Contacts of the strand formed by residues 342 - 346 (chain A) in PDB entry 2O1X
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 342 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL* 4.9 5.4 - - + -
335A TRP* 3.3 12.2 - - + -
336A ALA* 3.8 27.1 - - + +
339A ASP* 2.7 32.3 + - - +
340A PRO 3.4 2.0 - - - +
341A ARG* 1.3 78.6 - - - +
343A PHE* 1.3 64.4 + - - +
344A VAL* 4.4 17.0 - - + -
358A PHE* 4.9 1.6 - - + -
365A ARG* 3.5 23.9 - - - +
389A ARG 3.3 6.1 - - - -
391A VAL* 4.7 4.0 - - + -
468A GLN* 3.1 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG 4.4 0.7 - - - +
342A THR* 1.3 75.8 - - - +
344A VAL* 1.3 65.2 + - - +
345A VAL* 3.8 1.5 + - + -
364A HIS 4.1 14.1 - - - -
365A ARG* 3.5 16.6 - - - -
366A TYR 3.7 20.6 - - - -
367A LEU* 3.5 26.5 - - + -
383A MET* 3.5 42.0 - - + -
388A MET* 3.8 26.5 - - + -
389A ARG 3.5 5.5 + - - -
390A PRO* 3.1 8.1 - - + +
391A VAL 2.7 30.4 + - - +
137B LEU* 4.5 24.7 - - + -
141B ALA* 4.9 2.7 - - + -
172B MET* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 4.8 0.9 - - + -
332A VAL* 3.9 20.9 - - + -
342A THR* 4.4 4.0 - - + -
343A PHE* 1.3 74.8 - - - +
345A VAL* 1.3 60.8 + - - +
355A LEU* 3.6 35.9 - - + -
358A PHE* 3.3 37.9 - - + -
365A ARG 2.8 10.1 + - - -
366A TYR* 3.2 7.5 - - + -
367A LEU 2.8 30.0 + - - -
391A VAL* 3.3 19.5 - - + +
393A ALA* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE* 4.2 13.0 - - + +
344A VAL* 1.3 78.8 - - - +
346A THR* 1.3 62.8 + - - +
367A LEU* 3.3 29.6 - - + +
369A VAL* 4.1 4.5 - - + -
376A ALA* 3.8 37.5 - - + +
379A THR* 5.3 0.2 - - - -
380A ALA* 4.6 15.3 - - + +
383A MET* 4.3 21.5 - - - -
390A PRO* 4.8 0.9 - - + -
391A VAL 2.9 7.6 + - - +
392A VAL* 3.6 7.3 - - + +
393A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A VAL* 1.3 76.9 - - - +
347A PRO* 1.3 70.3 - - - +
348A ALA 3.2 2.9 + - - -
349A MET* 3.0 26.5 + - - +
350A ARG* 3.8 11.4 - - - +
353A SER* 5.0 0.6 + - - -
355A LEU* 4.1 11.9 - - + -
366A TYR* 3.3 40.4 - - + +
367A LEU 2.8 12.1 + - - +
368A ASP* 3.3 9.6 - - + -
369A VAL* 3.0 28.5 + - - +
393A ALA* 3.9 6.6 + - - -
----------------------------------------------------------
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