Contacts of the helix formed by residues 330 - 338 (chain F) in PDB entry 2VUT
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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F ASN* 4.1 3.8 - - - +
221F GLU* 3.2 20.2 - - - +
328F TRP* 3.4 30.3 + - + -
329F ARG* 1.3 76.4 - - - +
331F MET* 1.3 59.3 + - - +
332F GLU* 3.4 16.3 + - - +
333F GLU* 3.1 22.3 + - - +
334F TYR* 2.9 26.9 + - - +
680N THR* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F ASN* 3.0 33.3 - - - +
157F PHE* 4.2 4.7 - - + -
189F TRP* 3.5 37.5 - - + -
221F GLU* 2.6 15.3 + - - +
223F LEU* 3.5 17.7 - - + -
228F VAL* 4.0 22.7 - - + +
231F ALA* 3.8 17.5 - - + -
232F PHE* 4.1 20.6 - - + -
330F ASP* 1.3 72.2 - - - +
332F GLU* 1.3 57.8 + - - +
334F TYR* 3.6 9.6 - - - +
335F ALA* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ASN* 2.5 46.4 + - - +
231F ALA* 4.1 17.2 - - + +
234F ARG* 2.8 48.0 + - + +
235F ALA* 3.9 5.6 - - + +
330F ASP* 3.3 15.9 + - - +
331F MET* 1.3 77.4 - - - +
333F GLU* 1.3 57.9 + - - +
336F ARG* 2.9 34.2 + - + +
680N THR* 4.7 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F HIS* 4.6 7.4 + - - -
328F TRP 4.8 2.3 - - - +
329F ARG* 3.4 44.3 + - + +
330F ASP* 3.1 14.7 + - - +
332F GLU* 1.3 73.9 - - - +
334F TYR* 1.3 60.5 + - - +
336F ARG* 4.5 0.9 - - - -
337F GLU* 2.8 41.2 + - + +
676N CYS* 5.6 0.9 - - - -
678N THR* 3.2 20.4 + - - +
680N THR* 3.1 40.1 - - + +
681N THR* 4.4 5.4 - - - -
682N PRO* 5.0 4.0 - - - +
694N CYS* 5.7 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F ASN* 3.3 32.8 - - + +
155F ASN* 3.3 28.6 - - + -
157F PHE* 3.8 9.5 + - + -
191F ASP* 4.0 20.6 - - - +
232F PHE* 4.3 11.4 - + - -
329F ARG* 3.8 10.0 - - - +
330F ASP 2.9 16.9 + - - +
331F MET* 3.2 13.4 + - - +
333F GLU* 1.3 77.1 - - - +
335F ALA* 1.3 61.9 + - - +
338F VAL* 2.8 60.3 + - + -
339F PHE* 3.1 27.4 + + + -
342F GLU* 2.5 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F ALA 4.6 0.2 - - - +
232F PHE* 3.8 39.7 - - + -
235F ALA* 3.8 17.3 - - + -
236F LEU* 3.7 7.7 - - + +
331F MET 2.8 20.7 + - - +
334F TYR* 1.3 77.4 - - - +
336F ARG* 1.3 58.0 + - - +
339F PHE* 3.4 12.1 - - - +
340F PRO* 3.0 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 336 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ARG* 4.2 25.0 - - - +
237C ASN* 5.3 9.4 - - - +
336C ARG* 6.0 1.8 - - - +
234F ARG 5.4 0.4 - - - -
235F ALA* 3.1 38.3 - - + +
236F LEU* 5.1 0.7 - - - -
332F GLU* 2.9 21.2 + - + +
333F GLU 3.9 1.8 - - - +
335F ALA* 1.3 80.5 - - - +
337F GLU* 1.3 82.0 + - + +
340F PRO* 3.9 12.1 - - - +
679N GLN* 3.2 44.1 + - - +
680N THR* 3.5 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329F ARG* 5.8 0.9 - - - +
333F GLU* 2.8 32.6 + - + +
336F ARG* 1.3 102.1 + - - +
338F VAL* 1.3 64.2 + - + +
340F PRO* 4.4 2.9 - - - -
341F ILE* 3.6 22.8 - - - +
677N PHE 4.5 2.1 - - - +
678N THR* 3.6 28.8 - - - +
679N GLN* 3.4 15.0 + - - -
680N THR* 2.6 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F GLU* 5.8 2.0 - - - +
329F ARG* 3.3 43.1 - - - +
334F TYR* 2.8 33.1 + - + +
336F ARG 3.9 0.2 - - - -
337F GLU* 1.3 80.8 - - + +
339F PHE* 1.3 56.3 + - - +
340F PRO* 3.3 2.2 - - - +
341F ILE* 3.0 7.6 + - + +
342F GLU* 2.7 67.4 + - + +
----------------------------------------------------------
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