Contacts of the strand formed by residues 382 - 390 (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 GLY 382 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 4.1 7.2 - - - -
379A LYS* 2.8 34.6 + - - +
380A THR 3.3 1.6 + - - -
381A ASN* 1.3 79.4 - - - +
383A PRO* 1.3 77.8 - - - +
384A ARG* 3.4 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 4.0 11.2 - - + -
243A THR* 3.5 26.9 - - + -
248A LEU* 3.5 26.9 - - + -
376A MET* 4.3 6.9 - - + +
377A GLU 3.4 7.9 - - - +
378A LEU* 3.9 9.2 - - + -
382A GLY* 1.3 84.8 - - - +
384A ARG* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A MET* 3.3 7.3 - - - +
377A GLU 2.8 33.4 + - - -
379A LYS* 3.8 36.6 - - + +
382A GLY 3.4 1.5 + - - +
383A PRO* 1.3 75.0 - - - +
385A LYS* 1.3 79.9 + - - +
386A ILE* 3.4 6.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASP* 3.7 15.5 + - - +
372A THR* 5.8 0.4 - - - +
374A ASN* 3.2 38.8 + - + +
375A ILE 3.5 5.8 - - - +
376A MET* 3.8 15.7 - - + +
384A ARG* 1.3 87.6 + - - +
386A ILE* 1.3 60.5 + - - +
387A GLY 3.6 25.6 - - - +
388A TYR* 4.4 13.1 - - - +
398A THR* 4.3 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 4.1 24.0 - - + +
143A TYR* 4.0 3.8 - - - +
375A ILE* 2.9 35.7 + - + +
377A GLU* 3.3 50.0 - - + +
379A LYS* 4.2 11.7 - - - +
384A ARG* 3.8 15.9 - - + +
385A LYS* 1.3 77.4 - - - +
387A GLY* 1.3 59.3 + - - +
395A MET* 4.3 4.2 - - + +
397A VAL* 3.6 13.2 - - + +
398A THR* 2.8 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 2.9 25.2 + - - -
385A LYS* 3.5 14.6 - - - +
386A ILE* 1.3 85.6 - - - +
388A TYR* 1.3 65.9 + - - +
395A MET* 5.3 2.2 - - - -
396A VAL 3.1 14.4 - - - -
397A VAL* 4.2 0.4 - - - -
398A THR* 3.6 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A THR* 3.6 26.5 - - + -
373A ILE 3.3 11.9 - - - +
374A ASN* 3.9 7.2 - - - +
375A ILE* 4.0 6.8 - - - +
385A LYS* 4.4 13.0 - - - +
387A GLY* 1.3 78.8 - - - +
389A TRP* 1.3 67.2 + - - +
390A SER* 4.9 8.1 - - - -
393A ASP* 5.4 5.6 + - - -
395A MET* 3.4 3.3 - - - +
396A VAL* 2.7 80.3 + - + +
398A THR* 4.8 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP 5.0 1.6 - - - -
134A GLY* 3.4 26.2 + - - -
135A ALA* 3.5 31.6 - - + -
138A SER* 2.9 35.9 + - - -
371A TYR* 3.6 34.5 - + - -
372A THR* 3.4 5.7 - - - -
373A ILE* 2.8 38.4 + - + +
375A ILE* 4.4 8.3 - - + -
388A TYR* 1.3 78.5 - - - +
390A SER* 1.3 70.9 + - - +
391A GLU* 3.4 26.5 - - + -
394A LYS* 3.2 43.9 - - + +
395A MET* 3.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASN* 6.1 1.1 - - - -
371A TYR 3.6 18.2 - - - -
372A THR* 4.7 6.3 - - - -
388A TYR* 4.9 7.3 - - - -
389A TRP* 1.3 86.0 - - - +
391A GLU* 1.3 64.8 + - - +
392A VAL* 3.3 13.7 - - - +
393A ASP* 3.2 28.2 + - - +
394A LYS* 2.8 25.3 + - - -
----------------------------------------------------------
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