Contacts of the helix formed by residues 248 - 257 (chain A) in PDB entry 2VZC
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 248 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 1.3 74.9 - - - +
249A ALA* 1.3 64.9 + - - +
250A PHE* 2.9 14.8 + - - +
251A ASP* 2.9 12.5 + - - +
252A THR* 3.0 24.2 + - - -
343A LYS* 3.0 17.7 + - - +
359A ARG* 2.8 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASP* 1.3 76.8 - - - +
250A PHE* 1.3 56.8 + - - +
252A THR* 3.3 10.1 + - - -
253A LEU* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASP* 2.9 12.2 + - - +
249A ALA* 1.3 75.8 - - - +
251A ASP* 1.3 66.0 + - - +
253A LEU* 3.6 22.6 - - + +
254A PHE* 2.9 32.2 + + + +
261A LEU* 5.4 0.4 - - + -
264A VAL* 4.4 14.4 - - + -
355A LYS* 3.9 19.3 - - + -
358A LEU* 3.7 18.2 - - + -
359A ARG* 3.6 58.1 - - + +
362A TYR* 3.8 38.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU 4.6 1.2 - - - +
247A ARG* 3.3 37.5 - - + +
248A ASP* 2.9 30.0 + - - +
250A PHE* 1.3 76.6 - - - +
252A THR* 1.3 57.6 + - - +
255A ASP* 2.9 37.4 + - - +
343A LYS* 5.1 1.4 + - - -
355A LYS* 2.5 41.1 + - - +
359A ARG* 3.0 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 4.9 3.5 + - - +
248A ASP 3.0 14.3 + - - -
249A ALA* 3.6 11.8 - - - -
250A PHE 3.2 0.4 - - - -
251A ASP* 1.3 77.1 - - - +
253A LEU* 1.3 58.4 + - - +
256A HIS* 2.9 50.7 + - + +
257A ALA* 4.6 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA* 3.0 19.0 + - + +
250A PHE* 3.6 28.7 - - + +
252A THR* 1.3 77.0 - - - +
254A PHE* 1.4 75.0 + - + +
257A ALA* 2.8 37.2 + - + +
260A LYS* 3.8 35.2 - - + +
261A LEU* 3.8 35.2 - - + +
264A VAL* 4.3 16.6 - - + -
362A TYR* 6.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE* 2.9 24.3 + + + +
251A ASP 3.9 2.5 - - - +
253A LEU* 1.4 88.3 - - + +
255A ASP* 1.3 75.8 + - - +
257A ALA 4.6 1.2 + - - -
258A PRO* 6.0 0.2 - - - +
261A LEU* 3.9 35.5 - - + +
354A LEU* 3.9 29.4 - - + -
355A LYS* 3.6 53.8 - - + -
358A LEU* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 1.9 45.2 + - - -
251A ASP* 2.9 17.8 + - - +
254A PHE* 1.3 94.3 - - - +
256A HIS* 1.3 73.5 + - + +
258A PRO* 5.9 0.2 - - - -
355A LYS* 4.3 8.1 + - - -
1373A TRS 2.7 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 4.2 9.2 + - - -
252A THR* 2.9 37.0 + - + +
255A ASP* 1.3 98.6 + - + +
257A ALA* 1.3 59.5 + - + +
258A PRO* 3.4 12.9 - - - +
1373A TRS 2.9 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A THR 4.6 0.7 - - - +
253A LEU* 2.8 35.1 + - + +
254A PHE 4.6 0.8 + - - -
255A ASP 4.0 0.4 - - - -
256A HIS* 1.3 73.8 - - + +
258A PRO* 1.3 67.1 - - - +
259A ASP 3.3 2.7 - - - +
260A LYS* 3.1 21.6 + - + +
261A LEU* 2.9 19.2 + - - +
----------------------------------------------------------
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