3.1 18.2 + - - -
290A ALA* 3.4 8.8 + - - -
291A LEU 3.3 0.2 - - - -
292A ASP* 1.3 77.4 - - - +
294A LYS* 1.3 61.4 + - + +
296A LEU* 3.2 10.4 + - + +
297A ILE* 2.9 47.3 + - + +
----------------------------------------------------------
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 ALA* 2.8 24.0 + - + +
291A LEU* 3.9 11.7 - - + +
293A THR* 1.3 79.6 - - + +
295A ASN* 1.3 57.9 + - - +
297A ILE* 3.2 26.1 + - + +
298A LYS* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLY 4.8 0.7 - - - +
291A LEU* 2.6 49.7 + - - +
292A ASP* 4.1 6.3 + - - +
294A LYS* 1.3 78.6 - - - +
296A LEU* 1.3 64.3 + - + +
298A LYS* 3.4 33.6 + - - +
299A GLU* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASP 3.4 23.8 - - - +
255A GLY* 3.6 10.9 - - - +
256A GLU* 3.6 31.9 - - + +
283A LEU* 3.9 12.3 - - + -
288A ARG* 3.4 42.6 - - - +
292A ASP* 3.0 21.5 - - + +
293A THR* 3.2 9.3 + - - +
294A LYS 3.1 0.6 - - - -
295A ASN* 1.3 76.0 - - + +
297A ILE* 1.3 66.9 + - - +
299A GLU* 3.2 13.0 + - - +
300A ILE* 3.2 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.8 19.0 - - + +
293A THR* 2.9 37.8 + - + +
294A LYS* 3.2 25.1 + - + +
296A LEU* 1.3 75.4 - - - +
298A LYS* 1.3 64.6 + - - +
300A ILE* 3.1 11.2 + - - +
301A LYS* 2.9 54.4 + - + +
312A PHE* 4.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS 2.9 15.0 + - - +
295A ASN* 3.4 33.1 + - - +
297A ILE* 1.3 77.7 - - - +
299A GLU* 1.3 58.3 + - - +
301A LYS* 3.4 6.5 + - - +
302A ALA* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 4.6 4.3 + - - +
224A PHE* 3.8 26.0 - - + -
253A THR* 5.3 0.5 + - - +
255A GLY* 2.9 40.1 - - - +
257A SER* 2.7 32.9 + - - -
260A GLY* 4.5 4.7 - - - -
263A LEU* 5.3 7.7 - - + +
295A ASN 3.4 6.5 + - - +
296A LEU 3.2 5.1 + - - +
298A LYS* 1.3 80.4 - - - +
300A ILE* 1.3 64.2 + - - +
302A ALA* 3.1 15.6 + - - +
303A ILE* 3.1 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL 5.5 0.2 - - - +
253A THR* 3.4 27.1 - - + +
254A ASP* 3.6 15.0 - - - +
255A GLY* 3.6 13.9 - - - +
279A GLY* 4.0 23.8 - - - -
280A ILE 4.2 2.2 - - - +
281A ALA* 3.5 23.3 - - + +
283A LEU* 4.1 11.4 - - + -
296A LEU 3.3 13.0 - - - +
297A ILE* 3.1 7.5 + - - +
299A GLU* 1.3 78.0 - - - +
301A LYS* 1.3 60.4 + - - +
303A ILE* 3.2 19.9 + - + +
304A ALA* 3.4 8.1 + - - +
312A PHE* 3.6 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 2.9 41.2 + - + +
298A LYS* 3.9 5.8 - - - +
300A ILE* 1.3 76.4 - - - +
302A ALA* 1.3 60.4 + - - +
303A ILE 3.4 0.5 + - - -
304A ALA* 3.4 15.7 + - - +
308A THR* 3.7 34.0 + - + +
312A PHE* 3.7 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.2 26.2 - - + +
267A ILE* 4.3 18.7 - - - +
298A LYS* 2.9 20.8 + - + +
299A GLU* 3.1 11.4 + - - +
301A LYS* 1.3 77.3 - - - +
303A ILE* 1.3 62.3 + - + +
304A ALA 4.0 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 4.0 27.1 - - + -
224A PHE* 4.0 24.5 - - + -
227A ILE* 4.0 9.4 - - + -
251A VAL* 3.7 37.9 - - + -
253A THR* 4.5 11.2 - - + -
267A ILE* 4.3 6.3 - - + -
277A ARG* 2.7 40.0 + - + +
278A PHE 4.8 4.5 - - - +
279A GLY* 5.2 1.1 - - - -
299A GLU* 3.1 22.6 + - + +
300A ILE* 3.5 9.9 - - + +
301A LYS 3.2 0.4 - - - -
302A ALA* 1.3 77.8 - - + +
304A ALA* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 3.4 12.6 + - - +
279A GLY* 3.7 8.7 - - - +
300A ILE 3.4 7.3 + - - +
301A LYS 3.4 19.6 + - - +
302A ALA 4.0 4.5 - - - +
303A ILE* 1.3 84.7 - - - +
305A SER* 1.3 66.0 + - - +
306A ILE* 4.0 4.9 + - - +
308A THR* 4.5 8.2 + - + -
311A TYR* 3.4 32.1 - - + +
312A PHE* 4.5 2.0 - - + -
----------------------------------------------------------
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