Contacts of the helix formed by residues 123 - 132 (chain F) in PDB entry 1IES
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 PRO 123 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LEU* 3.7 26.9 - - + +
114D HIS* 3.5 46.7 - - + +
130D GLU* 4.2 4.0 - - - +
134D LEU* 3.7 11.9 - - + -
7F ASN* 3.9 8.1 - - - +
121F ALA 3.1 14.4 - - - +
122F ASP* 1.3 80.7 - - - +
124F HIS* 1.3 59.9 + - - +
126F CYS* 3.5 6.7 + - + +
127F ASP* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LEU* 6.3 1.1 - - + -
134D LEU* 4.2 11.8 - - + +
135D ASP* 3.1 38.4 + - - -
138D VAL* 3.8 39.5 - - + +
68F MET* 4.5 15.7 - - + +
71F GLN* 5.0 3.8 - - - -
72F ARG* 3.5 28.8 + - + +
122F ASP* 3.4 8.5 + - - +
123F PRO* 1.3 80.5 - - + +
125F LEU* 1.3 59.3 + - - +
127F ASP* 3.3 15.2 + - - +
128F PHE* 2.9 37.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 5.0 0.9 - - + -
12F VAL* 3.8 30.1 - - + -
16F VAL* 4.2 6.1 - - + -
68F MET* 3.6 34.3 - - + -
72F ARG* 5.7 1.6 - - - +
113F LEU* 3.9 25.6 - - + +
114F HIS* 5.1 0.2 - - - -
117F GLY* 3.6 28.3 - - - -
122F ASP* 3.3 21.9 + - - +
123F PRO 3.4 0.2 - - - -
124F HIS* 1.3 76.6 + - - +
126F CYS* 1.3 67.1 + - - +
128F PHE* 3.2 5.3 + - - +
129F LEU* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLU* 5.4 3.8 - - - +
114F HIS* 3.7 37.0 + - + +
117F GLY* 3.7 4.7 - - - -
118F SER* 3.5 32.5 - - - -
122F ASP 3.4 14.8 + - - +
123F PRO* 3.7 11.2 - - + +
125F LEU* 1.3 78.9 - - - +
127F ASP* 1.3 61.6 + - - +
129F LEU* 3.6 2.1 - - - +
130F GLU* 3.0 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLU* 3.6 49.9 + - + +
131D SER* 5.1 1.0 - - - -
134D LEU* 4.9 0.9 - - - +
135D ASP* 4.4 9.7 + - - +
204D CD 4.0 8.8 - - - -
123F PRO 2.9 18.4 + - - +
124F HIS* 3.4 21.3 - - - +
126F CYS* 1.3 73.8 - - - +
128F PHE* 1.3 54.0 + - - +
130F GLU* 3.1 8.4 + - - +
131F SER* 2.7 50.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ASP* 6.1 0.2 - - - -
64F ARG* 3.7 29.2 - - + -
65F LEU* 3.7 8.7 - - + -
68F MET* 3.6 46.9 - - + -
71F GLN* 6.2 1.6 - - - -
124F HIS* 2.9 31.5 + + + +
125F LEU* 3.5 7.0 - - - +
127F ASP* 1.3 73.3 - - - +
129F LEU* 1.3 66.7 + - + +
131F SER* 3.3 3.3 + - - -
132F HIS* 2.9 58.8 + + - +
133F PHE* 3.4 30.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 4.7 4.7 - - + -
110F LEU* 4.1 21.5 - - + +
113F LEU* 3.9 28.5 - - + -
114F HIS* 3.7 45.1 - - + +
125F LEU* 2.9 23.9 + - + +
126F CYS 3.6 3.4 - - - +
128F PHE* 1.3 91.1 - - + +
130F GLU* 1.3 60.4 + - - +
133F PHE* 2.9 38.8 + - + -
134F LEU* 3.0 17.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLU* 3.8 4.9 - - - +
203D CD 2.4 29.4 - - - -
123E PRO* 4.1 8.4 - - - +
126E CYS* 5.2 3.2 - - - +
127E ASP* 3.7 42.8 - - + +
130E GLU* 3.9 4.3 - - - +
114F HIS* 2.8 32.6 + - - +
126F CYS* 3.0 21.2 + - - +
127F ASP* 3.5 5.2 - - - +
129F LEU* 1.3 77.6 - - - +
131F SER* 1.3 62.7 + - - +
134F LEU* 3.8 26.7 + - + +
135F ASP* 4.2 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E ASP* 4.8 2.6 + - - -
127F ASP* 2.7 37.8 + - - -
128F PHE* 3.7 4.3 - - - -
130F GLU* 1.3 74.6 - - - +
132F HIS* 1.3 78.2 + - - +
135F ASP* 5.5 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F ARG* 3.7 30.7 + - - +
128F PHE* 2.9 56.7 + + - -
131F SER* 1.3 90.7 + - - +
133F PHE* 1.3 80.4 + - + +
135F ASP 5.4 0.7 - - - -
136F GLU* 3.5 24.5 - - - +
----------------------------------------------------------
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