Contacts of the strand formed by residues 338 - 343 (chain A) in PDB entry 2W8D
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 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASN 3.6 3.4 + - - -
337A TYR* 1.3 74.6 - - - +
339A SER* 1.3 67.0 + - - +
362A ASP* 3.5 13.2 - - + +
363A LYS* 4.1 26.7 - - + -
398A LEU* 4.8 5.4 - - + -
399A PRO* 3.4 41.0 + - + +
401A PRO 3.1 7.5 + - - -
402A PHE* 3.2 8.6 - - - +
403A TYR 2.8 24.1 + - - +
404A THR* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A PRO* 3.6 26.2 + - - +
333A LYS* 4.3 1.9 + - - -
337A TYR* 3.9 1.7 + - - -
338A THR* 1.3 76.9 - - - +
340A ALA* 1.3 62.9 + - - +
360A GLY 3.3 12.1 + - - -
361A ILE* 3.4 9.3 - - - -
362A ASP* 2.9 32.9 + - - +
363A LYS* 2.9 23.0 + - - +
403A TYR* 3.0 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 1.3 75.9 - - - +
341A THR* 1.3 61.8 + - - +
342A PHE* 4.1 4.0 - - + -
361A ILE* 3.8 3.5 - - - +
363A LYS* 3.0 26.0 - - + +
365A PHE* 4.0 20.4 - - + -
398A LEU* 4.0 18.6 - - + -
403A TYR 3.0 7.1 + - - +
404A THR* 3.1 10.1 - - + +
405A LYS* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ALA* 1.3 74.0 - - - +
342A PHE* 1.3 70.5 + - - +
343A HIS* 4.6 1.1 - - + -
356A TYR* 3.4 42.3 - - + +
361A ILE* 3.9 5.6 - - - +
363A LYS 2.9 7.6 + - - -
364A PHE* 3.8 14.5 - - + -
365A PHE* 2.8 34.0 + - - +
405A LYS* 3.2 34.8 - - + +
407A ILE* 4.1 10.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
340A ALA* 4.1 9.6 - - + -
341A THR* 1.3 76.3 - - - +
343A HIS* 1.3 65.1 + - - +
365A PHE* 3.3 37.2 - + + -
370A TYR* 3.5 21.5 - - - +
387A PHE* 3.7 3.3 - - + -
391A SER* 3.9 14.6 - - - -
394A LEU* 3.8 20.0 - - + -
395A LEU* 4.1 22.0 - - + -
398A LEU* 4.4 3.1 - - + -
404A THR* 3.9 22.7 - - + -
405A LYS 2.6 16.1 + - - +
406A PHE* 3.6 37.2 - + + -
407A ILE 3.1 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A THR* 4.6 0.9 - - + -
342A PHE* 1.3 77.5 - - - +
344A GLY* 1.3 58.6 + - - +
345A ASN* 3.1 42.7 + - + +
346A THR 4.8 3.1 - - - -
349A PHE* 5.7 0.2 - - - -
352A ARG* 3.5 30.2 + - - -
364A PHE* 4.2 16.6 - + + -
365A PHE 3.1 7.4 + - - +
366A ASP* 3.2 24.3 - - - -
370A TYR* 3.8 1.4 - - - -
387A PHE* 3.6 9.4 - - - -
407A ILE* 2.9 50.2 + - + +
409A LEU* 3.6 30.3 - - + +
----------------------------------------------------------
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