Contacts of the helix formed by residues 330 - 338 (chain B) in PDB entry 2VUU
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 ASP 330 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 4.3 2.0 - - - -
221B GLU* 3.0 24.0 - - - +
328B TRP* 3.6 20.8 + - + -
329B ARG* 1.3 78.2 - - - +
331B MET* 1.3 63.5 + - - +
332B GLU* 3.9 14.9 - - - +
333B GLU* 2.9 29.7 + - - +
334B TYR* 3.1 16.6 + - - +
680J THR* 5.2 1.9 - - - +
682J PRO* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 3.3 39.0 - - - +
157B PHE* 4.8 0.7 - - - -
189B TRP* 3.4 36.3 - - + -
221B GLU* 2.7 8.8 + - - +
223B LEU* 3.7 23.3 - - + -
228B VAL* 4.0 15.5 - - + -
231B ALA* 3.9 19.3 - - + -
232B PHE* 3.8 27.4 - - + -
330B ASP* 1.3 70.9 - - - +
332B GLU* 1.3 56.6 + - - +
334B TYR* 3.1 5.8 + - - +
335B ALA* 2.6 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASN* 4.6 7.4 + - - +
231B ALA* 4.3 18.4 - - + +
234B ARG* 3.2 41.5 + - + +
235B ALA* 3.6 13.2 - - + +
330B ASP* 3.4 14.9 + - - +
331B MET* 1.3 78.6 - - - +
333B GLU* 1.3 57.8 + - - +
335B ALA* 4.4 4.5 - - - -
336B ARG* 2.9 34.1 + - + +
680J THR* 4.1 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B HIS* 4.8 7.4 + - - -
328B TRP 4.7 2.4 - - - +
329B ARG* 3.5 40.6 + - + +
330B ASP* 2.9 20.1 + - - +
332B GLU* 1.3 73.8 - - - +
334B TYR* 1.3 59.8 + - - +
337B GLU* 2.7 46.9 + - + +
676J CYS* 5.3 2.3 - - - -
678J THR* 3.0 23.6 + - - +
680J THR* 3.4 35.6 - - + +
681J THR* 5.0 4.7 + - - -
682J PRO* 5.4 2.9 - - - +
694J CYS* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 3.0 35.9 - - + +
155B ASN* 3.1 23.5 - - + -
157B PHE* 3.6 9.1 + - + -
191B ASP* 4.0 19.7 - - - +
232B PHE* 4.0 15.7 - + - -
329B ARG* 4.0 3.1 - - - +
330B ASP 3.1 15.2 + - - +
331B MET* 3.1 15.2 + - - +
333B GLU* 1.3 77.8 - - - +
335B ALA* 1.3 56.1 + - - +
338B VAL* 2.7 58.3 + - + -
339B PHE* 2.8 30.3 + + + -
342B GLU* 2.7 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 3.7 46.7 - - + +
235B ALA* 3.9 6.5 - - + -
236B LEU* 3.8 10.3 - - - +
331B MET 2.6 20.8 + - - +
332B GLU* 3.8 4.0 - - - +
334B TYR* 1.3 75.0 - - - +
336B ARG* 1.3 57.5 + - - +
339B PHE* 3.3 14.1 - - - +
340B PRO* 3.0 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ALA* 3.2 30.2 + - + +
236B LEU* 5.1 1.5 - - - +
332B GLU* 2.9 20.9 + - - +
333B GLU 4.0 0.9 - - - +
335B ALA* 1.3 77.8 - - - +
337B GLU* 1.3 71.6 + - - +
340B PRO* 2.9 24.4 - - - +
679J GLN* 3.5 32.8 + - - +
680J THR* 3.2 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ARG* 5.5 0.9 - - - +
333B GLU* 2.7 31.3 + - + +
336B ARG* 1.3 90.9 + - - +
338B VAL* 1.3 62.0 + - + +
340B PRO* 4.3 0.6 - - - +
341B ILE* 3.1 27.9 - - - +
677J PHE 3.7 6.9 - - - +
678J THR* 3.4 30.5 - - - +
679J GLN* 3.2 29.3 + - - +
680J THR* 2.9 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU* 5.1 7.9 - - - +
329B ARG* 3.2 42.6 - - - +
334B TYR* 2.7 31.3 + - + +
337B GLU* 1.3 80.6 - - + +
339B PHE* 1.3 66.8 + - - +
340B PRO* 3.2 3.1 - - - -
341B ILE* 2.9 8.8 + - + -
342B GLU* 2.8 49.6 + - + +
----------------------------------------------------------
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