Contacts of the strand formed by residues 384 - 389 (chain A) in PDB entry 2WIN
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 384 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LYS* 3.8 17.5 - - + -
351A MET* 4.1 15.7 - - + -
352A VAL 3.2 7.9 - - - +
353A PHE* 3.7 19.5 - - + -
379A THR* 3.5 4.3 - - - +
380A GLN* 3.2 28.6 + - - +
382A ASP* 3.0 24.3 + - - +
383A GLY* 1.3 84.3 - - - +
385A ALA* 1.3 72.4 + - - +
440A ARG* 3.6 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU 3.5 15.3 - - - +
351A MET* 3.8 2.1 - - - +
352A VAL* 2.8 24.8 + - + +
367A VAL* 3.6 31.6 - - + -
377A SER* 3.9 1.3 - - - +
378A LEU 3.8 17.9 - - - +
379A THR* 3.9 12.3 - - - +
380A GLN* 5.5 0.2 - - - -
383A GLY 4.3 0.2 - - - -
384A VAL* 1.3 83.8 - - - +
386A LYS* 1.3 60.0 + - - +
387A LEU 3.9 0.2 - - - -
440A ARG* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASP* 4.7 14.6 - - - -
350A LEU 4.3 0.2 - - - -
351A MET* 3.6 23.3 - - + -
376A GLN 4.9 0.2 - - - +
377A SER* 3.2 23.6 + - - -
378A LEU 4.4 3.2 + - - -
380A GLN* 5.0 8.4 + - - +
384A VAL 4.3 0.4 + - - -
385A ALA* 1.3 72.3 - - - +
387A LEU* 1.3 70.5 + - - +
388A SER* 5.2 4.9 - - - -
438A VAL 4.1 17.9 + - - -
439A LEU* 4.8 4.2 - - - +
440A ARG* 4.0 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASP* 3.5 5.0 - - - +
350A LEU* 2.9 48.7 + - + +
352A VAL* 3.6 28.3 - - + -
367A VAL* 3.9 18.8 - - + +
368A ALA* 4.4 14.4 - - - -
369A VAL* 4.6 9.9 - - + -
375A VAL* 4.5 16.8 - - + -
376A GLN 4.5 5.8 - - - +
377A SER* 3.1 26.9 - - - +
386A LYS* 1.3 79.9 - - - +
388A SER* 1.3 64.7 + - - +
389A ILE* 5.7 0.9 - - + -
402A VAL* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO* 5.7 5.4 - - - -
348A PHE 3.5 5.8 - - - -
349A ASP* 4.1 14.4 - - - -
375A VAL* 4.9 11.7 - - - +
386A LYS* 5.2 6.5 - - - -
387A LEU* 1.3 80.9 - - - +
389A ILE* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO* 3.4 4.6 - - - +
348A PHE* 2.9 46.1 + - + +
350A LEU* 3.7 20.0 - - + -
369A VAL* 4.0 29.4 - - + -
372A GLU* 6.4 1.3 - - + -
375A VAL* 6.1 1.8 - - + -
387A LEU* 5.7 0.7 - - + -
388A SER* 1.3 81.0 - - - +
390A ASN* 1.3 66.6 + - - +
391A THR* 4.0 3.7 + - - +
398A LEU* 4.1 19.3 - - + -
400A ILE* 4.0 25.8 - - + -
----------------------------------------------------------
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