Contacts of the helix formed by residues 356 - 367 (chain A) in PDB entry 5ZE3
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 356 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LYS 3.2 14.1 - - - +
355A TRP* 1.3 80.0 - - - +
357A LEU* 1.3 60.2 + - - +
358A VAL* 3.1 14.1 + - + +
359A SER* 2.7 44.1 + - - -
360A ALA* 3.0 28.6 + - - +
375A ALA* 3.6 8.2 - - - +
393A ILE 3.2 6.9 - - - +
394A GLN* 4.3 4.9 - - - +
395A CYS 4.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASP* 1.3 72.5 - - - +
358A VAL* 1.3 73.5 + - + +
360A ALA* 3.2 0.8 + - - +
361A SER* 2.8 33.6 + - - -
372A ALA* 3.0 39.5 - - + +
373A LYS 4.5 7.9 - - - +
374A GLU 4.9 0.4 - - - +
375A ALA* 3.9 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASP* 3.1 9.7 + - + +
357A LEU* 1.3 87.3 - - + +
359A SER* 1.3 65.1 + - - +
361A SER* 3.3 6.6 + - - -
362A VAL* 3.0 22.2 + - - +
365A ARG* 5.4 0.2 + - - -
395A CYS* 3.9 8.1 - - - +
396A THR 3.5 28.0 - - - +
397A GLY* 3.8 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TRP* 3.7 12.8 - - - -
356A ASP* 2.7 37.8 + - - -
358A VAL* 1.3 72.9 - - - +
360A ALA* 1.3 55.7 + - - +
362A VAL* 2.7 28.4 + - - +
363A VAL 3.1 4.9 + - - -
393A ILE* 3.5 24.2 - - - +
395A CYS* 3.0 32.8 + - - -
402A ILE* 3.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TRP* 3.6 18.5 - - + -
356A ASP 3.0 19.4 + - - +
357A LEU 3.5 5.4 - - - +
359A SER* 1.3 74.4 - - - +
361A SER* 1.3 58.7 + - - +
363A VAL* 2.8 28.4 + - - +
364A CYS* 3.0 8.3 + - - -
372A ALA* 3.6 17.9 - - + -
375A ALA* 4.0 12.8 - - + -
422A VAL* 3.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 2.8 22.4 + - - -
358A VAL* 3.8 6.8 + - - +
360A ALA* 1.3 73.2 - - - +
362A VAL* 1.3 59.4 + - - +
364A CYS* 3.7 3.3 - - - +
365A ARG* 2.9 40.6 + - - +
370A GLY 4.8 0.2 - - - +
371A SER* 3.9 15.0 - - - -
372A ALA* 3.4 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL 3.0 14.7 + - - +
359A SER 2.7 19.4 + - - +
361A SER* 1.3 68.8 - - - +
363A VAL* 1.3 63.5 + - - +
365A ARG* 3.9 8.3 - - - +
366A GLU* 3.0 22.3 + - - +
395A CYS* 4.0 13.5 - - + -
397A GLY* 4.0 19.3 - - - +
399A GLU* 3.7 33.8 - - - +
400A LYS 5.7 0.2 - - - -
401A SER* 3.9 5.8 - - - -
402A ILE* 3.6 34.8 - - + +
405A CYS* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A VAL* 3.6 23.1 - - + -
328A LEU* 5.5 0.2 - - + -
339A VAL* 3.9 13.0 - - + -
355A TRP* 4.4 0.2 - - + -
359A SER 3.1 4.5 + - - +
360A ALA* 2.8 29.6 + - - +
362A VAL* 1.3 73.8 - - - +
364A CYS* 1.3 67.1 + - - +
366A GLU* 3.2 6.8 + - - +
367A LEU* 2.9 32.5 + - + +
402A ILE* 3.5 43.1 - - + -
422A VAL* 3.5 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ALA 3.0 14.2 + - - +
361A SER 3.7 3.1 - - - +
362A VAL 3.4 0.2 - - - -
363A VAL* 1.3 76.4 - - - +
365A ARG* 1.3 57.8 + - - +
367A LEU* 3.3 2.0 + - - -
368A GLY 3.0 7.8 + - - -
369A PHE* 2.9 30.1 + - - +
371A SER* 3.7 22.0 - - - +
372A ALA* 3.6 19.3 - - - +
422A VAL* 4.3 5.8 - - - -
424A CYS* 2.0 61.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL 5.4 0.2 + - - -
361A SER* 2.9 34.1 + - - +
362A VAL* 3.9 12.9 - - - +
364A CYS* 1.3 73.4 - - - +
366A GLU* 1.3 62.0 + - - +
368A GLY* 2.8 21.2 + - - -
369A PHE 3.6 8.0 + - - +
370A GLY 4.4 12.3 + - - +
397A GLY* 2.4 32.5 + - - -
398A ASN* 4.0 5.1 - - - +
399A GLU 3.3 22.8 + - - -
400A LYS* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 4.4 15.1 + - - +
326A VAL* 3.4 30.7 - - + +
362A VAL 3.0 17.4 + - - +
363A VAL* 3.2 5.9 + - - +
365A ARG* 1.3 77.4 - - - +
367A LEU* 1.3 61.5 + - + +
368A GLY* 3.4 0.5 + - - -
400A LYS 4.1 15.5 - - - +
401A SER* 2.8 25.5 + - - -
402A ILE* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PRO* 5.9 2.7 - - + -
326A VAL* 3.8 36.1 - - + +
327A ARG* 4.5 5.4 - - - -
328A LEU* 4.0 37.5 - - + +
363A VAL* 2.9 27.1 + - + +
364A CYS* 5.1 1.3 - - - -
366A GLU* 1.3 77.1 - - + +
368A GLY* 1.3 61.1 + - - +
369A PHE* 3.4 24.7 - - + -
422A VAL* 5.9 0.2 - - + -
424A CYS* 5.6 0.2 - - - -
455B GLN 4.5 13.0 - - - +
456B GLY* 4.5 6.3 - - - +
457B SER* 2.7 37.6 + - - +
458B LEU 5.0 0.3 + - - -
----------------------------------------------------------
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