Contacts of the helix formed by residues 126 - 130 (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 PHE 126 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C MET* 4.5 19.1 - - + -
83C GLU 4.3 14.8 - - - -
84C PHE 3.7 14.5 + - - +
85C PHE* 3.2 39.9 - + + -
102C PHE* 5.1 4.9 - + - -
106C MET* 5.4 4.3 - - - -
122C PRO 4.8 3.6 + - - -
123C HIS 5.0 1.2 + - - -
124C GLN 3.1 0.4 - - - -
125C VAL* 1.3 94.6 - - + +
127C THR* 1.3 56.4 + - - -
128C TRP* 2.9 22.7 - + - +
129C THR* 2.7 43.6 + - + +
130C GLN* 3.7 5.2 - - - +
207C LEU* 4.1 10.3 - - + -
222C TRP* 4.0 19.5 - + - -
225C PHE* 4.0 16.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C HIS 4.5 1.0 + - - -
124C GLN* 3.1 22.5 + - - +
125C VAL 3.6 1.0 + - - -
126C PHE* 1.3 76.5 - - - +
128C TRP* 1.3 58.1 + - - +
130C GLN* 3.0 29.7 + - + +
131C MET* 3.3 43.2 + - + +
154C HIS* 2.6 31.8 + - - +
155C GLY* 3.8 6.1 - - - -
156C LEU* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 4.7 0.4 - + - -
89C TRP* 3.5 49.5 - + - -
93C LEU* 4.6 2.2 - - + -
125C VAL 3.4 21.6 + - - -
126C PHE* 3.7 17.1 - + - +
127C THR* 1.3 78.9 - - - +
129C THR* 1.3 69.3 + - + +
130C GLN 3.3 1.5 + - - -
131C MET* 4.6 5.4 + - - +
132C CYS* 4.7 5.4 + - - +
155C GLY 3.3 21.2 + - - +
156C LEU* 4.0 14.6 - - + -
196C ALA* 6.1 0.2 - - - -
201C LEU* 3.8 30.6 - - + +
202C LEU 4.2 5.2 - - - +
203C LEU* 3.8 18.2 - - + -
204C ASN 6.1 0.2 - - - -
207C LEU* 3.6 31.3 - - + +
225C PHE* 4.1 11.4 - + - -
229C VAL* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 3.9 20.4 - - + -
86C GLY* 2.7 37.3 + - - -
89C TRP* 3.2 39.8 + - + -
126C PHE* 2.7 25.2 + - + +
128C TRP* 1.3 113.6 - - + +
130C GLN* 1.3 58.3 + - - +
131C MET 3.8 0.4 - - - -
132C CYS 4.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C PHE* 3.4 30.8 + - - +
85C PHE 4.7 0.3 - - - -
86C GLY* 4.0 9.0 + - - +
123C HIS 4.0 16.0 + - - -
126C PHE 3.7 6.0 + - - +
127C THR* 3.0 16.5 + - + +
129C THR* 1.3 94.0 - - - +
131C MET* 1.3 66.9 + - + +
132C CYS 3.3 3.4 + - - -
----------------------------------------------------------
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