Contacts of the helix formed by residues 50 - 60 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PHE* 4.4 9.6 - - + -
46C PHE* 3.1 43.4 + - + +
49C ASP* 1.3 84.6 - - - +
51C LEU* 1.3 68.8 + - - +
52C ASP 3.3 1.1 - - - -
53C HIS* 3.2 19.3 + - - +
54C TRP* 3.5 10.3 + - - +
243C LYS* 3.9 28.9 - - + -
277C TRP 3.3 24.9 - - - +
278C ALA* 3.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 3.1 14.4 + - + +
47C ALA* 3.3 10.5 - - - +
50C VAL* 1.3 81.4 - - - +
52C ASP* 1.3 59.2 + - - +
54C TRP* 3.2 22.2 + - - +
55C ALA* 3.3 10.0 + - - +
83C PHE* 4.0 17.9 - - + +
86C LEU* 3.5 28.3 - - + -
87C SER* 4.4 8.3 - - - -
90C SER* 4.3 2.5 - - - +
124C LEU* 3.9 30.3 - - + -
128C ARG* 3.4 26.9 - - - +
277C TRP* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA 2.9 18.5 + - - +
48C SER* 3.6 19.9 - - - +
50C VAL 3.3 0.4 - - - -
51C LEU* 1.3 72.7 - - - +
53C HIS* 1.3 65.7 + - - +
55C ALA* 3.7 6.0 - - + +
56C ASP* 3.0 35.2 + - - +
87C SER* 3.1 18.3 + - - -
91C GLN* 5.1 2.2 + - - -
128C ARG* 2.9 41.7 + - - -
207C CYS* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C SER 4.4 4.2 + - - -
49C ASP 4.3 10.1 - - - +
50C VAL* 3.2 14.9 + - - +
52C ASP* 1.3 78.6 - - - +
54C TRP* 1.3 94.8 + + - +
56C ASP* 3.3 6.3 + - - +
57C MET* 3.1 52.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C VAL* 3.6 19.4 + - - +
51C LEU* 3.2 9.6 + - - +
53C HIS* 1.3 93.7 - + - +
55C ALA* 1.3 66.1 - - - +
57C MET* 3.4 29.6 - - + +
58C GLU* 3.4 22.3 + - - +
63C ARG* 3.7 29.5 + - - -
83C PHE* 3.8 26.5 - + + -
253C ALA* 5.4 4.0 - - + -
277C TRP 3.1 28.0 + - - -
278C ALA 3.4 11.1 + - - -
279C LEU* 3.5 22.9 - - - -
280C GLY* 3.2 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU 3.3 4.3 + - - +
52C ASP* 3.7 13.7 - - + +
53C HIS 3.3 0.2 - - - -
54C TRP* 1.3 78.7 - - - +
56C ASP* 1.3 60.6 + - - +
58C GLU* 2.9 20.1 + - - +
59C LYS* 3.0 23.1 + - - +
83C PHE* 3.7 29.0 - - - +
84C ARG* 4.1 7.8 - - + +
87C SER* 3.7 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ASP* 3.0 28.3 + - - +
53C HIS* 3.7 6.6 - - - +
55C ALA* 1.3 75.2 - - - +
57C MET* 1.3 64.7 + - + +
59C LYS* 3.9 21.2 + - - +
60C ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C HIS* 3.1 49.7 + - + +
54C TRP* 3.4 32.3 - - + +
55C ALA 3.2 0.2 - - - -
56C ASP* 1.3 76.4 - - - +
58C GLU* 1.3 60.0 + - - +
60C ALA* 3.8 0.8 + - - -
61C GLY 3.4 1.7 + - - -
62C LYS* 2.9 60.6 + - + +
63C ARG* 3.2 31.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TRP 3.4 10.3 + - - +
55C ALA 2.9 7.9 + - - +
57C MET* 1.3 73.7 - - - +
59C LYS* 1.3 68.5 - - - +
61C GLY* 3.0 14.9 + - - -
63C ARG* 3.6 15.6 + - + +
64C PRO 4.0 13.2 - - - +
65C PRO* 3.7 17.1 - - + +
66C SER* 3.0 20.6 + - - +
82C ASN* 3.4 14.2 + - - -
83C PHE* 3.1 29.3 + - - +
84C ARG* 3.3 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 3.0 23.7 + - - +
56C ASP* 4.0 19.9 + - - +
58C GLU* 1.3 76.6 - - - +
60C ALA* 1.3 60.0 + - + +
61C GLY* 3.4 0.9 + - - -
84C ARG* 3.8 54.6 + - - +
87C SER* 5.0 9.2 + - - -
88C GLU* 4.6 10.5 + - - +
91C GLN* 5.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASP 3.0 19.9 + - - +
57C MET 4.4 1.6 - - - +
58C GLU 3.2 0.2 - - - -
59C LYS* 1.3 75.3 - - + +
61C GLY* 1.3 60.6 + - - +
62C LYS* 3.3 24.3 + - + +
----------------------------------------------------------
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