Contacts of the helix formed by residues 5081 - 5087 (chain v) in PDB entry 2AXT
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 ARG5081 (chain v).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5343d GLU* 5.4 1.2 + - - -
5134u LYS* 3.5 10.3 - - - +
5070v GLY 4.6 0.6 + - - -
5079v ASP* 2.7 28.1 + - - +
5080v LEU* 1.3 78.1 - - - +
5082v THR* 1.3 66.2 + - - +
5083v GLU* 3.8 20.4 - - + +
5084v THR* 2.9 23.3 + - - +
5085v LEU* 3.1 10.7 + - - +
5149v PRO* 6.3 1.3 - - - -
5153v GLY 5.4 2.0 - - - -
5154v ASP* 3.6 24.0 + - - +
5156v TRP* 4.1 8.0 - - - +
5157v GLY* 3.1 30.6 - - - +
5158v GLY* 3.0 21.2 - - - +
5162v TYR* 4.3 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR5082 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5080v LEU 3.4 3.5 + - - -
5081v ARG* 1.3 71.7 - - - +
5083v GLU* 1.3 71.9 + - - +
5085v LEU* 3.3 11.2 + - - +
5086v ALA* 3.0 21.0 + - + +
5093v ASP* 4.0 18.5 - - + +
5145v ILE 4.4 5.4 + - - -
5146v LEU* 4.4 16.0 + - + +
5149v PRO* 3.5 27.4 - - - +
5156v TRP* 4.8 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU5083 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5081v ARG* 3.2 24.5 - - + -
5082v THR* 1.3 86.8 - - + +
5084v THR* 1.3 62.4 + - - +
5086v ALA* 3.2 20.9 - - - +
5087v LEU* 3.4 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR5084 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5066u ILE* 5.6 2.7 - - + +
5078v LEU* 5.0 4.5 - - + -
5079v ASP* 2.8 40.6 + - - +
5081v ARG* 2.9 11.7 + - - +
5083v GLU* 1.3 76.5 - - - +
5085v LEU* 1.3 65.7 + - - +
5087v LEU* 3.1 6.7 + - - -
5088v ALA 3.3 2.1 + - - -
5108v TYR* 2.5 38.6 + - + +
5552v HEM 3.2 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5085 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5080v LEU* 3.6 25.6 - - + +
5081v ARG 3.1 7.0 + - - +
5082v THR* 3.6 12.8 - - - +
5084v THR* 1.3 80.3 - - - +
5086v ALA* 1.3 62.6 + - - +
5088v ALA* 2.9 21.8 - - - +
5092v ARG* 3.1 51.8 + - + +
5093v ASP 3.8 2.5 - - - +
5098v LEU* 4.1 11.2 - - + -
5145v ILE* 4.0 19.3 - - + +
5146v LEU* 4.4 9.6 - - + -
5552v HEM 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5086 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5069u ARG* 2.9 25.9 + - - -
5082v THR* 3.0 12.1 + - + +
5083v GLU* 3.2 16.4 - - - +
5084v THR 3.1 0.4 - - - -
5085v LEU* 1.3 79.1 - - - +
5087v LEU* 1.3 61.2 + - + +
5088v ALA 3.2 1.6 + - - +
5091v PRO* 4.4 6.1 - - - +
5093v ASP* 3.6 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5087 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5067u GLN* 3.7 24.9 - - + +
5068u TYR* 4.9 1.1 - - + -
5069u ARG* 3.9 52.2 - - + +
5070u GLY 4.1 0.5 + - - -
5083v GLU* 3.4 16.8 + - + +
5084v THR* 3.1 3.6 + - - +
5086v ALA* 1.3 76.5 - - + +
5088v ALA* 1.3 65.6 + - - +
5089v THR* 3.9 1.4 + - - -
5108v TYR* 3.3 27.5 + - + +
----------------------------------------------------------
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