Contacts of the strand formed by residues 346 - 350 (chain A) in PDB entry 2ZB5
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 ILE 346 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 3.7 27.2 - - + +
340A SER 5.7 1.6 - - - +
343A ASP* 3.1 45.5 + - + +
344A PRO 5.1 1.7 - - - -
345A VAL* 1.3 74.3 - - - +
347A ASP* 1.3 65.0 + - - +
369A THR* 3.8 17.5 - - + -
370A THR 3.7 2.5 - - - -
371A ARG* 3.7 13.9 - - + +
372A THR* 5.2 0.2 - - - -
427A ILE* 3.6 43.1 - - + -
429A SER* 3.5 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A THR* 3.9 5.2 - - - +
308A ILE* 3.0 27.0 + - - +
345A VAL 3.2 2.8 + - - -
346A ILE* 1.3 73.5 - - - +
348A ARG* 1.3 78.8 + - - +
370A THR* 2.9 23.6 + - - +
371A ARG* 4.2 1.1 - - - +
372A THR* 3.5 18.4 - - - +
406A ARG* 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER* 2.8 41.2 + - - -
306A ILE 3.0 9.9 - - - +
307A THR* 2.8 30.5 + - + +
308A ILE* 4.3 4.2 - - - +
346A ILE 4.0 0.2 - - - -
347A ASP* 1.3 100.6 - - - +
349A LEU* 1.3 65.3 + - - +
350A TYR* 3.1 31.8 + - + -
369A THR* 3.3 9.0 - - - +
370A THR* 3.0 33.6 + - - +
406A ARG* 5.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER* 3.4 5.7 + - - -
306A ILE* 2.7 45.6 + - + +
308A ILE* 3.8 23.3 - - + -
319A PHE* 4.1 18.4 - - + -
339A LEU* 4.5 15.3 - - + -
348A ARG* 1.3 74.2 - - - +
350A TYR* 1.3 64.5 + - - +
351A LEU* 3.9 11.6 + - + -
367A VAL* 3.8 12.6 - - + -
368A PRO 3.8 0.7 - - - -
369A THR* 3.2 26.5 - - + +
413A LEU* 4.0 32.8 - - + -
427A ILE* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASP 3.8 3.8 - - - -
305A SER* 3.6 25.6 - - - -
348A ARG* 3.1 34.8 + - + -
349A LEU* 1.3 76.0 - - - +
351A LEU* 1.3 63.9 + - - +
352A SER* 4.1 0.9 + - - -
354A HIS* 4.2 0.3 + - - -
368A PRO* 3.1 51.3 + - + +
369A THR 5.6 0.2 - - - -
370A THR* 3.9 25.5 - - + +
399A TRP* 4.3 13.6 - + + +
400A ALA* 4.1 13.4 - - + +
401A PRO* 3.5 49.5 - - + +
404A ASP* 5.2 6.8 + - - +
406A ARG* 6.0 1.0 - - - +
408A PRO* 5.7 0.4 - - + -
----------------------------------------------------------
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