Contacts of the helix formed by residues 1043 - 1051 (chain X) in PDB entry 2OO8
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 THR1043 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003X ARG* 4.1 3.8 - - - +
1041X GLY 5.8 0.4 - - - +
1042X MET* 1.3 77.0 - - - +
1044X CYS* 1.3 63.7 + - - +
1045X ALA* 3.5 9.2 + - - +
1046X GLU* 2.9 49.5 + - - +
1047X LEU* 3.3 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1044 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999X ARG* 3.1 33.2 - - - +
1002X VAL* 3.8 29.5 - - + +
1003X ARG* 4.0 28.5 - - - +
1043X THR* 1.3 72.9 - - - +
1045X ALA* 1.3 60.0 + - - +
1047X LEU* 3.2 16.0 + - - +
1048X TYR* 3.1 25.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1045 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043X THR* 3.2 8.4 - - - +
1044X CYS* 1.3 77.1 - - - +
1046X GLU* 1.3 63.8 + - - +
1047X LEU 3.1 1.1 + - - -
1048X TYR* 3.4 13.8 + - - +
1049X GLU* 3.3 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1046 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041X GLY 4.4 3.3 - - - +
1042X MET* 3.4 19.0 - - + +
1043X THR* 2.9 49.7 + - - +
1045X ALA* 1.3 74.5 - - - +
1047X LEU* 1.3 59.1 + - - +
1049X GLU* 3.7 12.5 - - - +
1050X LYS* 2.9 67.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1047 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002X VAL* 4.1 15.0 - - + +
1003X ARG* 3.8 27.1 - - + +
1010X LEU* 5.5 0.2 - - - -
1039X TYR* 3.5 61.0 - - + -
1042X MET* 4.4 9.4 - - - -
1043X THR 3.3 7.8 + - - +
1044X CYS* 3.2 14.7 + - - +
1045X ALA 3.1 0.8 - - - -
1046X GLU* 1.3 75.9 - - - +
1048X TYR* 1.3 66.1 + - - +
1049X GLU 3.0 1.3 - - - -
1050X LYS* 4.3 0.4 - - - +
1051X LEU* 3.0 55.2 + - + +
1055X TYR* 5.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1048 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000X LEU* 4.8 11.1 - - - +
1002X VAL* 3.7 30.5 - - + +
1010X LEU* 3.7 48.8 + - + +
1011X ASN* 4.4 11.6 + - - +
1044X CYS* 3.1 30.4 + - + -
1045X ALA* 3.6 10.3 - - - +
1047X LEU* 1.3 77.7 - - - +
1049X GLU* 1.3 57.1 + - - +
1052X PRO* 3.3 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1049 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045X ALA 3.3 9.6 + - - +
1046X GLU* 3.7 17.6 - - - +
1047X LEU 3.0 0.4 - - - -
1048X TYR* 1.3 80.1 - - - +
1050X LYS* 1.3 77.9 + - + +
1052X PRO* 3.3 11.4 - - - +
1053X GLN* 3.4 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1050 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042X MET* 4.5 22.5 - - + +
1046X GLU* 2.9 59.4 + - - +
1047X LEU* 5.0 1.3 - - - -
1049X GLU* 1.3 87.0 - - + +
1051X LEU* 1.3 65.1 + - - +
1053X GLN* 3.0 34.4 + - - +
1055X TYR* 3.2 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1051 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002X VAL 5.4 1.3 - - - +
1005X MET 4.9 2.7 - - - +
1007X ILE* 4.3 12.2 - - + +
1010X LEU* 4.0 22.9 - - + -
1022X TRP* 4.2 15.0 - - + -
1039X TYR* 3.7 24.0 - - + +
1047X LEU* 3.0 52.1 + - + +
1048X TYR* 5.6 0.2 - - - -
1050X LYS* 1.3 75.8 - - - +
1052X PRO* 1.4 57.9 - - + +
1054X GLY* 2.7 14.6 + - - -
1055X TYR* 3.3 26.2 - - + +
1056X ARG* 2.5 37.1 + - - +
----------------------------------------------------------
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