Contacts of the strand formed by residues 341 - 348 (chain A) in PDB entry 2ZHA
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 VAL 341 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 2.8 29.5 + - - +
340A ARG* 1.3 78.6 - - + +
342A PHE* 1.3 61.4 + - - +
365A PHE* 3.8 21.8 - - + -
377A PHE* 4.7 20.4 - - + -
378A GLU 3.0 7.6 - - - +
379A MET* 3.2 25.4 - - + -
380A ARG* 3.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 1.3 75.9 - - - +
343A ARG* 1.3 75.2 + - - +
344A ARG* 4.2 29.8 - - + -
377A PHE* 3.5 7.5 - - - -
378A GLU* 2.8 60.6 + - + -
379A MET 3.6 24.7 - - - -
380A ARG* 3.3 49.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PHE* 1.3 88.0 - - - +
344A ARG* 1.3 60.8 + - - +
345A MET 4.2 0.6 + - - -
368A PHE* 3.6 25.7 - - + -
370A GLU* 3.1 27.2 + - - -
375A TRP* 3.1 56.2 - - + -
376A ALA 3.4 7.0 - - - +
377A PHE* 4.6 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PHE* 4.2 23.3 - - + -
343A ARG* 1.3 73.7 - - - +
345A MET* 1.3 74.4 + - - +
358A PHE* 4.0 6.9 - - + -
363A ARG* 4.8 0.4 - - - +
375A TRP* 3.6 3.9 - - - -
376A ALA* 3.0 32.8 + - + +
378A GLU* 3.2 42.3 + - - +
13B U 4.7 5.7 + - - -
14B U 4.1 47.6 + - - -
15B C 4.5 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG 4.3 0.4 + - - -
344A ARG* 1.3 86.8 - - - +
346A GLY* 1.3 69.2 + - - +
358A PHE* 4.0 4.2 - - - -
373A ARG* 3.7 35.2 - - - +
375A TRP* 3.4 37.4 - - + -
15B C 4.0 26.5 + - - +
16B G 4.5 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG 3.7 0.2 + - - -
345A MET* 1.3 77.4 - - - +
347A PRO* 1.3 72.5 - - - +
358A PHE* 3.7 12.8 - - - -
373A ARG* 2.9 28.8 + - - -
374A TRP 2.8 20.5 + - - +
15B C 3.6 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLY* 1.3 85.4 - - - +
348A GLN* 1.3 67.6 + - - +
351A ASP* 4.5 5.8 - - - +
354A ASN* 3.9 10.5 - - + -
355A VAL* 3.9 35.0 - - + +
358A PHE* 3.7 22.7 - - + -
373A ARG* 3.2 5.6 - - - +
374A TRP* 3.1 27.8 + - + +
15B C 3.5 33.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO* 1.3 75.0 - - - +
349A PHE* 1.3 67.0 + - - +
350A GLU* 3.3 20.2 + - + +
351A ASP* 3.0 23.8 + - + +
355A VAL* 3.9 4.8 - - - +
371A ASN 5.7 1.6 + - - -
372A GLY* 4.1 6.1 + - - +
373A ARG* 3.6 37.2 - - + +
----------------------------------------------------------
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