Contacts of the helix formed by residues 333 - 342 (chain B) in PDB entry 5ZR1
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 TYR 333 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.5 57.4 - + + -
302B PRO* 3.4 28.1 - - + +
305B TRP* 4.0 17.5 - + + -
328B GLU 3.5 0.8 + - - +
329B PHE* 3.4 21.2 + + - +
332B ASP* 1.3 81.0 - - + +
334B LEU* 1.3 69.6 + - - +
335B SER 3.6 0.7 - - - -
336B PRO* 3.7 2.0 - - - +
337B LYS* 3.3 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TRP* 3.7 34.5 - - + -
308B LEU* 3.7 30.5 - - + -
329B PHE* 2.8 41.8 + - + +
330B ALA* 3.6 7.3 + - - +
333B TYR* 1.3 76.6 - - - +
335B SER* 1.3 59.9 + - - +
337B LYS* 3.3 3.1 + - - +
338B ILE* 3.1 46.2 + - + +
421B ILE* 3.7 33.4 - - + -
451B ALA* 5.4 0.7 - - + -
453B VAL* 4.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA 3.3 16.3 + - - -
331B ILE* 3.9 1.6 - - - -
334B LEU* 1.3 78.7 - - - +
336B PRO* 1.3 67.7 - - - +
337B LYS 3.5 0.3 + - - -
339B ALA* 3.6 16.8 + - - +
357B SER* 3.5 1.9 - - - -
358B ILE* 2.9 41.0 + - - +
360B CYS* 5.1 2.7 - - - -
421B ILE* 4.1 15.3 - - - -
27C PRO* 3.3 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE 3.3 19.3 - - - +
332B ASP 3.5 20.6 - - - +
333B TYR 3.7 4.7 - - - +
335B SER* 1.3 90.9 - - - +
337B LYS* 1.3 59.1 + - + +
339B ALA* 3.5 4.2 + - + +
340B TYR* 3.2 38.3 + - + -
357B SER* 4.4 9.4 - - - +
27C PRO* 5.6 1.6 - - + -
28C SER 4.5 15.5 - - - +
29C LEU* 4.6 5.6 - - + -
30C PRO* 4.3 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TRP* 3.2 45.0 - - + -
333B TYR* 3.3 59.2 + - + +
334B LEU* 3.3 4.2 + - - +
336B PRO* 1.3 81.8 - - + +
338B ILE* 1.3 62.6 + - - +
340B TYR* 4.1 9.5 - - + +
341B SER* 3.2 12.8 + - - -
33C ASN* 5.7 6.2 - - - +
37C LYS 5.1 5.7 + - - -
38C HIS* 4.1 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TRP* 3.5 22.2 - - + +
308B LEU* 5.7 3.1 - - + -
309B THR* 5.5 2.9 - - + -
334B LEU* 3.1 38.5 + - + +
337B LYS* 1.3 78.0 - - - +
339B ALA* 1.3 61.7 + - - +
341B SER* 2.7 21.9 + - - +
342B GLN* 3.1 36.9 + - + +
358B ILE* 3.7 14.1 - - + -
418B ILE* 3.8 28.0 - - + -
421B ILE* 3.9 15.7 - - + -
451B ALA* 5.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B SER 3.6 13.9 + - - +
336B PRO* 3.5 6.4 + - + +
337B LYS 3.4 0.2 - - - -
338B ILE* 1.3 80.5 - - - +
340B TYR* 1.3 62.4 + - - +
342B GLN* 3.5 14.9 + - - +
343B LEU* 3.6 18.6 + - - +
355B VAL* 5.1 4.1 - - + +
356B ASN 4.0 19.3 - - - +
357B SER* 4.2 5.8 - - - -
358B ILE* 3.4 16.1 - - + +
29C LEU* 4.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B PRO* 3.2 26.1 + - + +
337B LYS* 4.4 4.3 - - + +
338B ILE 3.3 0.2 - - - -
339B ALA* 1.3 78.0 - - - +
341B SER* 1.3 61.6 + - - +
342B GLN 3.4 0.5 + - - -
343B LEU* 3.5 28.5 + - + +
355B VAL* 5.5 3.6 - - + -
29C LEU* 3.6 25.6 - - + +
30C PRO* 2.4 49.2 + - + +
31C GLN 4.4 4.6 - - - -
32C SER* 4.6 6.1 + - - -
33C ASN* 4.0 23.3 - - - -
38C HIS* 3.3 47.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TRP* 4.0 10.4 + - - -
309B THR* 6.0 1.0 - - - +
337B LYS 3.2 15.2 + - - -
338B ILE* 2.7 24.3 + - - +
340B TYR* 1.3 78.2 - - - +
342B GLN* 1.3 59.9 + - - +
343B LEU 3.4 4.0 + - - -
38C HIS* 3.5 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ILE* 3.1 30.2 + - + +
339B ALA* 3.5 7.2 + - - +
340B TYR 3.2 1.0 - - - -
341B SER* 1.3 79.0 - - - +
343B LEU* 1.3 67.5 + - + +
358B ILE* 4.5 6.6 - - - +
417B ASP* 3.6 25.8 - - - +
418B ILE* 2.9 46.9 + - - +
----------------------------------------------------------
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