Contacts of the helix formed by residues 1228 - 1237 (chain A) in PDB entry 2OJ9
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 SER1228 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161A THR* 6.1 0.9 - - - -
1165A VAL* 4.4 3.4 - - - -
1226A ARG 3.8 0.4 + - - -
1227A PRO* 1.3 75.7 - - - +
1229A PHE* 1.3 63.6 + - - +
1230A LEU* 3.3 11.2 + - - +
1231A GLU* 2.9 40.4 + - - +
1232A ILE* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090A ALA* 3.7 27.8 - - + +
1093A MET* 3.5 37.0 - - + -
1094A ALA* 3.7 11.4 - - + -
1097A ASN* 3.0 33.8 - - - +
1106A LEU* 4.2 0.2 - - + -
1161A THR* 4.5 0.4 + - - -
1164A ASP* 3.6 35.0 - - + -
1165A VAL* 3.6 16.5 - - + +
1168A PHE* 3.5 31.4 - + + -
1228A SER* 1.3 73.5 - - - +
1230A LEU* 1.3 62.8 + - - +
1232A ILE* 3.2 13.1 + - + +
1233A ILE* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A ALA* 4.1 20.4 - - + +
1098A ALA* 6.4 1.3 - - + -
1228A SER* 3.1 9.7 + - - +
1229A PHE* 1.3 78.7 - - - +
1231A GLU* 1.3 57.1 + - + +
1233A ILE* 3.3 5.8 + - - +
1234A SER* 3.0 28.6 + - - -
1249A PHE* 4.4 8.5 - - + -
1250A TYR* 3.7 28.5 - - + -
1255A ASN* 3.8 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1226A ARG 4.5 1.2 - - - +
1227A PRO* 3.4 16.4 - - + +
1228A SER* 2.9 39.6 + - - +
1230A LEU* 1.3 74.3 - - + +
1232A ILE* 1.3 66.5 + - - +
1234A SER* 3.4 7.6 + - - -
1235A SER* 3.2 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090A ALA* 4.1 12.1 - - + -
1165A VAL* 4.4 5.4 - - + -
1168A PHE* 3.8 41.3 - - + -
1214A LEU* 4.0 23.8 - - + -
1218A CYS* 4.0 13.7 - - - -
1227A PRO* 3.8 20.2 - - + -
1228A SER 3.0 19.7 + - - +
1229A PHE* 3.2 21.1 + - + +
1231A GLU* 1.3 76.1 - - - +
1233A ILE* 1.3 64.5 + - - +
1235A SER* 2.8 25.0 + - - -
1236A ILE* 3.3 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087A GLY* 4.3 7.2 - - - +
1090A ALA* 3.6 19.7 - - + +
1091A ASP* 3.5 40.2 - - + +
1094A ALA* 4.0 9.6 - - + -
1229A PHE 3.0 19.7 + - - +
1230A LEU* 3.7 5.8 - - - +
1232A ILE* 1.3 76.9 - - - +
1234A SER* 1.3 53.6 + - - +
1236A ILE* 3.0 9.4 + - + -
1237A LYS* 2.7 39.0 + - + -
1240A MET* 5.7 1.3 - - + -
1244A PHE* 4.1 17.7 - - + -
1250A TYR* 3.4 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230A LEU 3.0 15.6 + - - -
1231A GLU* 3.8 8.7 - - - -
1232A ILE 3.3 0.2 - - - -
1233A ILE* 1.3 76.3 - - - +
1235A SER* 1.3 60.1 + - - +
1236A ILE 3.5 0.3 + - - -
1237A LYS* 3.7 25.7 + - - +
1238A GLU* 3.9 4.2 - - - +
1250A TYR* 3.3 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1214A LEU* 4.9 8.3 - - - +
1217A MET* 5.8 3.6 - - - +
1231A GLU 3.2 11.4 + - - -
1232A ILE* 2.8 19.0 + - - -
1233A ILE 3.1 0.8 - - - -
1234A SER* 1.3 78.7 - - - +
1236A ILE* 1.3 67.0 + - - +
1238A GLU* 2.9 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083A ILE* 3.9 30.5 - - + +
1086A ALA* 4.4 9.6 - - + -
1087A GLY* 3.7 34.3 - - - +
1210A MET* 5.0 13.5 - - + -
1214A LEU* 4.8 13.2 - - + -
1232A ILE* 3.3 24.2 - - + +
1233A ILE* 3.6 8.3 - - - +
1235A SER* 1.3 88.9 - - - +
1237A LYS* 1.3 56.1 + - - +
1238A GLU* 3.1 8.5 - - - -
1239A GLU* 2.7 33.3 + - + +
1240A MET* 3.6 9.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233A ILE* 2.7 19.2 + - + +
1234A SER* 3.7 19.3 + - - +
1236A ILE* 1.3 76.4 - - - +
1238A GLU* 1.3 65.2 + - - +
1239A GLU 3.3 0.9 + - - -
1240A MET* 3.3 26.5 + - - +
1244A PHE* 5.2 1.7 - - + -
1250A TYR* 3.0 44.3 + - + +
1251A TYR* 2.8 39.4 + - + +
----------------------------------------------------------
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