Contacts of the helix formed by residues 1043 - 1052 (chain Z) in PDB entry 5WTI
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 ASP1043 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290Z LYS* 5.4 4.9 + - - -
356Z TYR* 4.2 24.3 + - + -
1042Z LYS* 1.3 80.7 - - + +
1044Z SER* 1.3 62.0 + - - +
1046Z ASP* 3.6 5.6 + - - +
1047Z LEU* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1044 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353Z GLU* 3.8 18.2 + - - +
356Z TYR* 4.8 10.3 - - - -
357Z LEU* 3.5 41.8 - - - +
360Z THR* 5.9 2.0 - - - -
1042Z LYS* 3.4 11.9 - - - +
1043Z ASP* 1.3 76.7 - - - +
1045Z PHE* 1.3 62.6 + - - +
1047Z LEU* 3.3 10.0 + - - +
1048Z ALA* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1045 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353Z GLU* 5.3 4.0 - - - -
1042Z LYS* 3.2 31.1 + - + +
1044Z SER* 1.3 80.1 + - - +
1046Z ASP* 1.3 70.5 + - - +
1048Z ALA* 3.2 18.0 + - + +
1049Z SER* 3.3 28.5 + - - -
1055Z LYS* 5.8 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1046 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974Z TYR* 4.4 19.6 + - - +
1042Z LYS 2.8 36.5 + - - +
1043Z ASP* 4.0 5.7 - - - +
1045Z PHE* 1.3 80.9 - - - +
1047Z LEU* 1.3 61.1 + - - +
1049Z SER* 4.6 3.2 - - - -
1050Z GLU* 3.2 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1047 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296Z TRP* 4.0 29.2 - - + +
297Z ARG* 3.2 53.4 - - + +
353Z GLU* 4.3 11.0 - - - -
356Z TYR* 4.0 28.5 - - + -
1043Z ASP 3.2 15.2 + - - +
1044Z SER* 3.4 11.7 - - - +
1045Z PHE 3.1 0.8 - - - -
1046Z ASP* 1.3 76.6 - - - +
1048Z ALA* 1.3 64.0 + - - +
1050Z GLU* 3.7 4.9 + - - +
1051Z LEU* 3.2 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1048 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352Z PRO* 4.8 9.1 - - + +
353Z GLU* 3.3 40.8 - - + +
1044Z SER 3.1 8.4 + - - +
1045Z PHE* 3.2 14.8 + - + +
1047Z LEU* 1.3 78.1 - - - +
1049Z SER* 1.3 62.4 + - - +
1051Z LEU* 3.2 18.4 + - - +
1052Z LYS* 3.7 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1049 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045Z PHE* 3.3 33.1 + - - -
1046Z ASP* 4.6 3.4 - - - -
1048Z ALA* 1.3 73.4 - - - +
1050Z GLU* 1.3 64.9 + - - +
1051Z LEU 3.1 1.8 - - - -
1052Z LYS* 6.3 0.2 - - - -
1053Z GLY 3.2 2.9 + - - -
1054Z GLU* 3.0 42.7 + - - +
1055Z LYS* 3.3 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1050 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297Z ARG* 3.2 37.4 + - - -
301Z GLN* 5.7 2.0 + - - +
974Z TYR* 4.5 17.0 + - + +
1046Z ASP* 3.2 26.8 + - - +
1047Z LEU* 3.9 6.5 - - - +
1049Z SER* 1.3 76.5 - - - +
1051Z LEU* 1.3 64.1 + - - +
1053Z GLY 3.7 0.2 + - - -
1055Z LYS* 3.3 19.6 + - - +
1056Z LEU* 3.2 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1051 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297Z ARG* 5.3 2.5 - - - -
300Z ILE* 3.9 24.2 - - + -
301Z GLN* 3.7 45.9 - - + +
304Z LEU* 4.0 16.9 - - + +
352Z PRO* 3.5 38.1 - - + +
1047Z LEU* 3.2 38.7 + - + +
1048Z ALA 3.5 6.5 - - - +
1049Z SER 3.1 1.8 - - - -
1050Z GLU* 1.3 79.4 - - - +
1052Z LYS* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1052 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304Z LEU* 4.3 19.5 - - + -
351Z HIS* 5.9 3.4 - - - +
352Z PRO* 5.2 12.3 - - + +
1048Z ALA 3.7 7.3 + - - +
1049Z SER* 4.0 0.4 + - - -
1051Z LEU* 1.3 78.5 - - - +
1053Z GLY* 1.3 57.8 + - - +
1054Z GLU* 3.8 7.4 - - + +
----------------------------------------------------------
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