Contacts of the strand formed by residues 373 - 379 (chain A) in PDB entry 2WJW
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 ILE 373 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PRO* 4.7 2.2 - - + -
131A ASP 3.6 23.3 - - - +
132A LEU* 4.2 2.2 - - + -
135A ALA* 4.0 22.4 - - + -
240A LEU* 3.9 18.8 - - + -
260A PHE* 3.8 29.8 - - + -
261A GLN 4.1 7.4 - - - +
262A ILE* 4.1 12.1 - - + -
371A TYR* 3.9 18.4 - - + -
372A THR* 1.3 77.5 - - - +
374A ASN* 1.3 76.0 + - - +
375A ILE* 3.7 1.1 + - + +
388A TYR* 3.3 0.9 - - - -
389A TRP* 2.8 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 3.3 6.6 - - - -
261A GLN* 2.9 44.7 + - + +
262A ILE* 5.6 1.0 - - - -
263A VAL 5.1 0.8 + - - -
264A ASP* 3.1 42.4 + - - +
372A THR* 4.1 8.6 + - - +
373A ILE* 1.3 75.9 - - - +
375A ILE* 1.3 60.8 + - - +
376A MET* 4.0 12.4 - - - +
385A LYS* 3.2 36.1 + - + +
387A GLY 3.7 2.2 - - - -
388A TYR* 3.9 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA* 4.8 3.1 - - + +
139A LEU* 3.8 27.8 - - + -
143A TYR* 5.2 0.2 - - - +
259A GLY 3.7 4.9 - - - +
260A PHE* 3.6 32.5 - - + -
373A ILE* 4.1 6.5 - - + +
374A ASN* 1.3 75.4 - - - +
376A MET* 1.3 64.6 + - - +
385A LYS* 3.5 4.5 - - - -
386A ILE* 2.9 46.4 + - + -
387A GLY 2.9 21.4 + - - +
388A TYR* 4.0 14.4 - - - +
389A TRP* 4.4 13.2 - - + -
395A MET* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 3.4 25.8 - - + -
243A THR* 4.5 9.9 - - + -
258A SER* 3.2 7.4 - - - -
259A GLY 2.9 34.0 + - - +
261A GLN* 3.8 34.3 - - + -
374A ASN* 4.0 11.0 - - - +
375A ILE* 1.3 78.6 - - - +
377A GLU* 1.3 65.2 + - - +
383A PRO* 4.3 13.9 - - + +
384A ARG 3.3 13.0 - - - +
385A LYS* 3.8 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 4.6 1.4 + - - -
143A TYR* 2.5 42.5 + - - +
234A HIS* 5.4 0.6 - - - -
242A PHE* 4.2 4.7 - - - -
257A VAL 3.5 6.5 - - - +
258A SER* 3.7 5.2 - - - +
376A MET* 1.3 77.1 - - - +
378A LEU* 1.3 61.4 + - - +
379A LYS* 3.2 35.2 + - + +
383A PRO* 3.4 0.5 - - - +
384A ARG 2.8 37.7 + - - +
386A ILE* 3.3 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 4.0 7.0 - - + -
248A LEU* 4.3 22.2 - - + +
252A PHE* 4.1 30.5 - - + -
255A ALA 5.4 3.6 - - - +
256A ASN* 5.6 2.4 - - - +
257A VAL* 2.9 37.5 + - + +
377A GLU* 1.3 72.8 - - - +
379A LYS* 1.3 63.7 + - - +
382A GLY* 4.1 6.7 - - - -
383A PRO* 3.9 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU* 3.2 43.3 + - + +
378A LEU* 1.3 80.0 - - - +
380A THR* 1.3 68.7 + - - +
381A ASN 3.2 3.6 - - - +
382A GLY* 2.8 22.9 + - - +
384A ARG* 3.8 36.6 - - + +
386A ILE* 4.2 8.8 - - + +
----------------------------------------------------------
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