Contacts of the helix formed by residues 26 - 36 (chain C) in PDB entry 2V5Q
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 GLN 26 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 3.0 15.6 + - + +
24C ALA* 4.2 20.6 - - + +
25C GLY* 1.3 73.7 - - - +
27C ASP* 1.3 59.8 + - - +
28C ASP* 3.4 4.8 - - - +
29C GLU* 3.3 26.7 + - + +
30C VAL* 3.0 30.0 + - - +
62C ILE* 3.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY 3.1 14.0 + - - +
26C GLN* 1.3 69.8 - - - +
28C ASP* 1.3 70.5 + - - +
30C VAL* 3.3 5.0 + - - +
31C ARG* 3.2 40.7 + - - +
59C HIS* 6.1 0.3 - - - +
61C GLU* 3.5 28.6 - - - +
62C ILE* 3.4 27.2 + - - +
65C VAL* 5.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN* 3.4 3.9 - - - +
27C ASP* 1.3 77.6 - - - +
29C GLU* 1.3 57.1 + - - +
31C ARG* 3.2 23.8 + - - +
32C ILE* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LYS* 5.3 3.6 - - - +
21C ALA* 4.0 8.7 - - + +
26C GLN* 3.3 32.2 + - + +
28C ASP* 1.3 73.8 - - - +
30C VAL* 1.3 59.3 + - - +
32C ILE* 3.8 21.0 - - + +
33C LEU* 2.9 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 4.1 16.1 - - + +
21C ALA* 3.8 27.1 - - + -
22C ALA* 3.9 6.7 - - + +
26C GLN 3.0 18.4 + - - +
27C ASP 3.5 8.5 - - - +
29C GLU* 1.3 77.0 - - - +
31C ARG* 1.3 62.2 - - + +
33C LEU* 3.8 1.4 - - - +
34C ILE* 3.1 47.7 + - + +
62C ILE* 3.9 30.7 - - + -
65C VAL* 4.2 13.9 - - + -
66C LEU* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 3.2 28.4 + - - +
28C ASP* 3.6 29.1 + - - +
30C VAL* 1.3 73.6 - - + +
32C ILE* 1.3 61.1 + - + +
34C ILE* 3.4 7.9 + - - +
35C ALA* 3.0 29.1 + - - +
61C GLU* 5.3 5.5 - - - +
65C VAL* 4.0 36.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ASP* 2.9 34.1 + - + +
29C GLU* 3.8 21.8 - - + +
31C ARG* 1.3 77.5 - - + +
33C LEU* 1.3 64.9 + - + +
35C ALA* 3.2 8.0 + - - +
36C ASN* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 3.8 25.4 - - + +
17C LYS* 3.5 53.6 - - + +
18C LEU* 3.6 11.4 - - + +
21C ALA* 3.9 8.1 - - + -
29C GLU* 2.9 45.3 + - - +
30C VAL 3.8 2.7 - - - +
32C ILE* 1.3 75.7 - - + +
34C ILE* 1.3 59.0 + - - +
36C ASN* 3.2 9.1 + - - +
37C GLY 3.2 6.2 + - - -
38C ALA* 3.0 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 4.2 11.9 - - + -
30C VAL* 3.1 35.3 + - + +
31C ARG* 3.7 5.6 - - - +
32C ILE 3.3 0.2 - - - -
33C LEU* 1.3 72.3 - - - +
35C ALA* 1.3 65.9 + - - +
37C GLY* 3.2 12.8 + - - -
38C ALA* 4.1 9.0 + - - +
40C VAL* 4.1 25.1 - - + -
65C VAL* 3.9 18.8 - - + +
66C LEU* 4.1 9.2 - - + -
69C HIS* 3.5 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG 3.0 17.3 + - - +
32C ILE* 3.2 8.3 + - - +
34C ILE* 1.3 78.0 - - - +
36C ASN* 1.3 63.5 + - - +
37C GLY* 3.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 3.5 27.3 - - + +
32C ILE* 3.1 34.9 + - - +
33C LEU* 3.6 10.4 - - - +
34C ILE 3.2 0.4 - - - -
35C ALA* 1.3 80.6 - - - +
37C GLY* 1.3 56.0 + - - +
38C ALA 3.7 0.2 - - - -
----------------------------------------------------------
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