Contacts of the strand formed by residues 438 - 443 (chain A) in PDB entry 2W93
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 438 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 3.5 16.4 - - + +
385A ILE* 3.9 27.4 - - + -
422A THR* 3.9 24.7 - - + +
425A ALA* 4.1 4.3 - - + +
426A ALA* 3.9 26.5 - - + +
429A ALA* 4.1 15.5 - - + -
436A LYS 5.0 1.3 - - - +
437A ARG* 1.3 79.4 - - - +
439A ILE* 1.3 58.4 + - - +
440A LEU 4.2 0.2 - - - -
463A LYS 5.4 1.6 + - - -
464A PRO* 3.3 13.0 - - + +
465A TYR* 2.8 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A PHE* 3.7 26.0 - - + -
378A LEU* 3.9 14.1 - - + -
382A ASP* 3.2 38.8 - - + +
383A VAL 2.8 11.7 + - - +
384A VAL* 3.4 7.0 - - + +
385A ILE* 2.8 34.9 + - - +
437A ARG* 3.9 8.3 - - + +
438A VAL* 1.3 80.2 - - - +
440A LEU* 1.3 57.1 + - - +
441A PHE* 3.7 28.7 - - + -
465A TYR* 3.7 16.2 - - + -
467A PHE* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ILE* 3.5 11.7 - - + +
418A THR* 3.4 38.4 - - - +
419A THR* 4.6 7.2 - - + +
422A THR* 3.5 26.2 - - + +
438A VAL 4.2 0.4 - - - -
439A ILE* 1.3 74.2 - - - +
441A PHE* 1.3 75.0 + - - +
442A ILE* 3.9 28.9 - - + +
447A LEU* 5.9 1.3 - - + -
465A TYR 2.9 12.6 + - - +
466A LEU* 3.8 25.6 - - + -
467A PHE* 2.8 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A MET* 4.4 8.3 - - + -
371A TRP* 3.7 27.4 - + + -
374A LEU* 3.6 40.6 - - + -
384A VAL* 5.0 6.5 - - + -
385A ILE 2.8 15.4 + - - +
386A ALA* 3.5 4.4 - - + -
387A GLU* 2.9 26.3 + - - +
391A SER* 3.6 16.8 + - - +
395A ILE* 5.2 0.9 - - + -
439A ILE* 3.7 24.2 - - + -
440A LEU* 1.3 75.7 - - - +
442A ILE* 1.3 59.2 + - - +
467A PHE* 3.5 38.6 - + + -
469A LEU* 4.1 12.8 - - + -
518A TRP* 3.9 12.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLU* 3.9 8.1 - - + +
391A SER* 4.2 4.5 + - - -
416A GLY* 5.1 0.2 - - - -
418A THR* 3.3 23.6 - - - +
419A THR* 3.1 28.5 - - - +
440A LEU* 3.9 18.8 - - + -
441A PHE* 1.3 75.2 - - - +
443A GLY* 1.3 72.3 + - - +
446A SER* 3.9 13.0 - - - +
447A LEU* 3.6 27.1 - - + +
450A THR* 4.9 0.2 - - - +
466A LEU* 5.8 0.7 - - + -
467A PHE 2.9 15.5 + - - +
468A VAL* 3.3 17.1 - - + -
469A LEU* 2.9 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLU* 4.3 6.3 - - - +
388A THR 5.7 0.2 + - - -
391A SER* 4.5 4.0 + - - -
442A ILE* 1.3 78.1 - - - +
444A ASP* 1.3 66.2 + - - -
445A GLY 3.2 2.4 + - - -
446A SER 3.3 0.9 + - - -
447A LEU* 3.0 24.1 + - - +
468A VAL* 4.6 0.7 - - - -
469A LEU* 4.0 12.6 - - - -
600A TPP 3.3 27.5 + - - -
----------------------------------------------------------
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