Contacts of the helix formed by residues 106 - 111 (chain C) in PDB entry 4AEJ
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 TRP 106 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C HIS* 4.9 7.6 + - - +
105C VAL* 1.3 72.0 - - - +
107C PHE* 1.3 66.6 + - - +
109C GLU* 3.6 33.2 - - + -
110C SER* 3.0 29.2 + - - +
111C MSE 3.7 3.0 + - - +
170C LYS* 3.9 12.5 - - + +
171C LEU 3.7 7.6 - - - -
172C MSE 3.5 43.5 - - + -
178C GLU* 2.9 33.4 + - + -
222C ASP* 3.4 25.4 - - + +
223C ILE 3.5 19.3 - - - -
224C ALA* 3.6 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 3.6 44.9 - - + -
94C TRP* 3.9 21.3 - + - -
105C VAL 3.5 2.2 + - - -
106C TRP* 1.3 73.0 - - - +
108C GLY* 1.3 60.7 + - - +
111C MSE 3.4 39.1 + - + +
113C GLY 4.4 1.6 - - - -
114C GLY* 3.4 32.4 - - - -
115C PHE* 3.2 50.3 - + - -
117C PHE* 4.2 12.6 - + - -
222C ASP* 3.5 3.3 + - - +
223C ILE* 3.0 29.8 + - + +
235C PHE* 4.5 9.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 1.3 75.2 - - - +
109C GLU* 1.3 61.5 + - - +
111C MSE 5.2 1.0 + - - +
114C GLY* 4.1 10.7 - - - +
115C PHE* 3.4 29.1 - - - -
116C GLN* 3.9 8.5 - - - +
222C ASP* 2.7 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TRP* 3.4 33.2 + - + -
107C PHE 3.4 0.2 - - - -
108C GLY* 1.3 78.8 - - - +
110C SER* 1.3 64.1 + - - +
111C MSE 5.6 0.2 - - - -
116C GLN* 3.6 15.2 + - - +
172C MSE 6.1 0.7 - - - +
222C ASP* 3.5 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TRP* 3.7 16.2 - - - -
105C VAL* 3.8 19.0 - - - +
106C TRP* 3.0 16.7 + - - +
109C GLU* 1.3 86.0 + - - +
111C MSE 1.3 65.9 + - - +
112C ASP 3.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C TRP* 3.8 21.1 - - + +
95C TRP* 3.8 24.9 - - + -
105C VAL* 3.2 34.3 - - + +
106C TRP 3.9 2.5 - - - +
107C PHE* 3.4 36.8 + - + +
108C GLY 5.3 1.0 - - - +
110C SER* 1.3 78.0 - - - +
112C ASP* 1.3 58.4 + - - +
113C GLY 3.1 1.0 + - - -
114C GLY* 2.8 26.7 + - - -
225C PRO* 3.9 11.4 - - + -
228C ILE* 3.6 26.5 - - + -
235C PHE* 3.8 21.8 - - + -
----------------------------------------------------------
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