Contacts of the helix formed by residues 386 - 395 (chain C) in PDB entry 2ZZ0
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 SER 386 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLY 5.0 1.8 - - - -
228C PHE 4.8 1.8 - - - -
229C ASP* 3.8 19.3 - - - -
385C LEU* 1.3 77.9 - - - +
387C GLU* 1.3 64.9 + - - +
388C GLU* 3.1 20.0 + - - +
389C LYS* 2.8 47.1 + - - +
390C ALA* 3.0 19.9 + - - +
426C ILE* 4.2 2.7 - - - -
439C HIS* 3.7 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ASP* 3.0 17.7 + - - +
231C ASP* 4.7 2.8 - - + +
386C SER* 1.3 71.6 - - - +
388C GLU* 1.3 66.2 + - + +
390C ALA* 3.2 3.7 + - - +
391C VAL* 3.0 35.4 + - + +
401C VAL* 3.8 29.3 - - + +
424C LYS* 3.2 19.6 + - - +
426C ILE* 4.1 15.1 - - + +
486C LYS* 2.6 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PHE 3.9 2.0 - - - +
229C ASP* 3.3 13.9 - - - +
230C GLN* 2.7 45.8 + - + +
231C ASP 5.1 0.9 - - - -
386C SER* 3.1 26.3 + - - +
387C GLU* 1.3 81.0 + - + +
389C LYS* 1.3 63.7 + - - +
390C ALA 3.1 0.5 + - - -
391C VAL* 3.2 8.2 + - - +
392C GLU* 3.0 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLY 4.4 12.5 + - - -
384C GLY 3.7 12.9 + - - -
385C LEU* 3.4 28.9 - - + +
386C SER* 2.8 48.6 + - - +
388C GLU* 1.3 74.6 - - - +
390C ALA* 1.3 61.2 + - - +
392C GLU* 3.6 17.6 - - - +
393C LYS* 3.1 26.5 + - + +
439C HIS* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C LEU* 4.1 13.0 - - + +
386C SER 3.0 19.4 + - - +
387C GLU 3.4 4.7 - - - +
389C LYS* 1.3 73.0 - - - +
391C VAL* 1.3 66.9 + - - +
393C LYS 3.3 1.0 + - - -
394C PHE* 2.9 35.3 + - - +
399C ILE* 3.6 11.6 - - + +
426C ILE* 3.4 29.4 - - + -
436C VAL* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C GLU* 3.0 25.6 + - + +
388C GLU* 3.6 6.7 - - - +
390C ALA* 1.3 75.2 - - - +
392C GLU* 1.3 60.0 + - - +
395C GLY* 2.5 33.6 + - - -
396C GLU* 3.2 46.2 - - + +
399C ILE* 4.1 19.5 - - + -
401C VAL* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C GLU 3.0 14.5 + - - +
389C LYS* 3.6 18.4 - - - +
391C VAL* 1.3 83.0 - - - +
393C LYS* 1.3 64.9 + - - +
394C PHE 3.5 0.2 + - - -
395C GLY* 4.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C GLU* 5.6 3.4 + - - -
385C LEU* 4.7 17.4 - - + +
389C LYS* 3.1 15.8 + - + +
390C ALA 3.9 2.5 - - - +
392C GLU* 1.3 86.6 - - + +
394C PHE* 1.3 94.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C LEU* 3.7 21.3 - - + -
390C ALA* 2.9 22.4 + - - +
393C LYS* 1.3 112.5 - - + +
395C GLY* 1.3 57.4 + - - +
398C ASN* 2.7 33.2 + - + -
399C ILE* 4.1 20.6 - - + -
428C ASN* 3.5 35.7 - - - +
430C LYS* 6.0 1.1 - - + -
436C VAL* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C VAL* 2.5 24.0 + - - -
392C GLU 4.0 2.9 + - - -
393C LYS 3.8 0.6 - - - -
394C PHE* 1.3 74.6 - - - +
396C GLU* 1.3 57.1 + - - -
397C GLU* 3.0 3.6 - - - -
398C ASN* 2.6 31.7 + - - -
399C ILE* 3.4 5.5 + - - +
----------------------------------------------------------
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