Contacts of the strand formed by residues 345 - 347 (chain A) in PDB entry 1MOX
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 LEU 345 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ILE* 4.2 2.0 - - + -
327A ILE* 3.6 28.9 - - + -
335A PHE* 3.8 18.8 - - + -
341A ILE* 4.1 27.1 - - + -
344A ASP* 1.3 81.3 - - - +
346A HIS* 1.3 65.0 + - - +
347A ILE* 5.5 1.8 - - + -
371A LEU* 4.4 14.4 - - + -
374A VAL* 5.0 2.5 - - + -
377A ILE* 4.1 13.1 - - + +
380A PHE 2.9 10.5 + - - +
381A LEU* 4.1 13.5 - - + +
382A LEU* 2.9 28.2 + - - +
396A PHE* 4.0 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ILE* 3.6 33.5 + - + +
317A GLY* 5.8 0.4 - - - -
325A LEU 3.6 20.5 + - - +
326A SER* 3.8 3.4 - - - -
327A ILE* 2.9 32.2 + - - +
344A ASP* 4.0 15.0 + - + +
345A LEU* 1.3 80.9 - - - +
347A ILE* 1.3 63.4 + - - +
348A LEU* 4.7 6.7 - - + -
380A PHE* 3.5 29.6 - + - -
382A LEU* 3.5 12.8 - - + +
408A GLN* 5.0 0.9 - - - -
45C HIS* 3.7 30.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A SER* 3.3 4.5 - - - +
327A ILE* 3.9 15.9 - - + -
345A LEU* 5.1 1.8 - - + -
346A HIS* 1.3 81.9 - - - +
348A LEU* 1.3 60.6 + - - +
351A ALA* 5.1 3.4 - - + -
352A PHE* 4.0 21.1 - - + -
363A LEU* 6.3 0.4 - - + -
368A LEU* 4.7 5.6 - - + -
371A LEU* 4.6 8.7 - - + -
381A LEU* 4.8 2.2 - - + -
382A LEU 3.0 11.1 + - - +
383A ILE* 4.4 9.6 - - + -
384A GLN 2.9 25.3 + - - -
385A ALA 3.3 24.3 + - - +
386A TRP* 3.7 25.6 - - + -
396A PHE* 3.8 25.8 - - + -
----------------------------------------------------------
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