Contacts of the helix formed by residues 1209 - 1216 (chain D) in PDB entry 5UHE
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 GLY1209 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035D PHE 3.7 1.6 - - - -
1036D GLU* 3.3 33.9 + - - -
1037D ALA* 4.4 1.8 - - - +
1161D MET* 4.1 0.4 - - - -
1207D LEU 4.2 0.6 + - - -
1208D MET* 1.3 74.1 - - - +
1210D ILE* 1.3 61.2 + - - -
1211D THR 3.2 3.6 - - - -
1212D LYS* 3.1 12.5 + - - +
1213D ALA* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873D LEU* 3.8 9.4 - - + -
876D ARG* 3.8 24.2 - - + +
877D LEU* 3.6 24.0 - - + +
880D VAL* 3.5 28.2 - - + +
1035D PHE* 3.0 32.7 + - + +
1036D GLU* 3.5 15.2 + - - +
1157D ILE* 4.0 23.1 - - + -
1161D MET* 4.1 13.0 - - + -
1208D MET 3.9 0.4 + - - -
1209D GLY* 1.3 71.9 - - - -
1211D THR* 1.3 59.3 + - - +
1213D ALA* 4.3 1.3 - - - -
1214D SER* 2.8 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872D TYR* 4.7 2.0 + - - +
876D ARG* 3.2 17.9 + - - +
1036D GLU* 2.6 31.6 + - - -
1209D GLY 3.2 0.8 - - - -
1210D ILE* 1.3 80.9 - - - +
1212D LYS* 1.3 64.9 + - + +
1214D SER* 3.6 2.6 - - - -
1215D LEU* 3.1 33.4 + - + +
1226D PHE* 4.0 9.4 - - + -
1227D GLN* 3.8 20.9 + - - +
1228D GLU* 5.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036D GLU* 4.8 0.2 + - - -
1180D LEU* 3.9 25.9 - - - +
1208D MET* 4.7 15.9 - - + -
1209D GLY* 3.1 15.5 + - - +
1211D THR* 1.3 82.2 - - + +
1213D ALA* 1.3 57.8 + - - +
1215D LEU* 3.1 12.8 + - + +
1216D ALA* 2.9 29.0 + - + +
20H G 4.6 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880D VAL* 4.1 14.8 - - + -
1160D GLN 4.4 9.6 - - - +
1161D MET* 5.1 1.1 - - - -
1164D ARG* 4.2 7.6 + - - +
1208D MET* 4.1 35.6 - - + +
1209D GLY 2.9 15.8 + - - +
1210D ILE* 4.1 4.0 - - - +
1212D LYS* 1.3 75.3 - - - +
1214D SER* 1.3 62.9 + - - +
1216D ALA* 3.1 20.4 + - - +
1217D THR* 3.7 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876D ARG 3.8 4.7 + - - -
879D ASP* 3.1 22.2 - - - +
880D VAL* 3.2 32.8 + - - +
1210D ILE 2.8 22.1 + - - -
1211D THR 3.6 4.3 - - - -
1213D ALA* 1.3 75.6 - - - +
1215D LEU* 1.3 61.5 + - - +
1217D THR* 3.3 23.9 - - - +
1223D ALA* 4.5 4.0 - - - +
1226D PHE* 3.8 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211D THR* 3.1 30.3 + - + +
1212D LYS* 3.1 15.2 + - + +
1214D SER* 1.3 72.4 - - - +
1216D ALA* 1.3 59.0 + - - +
1217D THR* 2.9 13.5 + - - +
1223D ALA* 3.8 24.3 - - + +
1226D PHE* 3.8 22.4 - - + -
1227D GLN* 4.0 18.8 - - + +
1228D GLU* 3.4 25.4 - - + +
1231D ARG* 3.8 19.7 - - - +
1232D VAL* 4.8 8.1 - - + -
1241D ARG* 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164D ARG* 2.5 49.3 + - - +
1180D LEU* 5.8 1.8 - - + +
1208D MET* 5.0 3.8 - - - -
1212D LYS* 2.9 17.4 + - + +
1213D ALA* 3.1 9.5 + - - +
1215D LEU* 1.3 75.1 - - - +
1217D THR* 1.3 57.4 + - - +
----------------------------------------------------------
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