Contacts of the helix formed by residues 384 - 395 (chain B) in PDB entry 1ZJA
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 384 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE* 3.6 1.1 - - - +
383B ASP* 1.3 82.6 + - - +
385B ILE* 1.3 81.8 + - - +
386B GLU* 2.9 16.8 + - - +
387B VAL* 3.0 27.4 + - + +
388B LYS* 3.5 10.3 + - - +
413B SER* 4.5 1.5 + - - +
414B ARG* 2.7 61.4 + - - +
415B ASP* 2.8 24.1 + - - +
418B ARG* 4.3 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 3.6 40.1 + - - +
61B ASP* 3.8 10.1 - - - +
145B PHE* 3.7 45.5 - - + +
165B GLY* 4.6 10.8 - - - -
166B ARG 5.7 0.4 - - - +
167B GLN* 5.3 6.5 - - - +
168B GLN* 5.0 1.3 - - - +
383B ASP* 3.3 5.3 + - - -
384B ASP* 1.3 83.3 + - - +
386B GLU* 1.3 63.8 + - - +
388B LYS* 3.1 18.7 + - + +
389B GLY* 3.0 18.5 + - - -
414B ARG* 3.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE 4.5 5.3 - - - +
145B PHE* 3.9 31.6 - - + -
284B ARG* 5.2 6.6 + - - -
287B ARG* 5.6 2.9 + - - -
291B ARG* 3.9 22.3 + - - +
384B ASP* 2.9 18.8 + - - +
385B ILE* 1.3 79.9 - - - +
387B VAL* 1.3 62.8 + - - +
389B GLY* 3.1 4.7 + - - +
390B PHE* 3.1 51.9 + - + -
412B THR 5.6 0.5 - - - +
413B SER* 5.2 4.2 - - - -
414B ARG* 3.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LEU* 4.4 22.2 - - + +
382B PHE* 3.9 31.0 - - + -
384B ASP* 3.0 20.9 + - + +
386B GLU* 1.3 74.8 - - + +
388B LYS* 1.3 66.8 + - + +
390B PHE* 3.2 11.2 + - + +
391B PHE* 3.0 21.9 + - + +
405B LEU* 4.2 5.1 - - + +
409B VAL* 4.2 23.8 - - + -
413B SER* 3.9 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE 4.6 4.8 + - - -
383B ASP* 3.3 30.1 + - - +
384B ASP 3.5 5.2 + - - +
385B ILE* 3.1 19.0 + - + +
387B VAL* 1.3 77.5 - - + +
389B GLY* 1.3 58.1 + - - +
391B PHE* 3.2 10.2 + - - +
392B GLN* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE 5.9 0.4 - - - -
145B PHE 3.3 29.6 + - - -
146B GLY* 4.0 4.3 - - - -
385B ILE 3.0 10.1 + - - -
386B GLU 3.1 5.4 + - - -
387B VAL 3.1 0.6 - - - -
388B LYS* 1.3 76.4 - - - +
390B PHE* 1.3 60.8 + - - +
392B GLN* 3.2 6.7 + - - +
393B ASP* 2.8 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE 5.0 2.0 - - - -
290B ASP 3.6 18.6 - - - -
291B ARG* 4.0 28.3 - - + -
292B TRP* 3.7 33.0 - + + -
386B GLU* 3.1 53.5 + - + -
387B VAL* 3.2 11.2 + - - +
389B GLY* 1.3 74.1 - - - +
391B PHE* 1.3 61.9 + - - +
393B ASP* 5.8 1.1 - - - -
394B TYR* 2.7 49.0 + + + +
405B LEU* 3.8 19.4 - - + +
409B VAL* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LEU* 3.8 29.4 - - + -
387B VAL 3.0 12.9 + - - +
388B LYS* 3.3 12.8 - - - +
390B PHE* 1.3 78.2 - - - +
392B GLN* 1.3 59.7 + - - +
395B VAL* 2.9 56.3 + - + +
396B GLU* 3.0 41.2 + - + -
402B ALA* 4.2 7.2 - - + -
405B LEU* 3.8 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE 4.2 1.7 - - - +
146B GLY* 3.6 8.1 - - - -
147B GLY* 3.6 26.2 - - - -
166B ARG* 3.1 33.2 + - - +
388B LYS 3.0 13.4 + - - +
389B GLY* 3.2 8.7 + - - +
391B PHE* 1.3 80.2 - - - +
393B ASP* 1.3 66.0 + - - +
396B GLU* 3.6 30.2 - - - +
397B THR* 3.6 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER 4.5 5.2 - - - +
144B PHE 5.6 0.3 - - - +
146B GLY* 3.5 16.6 + - - -
147B GLY* 2.8 27.9 + - - +
389B GLY 2.8 20.9 + - - +
390B PHE* 5.8 0.9 - - - -
392B GLN* 1.3 77.8 - - - +
394B TYR* 1.3 77.9 + - + +
397B THR* 2.6 26.2 + - - +
399B LYS* 3.7 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ASP* 3.4 25.7 + - + +
292B TRP* 3.4 48.7 - + + -
390B PHE* 2.7 35.9 + + + +
393B ASP* 1.3 91.5 - - + +
395B VAL* 1.3 62.8 + - + +
397B THR* 3.3 4.9 - - - -
399B LYS* 2.9 36.8 + - + -
400B ALA* 2.8 32.0 + - + -
405B LEU* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B PHE 4.4 0.7 - - - +
391B PHE* 2.9 58.3 + - + +
394B TYR* 1.3 74.6 - - + +
396B GLU* 1.3 67.5 + - - +
397B THR 3.1 1.8 - - - -
398B GLY* 3.0 14.2 + - - -
400B ALA* 3.4 18.3 - - + +
401B THR* 4.1 12.1 - - - +
402B ALA* 3.8 15.9 - - + +
405B LEU* 3.9 16.6 - - + -
----------------------------------------------------------
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