Contacts of the strand formed by residues 367 - 370 (chain A) in PDB entry 4ZZ7
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 THR 367 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PHE* 3.4 6.6 - - - -
305A MET* 4.2 3.1 - - - -
336A ILE* 3.8 29.6 - - + +
346A ILE* 5.7 0.4 - - - -
348A VAL 3.2 14.6 - - - -
349A ASP* 4.7 0.4 - - - -
350A GLY* 3.5 20.0 - - - +
364A VAL* 4.5 0.9 - - + -
365A GLY 2.9 18.2 - - - +
366A GLY* 1.3 73.0 - - - -
368A LEU* 1.3 60.3 + - - +
369A ILE* 4.3 6.0 - - - +
386A PRO 3.0 8.8 + - - +
387A VAL* 3.4 23.9 - - + +
388A LEU 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 4.3 10.1 - - + +
301A MET* 4.0 21.3 - - + -
302A THR* 4.1 17.3 - - - +
305A MET* 3.7 28.7 - - + -
346A ILE* 3.7 2.9 - - - +
347A VAL* 3.1 34.3 + - + -
348A VAL* 3.0 25.5 + - + +
367A THR* 1.3 73.2 - - - +
369A ILE* 1.3 79.3 + - - +
370A ASP* 4.6 0.9 - - + +
388A LEU* 3.5 17.0 - - + +
390A VAL* 3.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A TYR 5.1 0.7 - - - +
336A ILE* 4.5 12.8 - - + -
339A ALA* 3.8 22.2 - - + -
344A ALA* 3.5 30.1 - - + -
345A THR 3.3 7.0 - - - +
346A ILE* 3.8 20.2 - - + -
367A THR* 4.3 4.3 - - - +
368A LEU* 1.3 78.4 - - - +
370A ASP* 1.3 61.9 + - - +
372A VAL* 3.6 14.8 - - + -
383A ILE* 5.4 1.6 - - + -
387A VAL* 3.8 27.6 - - + -
388A LEU 2.9 5.7 + - - +
389A GLN* 4.1 15.0 - - + +
390A VAL* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 3.6 17.5 - - + +
344A ALA* 3.7 4.0 - - - +
345A THR* 2.7 31.6 + - - +
347A VAL* 3.5 23.0 - - + +
369A ILE* 1.3 73.9 - - - +
371A HIS* 1.3 102.0 + - - +
372A VAL 3.4 2.8 + - - -
390A VAL* 3.6 16.9 - - + +
392A ARG* 3.0 37.8 + - - -
----------------------------------------------------------
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