Contacts of the helix formed by residues 86 - 94 (chain C) in PDB entry 5AYR
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 GLY 86 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 1.3 75.7 - - - +
87C GLU* 1.3 60.3 + - - -
88C SER* 3.5 2.5 - - - -
89C TRP* 3.4 4.7 + - - +
90C LYS* 2.9 23.4 + - - +
129C THR* 2.7 38.5 + - - -
130C GLN* 4.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C MET 5.4 0.2 - - - +
85C PHE 4.3 4.5 - - - +
86C GLY* 1.3 68.4 - - - -
88C SER* 1.3 61.3 + - - +
89C TRP 3.0 1.6 - - - -
90C LYS* 3.0 33.7 + - - +
91C LYS* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLU* 1.3 78.3 + - - +
89C TRP* 1.3 67.8 + - - +
91C LYS* 3.5 14.3 - - - +
92C HIS* 3.2 28.8 - - - -
133C ASP* 3.3 34.7 - - - -
134C ILE* 3.3 22.1 + - - +
135C LYS* 4.1 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 3.7 15.7 - - + -
86C GLY 3.4 6.9 + - - +
87C GLU 3.0 0.2 - - - -
88C SER* 1.3 86.8 - - - +
90C LYS* 1.3 67.8 + - - +
91C LYS 3.0 1.3 - - - -
92C HIS* 2.9 13.5 + - - +
93C LEU* 3.0 23.7 + - + +
128C TRP* 3.5 46.9 - + - -
129C THR* 3.2 28.8 + - + +
132C CYS* 2.9 26.1 + - - -
134C ILE* 3.3 47.5 - - + +
137C VAL* 3.7 25.6 - - + -
201C LEU* 4.1 15.9 - - + -
229C VAL* 4.4 12.8 - - + -
233C LEU* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C MET* 2.8 54.9 + - - +
85C PHE* 3.4 20.7 - - + +
86C GLY 2.9 12.5 + - - +
87C GLU* 3.2 38.1 + - + +
89C TRP* 1.3 75.6 - - - +
91C LYS* 1.3 63.7 + - - +
94C SER* 3.0 33.6 + - - +
97C PHE* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLU 2.8 11.5 + - - +
88C SER* 3.5 20.7 - - - +
90C LYS* 1.3 78.4 - - - +
92C HIS* 1.3 85.4 + - + +
94C SER* 4.0 8.8 + - - -
135C LYS* 3.5 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C SER 3.2 24.2 - - - -
89C TRP 2.9 4.9 + - - +
91C LYS* 1.3 104.3 + - + +
93C LEU* 1.3 62.8 + - + +
94C SER 3.6 0.7 - - - -
95C GLY* 4.8 2.4 + - - -
134C ILE* 3.9 20.9 - - + +
135C LYS* 5.4 5.5 - - - +
232C TRP* 3.4 53.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 4.3 22.0 - - + -
89C TRP* 3.0 43.6 + - + +
92C HIS* 1.3 83.2 - - + +
94C SER* 1.3 62.6 + - - +
95C GLY* 3.0 7.6 + - - -
96C GLU* 3.1 24.3 + - + +
97C PHE* 4.1 6.6 - - - -
128C TRP* 4.6 1.1 - - + -
134C ILE* 4.7 4.5 - - + -
225C PHE* 4.7 7.6 - - + -
228C ALA* 4.5 7.2 - - + +
229C VAL* 4.0 33.2 - - + +
232C TRP* 4.0 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LYS* 3.0 22.0 + - - -
91C LYS* 4.0 8.5 + - - -
92C HIS 3.6 0.4 - - - -
93C LEU* 1.3 77.4 - - - +
95C GLY* 1.3 63.5 + - - +
96C GLU 3.0 1.7 + - - -
97C PHE* 3.1 42.3 + - - +
98C GLY 4.3 1.7 + - - -
----------------------------------------------------------
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