Contacts of the strand formed by residues 342 - 346 (chain B) in PDB entry 4WGK
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 342 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.0 20.0 - - + +
107B GLY* 3.9 27.6 - - - +
108B ARG* 3.7 15.0 - - + +
140B ARG* 3.6 32.5 - - + -
142B PHE* 3.8 16.4 - - + -
294B LEU 3.3 6.5 + - - -
295B GLY* 3.1 3.1 - - - -
296B LEU 3.0 24.9 + - - +
327B GLU* 3.7 4.3 - - - +
339B GLY 5.0 0.4 - - - +
340B PRO 3.5 11.4 - - - +
341B PHE* 1.3 78.5 - - - +
343B ALA* 1.3 63.0 + - - +
344B ALA 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 3.3 11.0 + - - -
296B LEU* 3.6 14.6 - - + -
323B SER* 3.3 21.9 - - - +
326B LEU* 3.7 24.2 - - + -
327B GLU* 3.1 21.9 + - + +
341B PHE* 3.6 20.9 - - + -
342B VAL* 1.3 73.4 - - - +
344B ALA* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 3.6 20.6 - - + +
142B PHE* 3.6 26.2 - - + -
157B SER* 3.8 22.0 - - - +
296B LEU* 3.0 8.3 + - - +
297B ILE* 3.3 7.3 - - + +
298B SER* 2.9 23.6 + - - -
323B SER* 4.1 0.7 - - - -
342B VAL 4.1 0.4 - - - -
343B ALA* 1.3 74.0 - - - +
345B PHE* 1.3 62.4 + - - +
346B ALA 3.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 5.7 0.2 - - - +
157B SER* 2.9 15.4 + - - -
193B THR* 3.6 15.0 - - + +
281B MET* 3.7 14.1 - - + -
298B SER* 3.3 33.9 - - - -
300B PHE* 4.8 7.9 - - + -
319B VAL* 3.9 34.7 - - + +
322B ALA* 3.5 23.3 - - + -
323B SER* 3.3 26.7 + - - +
326B LEU* 3.5 28.7 - - + -
344B ALA* 1.3 72.4 - - - +
346B ALA* 1.3 62.8 + - - +
404B MET* 3.7 33.2 - - + -
408B ALA* 3.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.6 26.0 - - + -
157B SER* 3.9 5.6 - - - +
191B SER* 5.2 1.1 - - - +
297B ILE* 4.0 5.4 - - + -
298B SER 2.7 18.5 + - - +
299B TRP* 3.4 33.8 - - + +
300B PHE 3.5 16.5 + - - +
319B VAL* 6.5 0.7 - - - -
344B ALA 3.7 1.4 + - - -
345B PHE* 1.3 74.7 - - - +
347B SER* 1.3 65.2 + - - +
348B SER 3.7 0.2 + - - -
----------------------------------------------------------
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