Contacts of the helix formed by residues 123 - 127 (chain D) in PDB entry 1IR1
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 ASN 123 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLU* 4.9 18.7 + - - +
119D SER 5.1 1.6 + - - -
122D GLY* 1.3 84.5 - - - +
124D VAL* 1.3 66.6 + - - +
125D PHE 3.2 4.6 + - - -
126D GLY* 3.2 13.2 + - - -
127D PHE* 3.9 15.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE* 4.7 0.2 - - + -
56D ALA 4.5 0.2 - - - +
57D VAL* 3.6 41.1 - - + +
60D GLU* 3.8 31.0 - - + +
61D SER* 4.1 4.0 - - - -
119D SER 5.5 0.2 - - - +
120D ILE 3.7 22.4 - - - +
121D VAL* 4.6 2.0 - - - -
122D GLY 3.9 0.2 - - - -
123D ASN* 1.3 77.4 - - - +
125D PHE* 1.3 75.5 + - + +
126D GLY 3.1 2.2 + - - -
127D PHE* 3.5 17.9 + - + +
130D LEU* 3.6 19.3 - - + +
133D LEU* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE* 4.3 5.2 - + - -
120D ILE 4.3 1.3 - - - -
121D VAL* 3.5 50.9 - - + +
123D ASN 3.2 2.2 + - - -
124D VAL* 1.3 86.4 - - + +
126D GLY* 1.3 56.5 + - - +
127D PHE 3.5 1.7 + - - +
130D LEU* 5.6 2.8 - - - +
132D ALA* 6.0 0.2 - - - -
133D LEU* 3.2 54.8 - - + +
134D ARG* 4.1 0.2 - - - -
135D LEU* 4.1 10.1 - - + -
307D HIS* 3.8 30.4 + + + +
308D GLY* 3.2 23.8 - - - -
309D MET* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASN 3.2 9.4 + - - -
124D VAL 3.1 1.0 - - - -
125D PHE* 1.3 79.3 - - - +
127D PHE* 1.3 67.2 + - - +
128D LYS* 3.3 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TYR* 3.8 21.8 - + - -
56D ALA* 4.9 12.8 - - + -
60D GLU* 3.2 48.9 - - + -
66D TRP* 6.3 0.4 - - + -
123D ASN* 3.9 20.9 - - + -
124D VAL* 3.5 20.3 + - + +
125D PHE 3.5 1.4 - - - +
126D GLY* 1.3 77.1 - - - +
128D LYS* 1.3 65.5 + - - +
129D ALA* 4.2 13.7 - - + +
130D LEU* 3.2 33.5 + - + +
----------------------------------------------------------
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