Contacts of the helix formed by residues 50 - 60 (chain A) in PDB entry 2VZE
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 50 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 4.4 11.2 - - + -
46A PHE* 3.2 36.5 + - + +
49A ASP* 1.3 84.1 - - + +
51A LEU* 1.3 70.5 + - - +
52A ASP 3.2 1.3 - - - -
53A HIS* 3.2 15.1 + - - +
54A TRP* 3.3 20.8 + - - +
243A LYS* 4.2 26.0 - - + -
277A TRP 3.4 25.8 - - - +
278A ALA* 3.7 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.2 14.3 + - + +
47A ALA* 3.3 11.9 - - - +
50A VAL* 1.3 82.3 - - - +
52A ASP* 1.3 62.7 + - - +
54A TRP* 3.2 17.2 + - - +
55A ALA* 3.2 10.0 + - - +
83A PHE* 3.9 21.3 - - + +
86A LEU* 3.4 29.4 - - + -
87A SER* 4.6 5.4 - - - -
90A SER* 4.4 1.3 - - - +
124A LEU* 3.5 35.0 - - + -
128A ARG* 3.6 23.3 - - - +
277A TRP* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 2.9 17.7 + - - +
48A SER* 3.7 20.4 + - - +
50A VAL 3.2 0.2 - - - -
51A LEU* 1.3 75.2 - - - +
53A HIS* 1.3 64.4 + - - +
54A TRP 3.2 0.2 - - - -
55A ALA* 3.7 4.7 - - + +
56A ASP* 2.8 36.2 + - - +
87A SER* 3.0 18.2 + - - -
91A GLN* 4.8 2.5 + - - -
128A ARG* 2.9 40.0 + - - -
207A CYS* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER 4.3 4.6 + - - +
49A ASP 4.3 10.8 - - - +
50A VAL* 3.2 13.4 + - - +
52A ASP* 1.3 77.5 - - - +
54A TRP* 1.3 98.9 + + - +
56A ASP* 3.2 6.9 + - - +
57A MET* 3.0 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.3 23.6 + - - +
51A LEU* 3.2 9.2 + - - +
53A HIS* 1.3 104.2 - + - +
55A ALA* 1.3 63.6 + - - +
57A MET* 3.4 20.9 + - + +
58A GLU* 3.4 15.8 + - - +
63A ARG* 3.8 37.4 + - - -
83A PHE* 3.6 26.5 - + + +
253A ALA* 5.5 3.1 - - + -
277A TRP 2.9 27.7 + - - -
278A ALA 3.5 12.0 + - - -
279A LEU* 3.5 24.9 - - - -
280A GLY* 3.4 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU 3.2 7.8 + - - +
52A ASP* 3.8 8.1 - - + +
53A HIS 3.3 0.2 - - - -
54A TRP* 1.3 78.7 - - - +
56A ASP* 1.3 65.8 + - - +
58A GLU* 3.0 15.6 + - - +
59A LYS* 3.1 21.9 + - - +
83A PHE* 3.5 30.4 - - - +
84A ARG* 3.9 8.5 - - + +
87A SER* 3.6 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 2.8 28.2 + - - +
53A HIS* 3.7 6.4 + - - +
55A ALA* 1.3 77.3 - - - +
57A MET* 1.3 61.6 + - - +
59A LYS* 3.9 25.0 + - - +
60A ALA* 3.1 27.7 + - - +
62A LYS* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS* 3.0 48.9 + - + +
54A TRP* 3.6 16.8 - - + +
55A ALA 3.2 0.2 - - - -
56A ASP* 1.3 75.2 - - - +
58A GLU* 1.3 59.4 + - - +
60A ALA* 3.7 1.3 + - - -
61A GLY 3.4 1.9 + - - -
62A LYS* 2.9 61.7 + - + +
63A ARG* 3.2 32.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TRP 3.4 6.2 + - - +
55A ALA 3.0 8.5 + - - +
57A MET* 1.3 75.8 - - - +
59A LYS* 1.3 67.1 + - - +
61A GLY* 3.1 14.0 + - - -
63A ARG* 3.6 13.8 + - + +
64A PRO 3.8 15.4 - - - +
65A PRO* 3.6 20.7 - - + +
66A SER* 2.9 22.6 + - - +
82A ASN* 3.4 13.2 + - - +
83A PHE* 3.3 28.9 + - - +
84A ARG* 3.1 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 3.1 19.6 + - - +
56A ASP* 3.5 28.3 + - - +
58A GLU* 1.3 76.0 - - - +
60A ALA* 1.3 60.3 + - + +
61A GLY 3.5 0.7 + - - -
84A ARG* 3.8 51.8 + - - +
87A SER* 5.1 7.6 + - - -
88A GLU* 5.2 8.7 + - - +
91A GLN* 5.1 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP 3.1 18.7 + - - +
57A MET 4.5 0.4 - - - +
59A LYS* 1.3 76.0 - - + +
61A GLY* 1.3 58.2 + - - +
62A LYS* 3.3 30.3 + - + +
----------------------------------------------------------
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