Contacts of the helix formed by residues 5061 - 5068 (chain u) in PDB entry 3A0B
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 ASN5061 (chain u).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5383b ALA* 6.5 0.4 - - + -
5320c ARG* 6.0 0.8 - - - +
5051u TYR* 5.9 0.2 + - - -
5059u ASN 4.2 0.2 - - - -
5060u THR* 1.3 77.1 - - - +
5062u ILE* 1.3 62.4 + - - +
5063u ALA* 3.5 20.0 + - - +
5064u ALA* 3.2 24.4 + - - +
5065u PHE* 5.3 1.4 - - - -
5126u ASP 3.8 2.7 - - - +
5127u ARG* 3.0 13.5 - - - +
5128u TYR 3.2 19.8 + - - -
5129u ASN* 4.9 0.2 - - - +
5130u ASN* 2.9 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5062 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5320c ARG* 6.0 1.1 - - - +
5324c LEU* 3.6 53.2 - - + +
5060u THR 3.7 1.6 + - - -
5061u ASN* 1.3 66.7 - - - +
5063u ALA* 1.3 62.8 + - + +
5064u ALA 2.5 19.4 + - - -
5065u PHE* 2.9 28.4 + - + +
5072u TYR* 4.0 9.1 - - + -
5076u ALA* 4.2 14.4 - - + -
5077u LYS* 3.9 20.2 - - - +
5080u VAL* 4.1 23.6 - - + -
5127u ARG* 2.7 15.1 + - - +
5128u TYR* 4.2 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5063 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5320c ARG* 5.7 2.7 - - - +
5324c LEU* 6.1 0.2 - - + -
5061u ASN* 3.4 15.6 + - - +
5062u ILE* 1.3 81.9 - - + +
5064u ALA* 1.3 57.1 + - - +
5065u PHE 3.1 3.8 - - - +
5066u ILE* 3.3 31.7 + - + +
5067u GLN 5.1 0.2 + - - -
5072u TYR* 4.2 4.7 - - + +
5077v SER* 3.1 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5064 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5055u ILE* 3.3 12.5 - - + +
5060u THR* 3.5 23.3 - - + -
5061u ASN* 3.2 21.6 + - - +
5062u ILE 2.5 8.1 + - - -
5063u ALA* 1.3 73.8 - - - +
5065u PHE* 1.3 54.5 + - + +
5066u ILE 3.2 4.3 - - - -
5067u GLN* 2.8 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5065 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5055u ILE* 3.2 43.1 - - + -
5056u ASP 5.4 0.7 - - - -
5057u LEU* 3.8 9.0 - - + -
5060u THR* 5.6 4.0 - - - -
5061u ASN 5.3 1.6 - - - -
5062u ILE* 2.9 20.7 + - + +
5064u ALA* 1.3 75.8 - - + +
5066u ILE* 1.3 56.1 + - - +
5067u GLN* 2.9 10.0 + - - -
5068u TYR* 3.2 19.8 + + - +
5071u LEU* 3.7 22.6 - - + +
5072u TYR* 3.9 9.8 + - + -
5076u ALA* 3.2 33.4 - - + -
5079u ILE* 3.5 49.6 - - + -
5080u VAL* 4.5 13.0 - - + -
5112u PHE* 4.8 7.2 - + - -
5127u ARG* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5066 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5063u ALA* 3.3 37.9 - - + +
5064u ALA 3.2 1.0 - - - -
5065u PHE* 1.3 76.3 - - - +
5067u GLN* 1.3 61.0 + - - +
5068u TYR* 3.2 6.4 + - - +
5072u TYR* 3.3 40.6 - - + -
5077v SER* 4.0 26.5 - - - +
5078v LEU* 4.1 15.5 - - + -
5079v ASP* 5.9 1.3 - - - +
5084v THR* 5.3 4.7 - - + -
5087v LEU* 4.8 4.5 - - - +
5108v TYR* 4.0 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN5067 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5055u ILE* 3.8 18.1 - - - +
5063u ALA 5.1 0.2 + - - -
5064u ALA* 2.8 27.0 + - - +
5065u PHE 2.9 0.2 - - - -
5066u ILE* 1.3 78.5 - - - +
5068u TYR* 1.3 90.6 + - + +
5087v LEU* 3.9 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR5068 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5054u LYS* 5.7 4.2 - - - -
5055u ILE* 5.0 11.1 - - + +
5064u ALA 5.2 0.7 - - - -
5065u PHE* 3.2 13.3 + + - +
5066u ILE* 4.0 6.5 - - - +
5067u GLN* 1.3 115.2 + - + +
5069u ARG* 1.3 60.1 + - - +
5070u GLY 4.0 0.7 + - - -
5071u LEU* 3.0 33.7 + - + +
5072u TYR 4.6 0.9 + - - -
5108u ASN* 3.9 12.6 - - - +
5111u HIS* 3.1 61.7 + + + +
5112u PHE* 5.4 3.1 - + - -
5087v LEU* 5.0 5.6 - - - -
5108v TYR* 4.5 5.5 - - - -
----------------------------------------------------------
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