Contacts of the helix formed by residues 723 - 731 (chain A) in PDB entry 1WER
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 TYR 723 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A MET* 3.1 59.9 + - + +
719A PRO 3.5 7.2 - - - -
720A GLU 3.0 8.2 + - - +
722A GLU* 1.3 76.0 - - - +
724A SER* 1.3 58.3 - - - +
725A GLU* 3.3 8.5 - - - -
726A PHE* 3.2 6.9 + + + +
727A LYS* 2.9 28.6 + - - +
992A SER* 3.5 28.3 - - - -
995A LEU* 3.7 32.3 - - + -
996A ALA* 3.7 32.0 - - + +
999A HIS* 4.8 7.4 - + + -
1033A LEU* 4.2 20.9 - - + -
1037A GLN* 4.6 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A GLU 3.8 2.8 + - - -
721A GLU* 2.9 25.2 + - - -
723A TYR* 1.3 78.7 - - - +
725A GLU* 1.3 64.4 + - - +
727A LYS* 3.9 8.5 - - - +
728A GLU* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A GLU 4.3 0.3 - - - +
722A GLU* 2.7 30.3 - - - +
723A TYR 3.4 2.9 - - - -
724A SER* 1.3 82.9 + - - +
726A PHE* 1.3 87.7 + - - +
728A GLU* 3.4 4.7 + - - +
729A LEU* 3.3 16.8 + - - +
1029A ILE* 3.6 33.0 - - + +
1032A LEU* 5.1 13.7 - - + -
1033A LEU* 3.4 15.0 - - - +
1036A LYS* 5.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A TYR* 3.2 7.2 + + - +
725A GLU* 1.3 94.4 + - - +
727A LYS* 1.3 64.4 + - - +
729A LEU* 3.2 7.7 - - + +
730A ILE* 3.1 53.0 + - + +
737A VAL* 5.3 0.7 - - + -
995A LEU* 3.4 35.4 - - + -
998A LEU* 4.0 9.9 - - + -
999A HIS* 3.7 24.2 - - + -
1002A CYS* 3.9 13.7 - - - -
1026A LEU* 3.7 28.9 - - + -
1029A ILE* 3.5 24.0 - - + -
1030A THR* 5.0 2.9 - - - -
1033A LEU* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A GLU* 4.4 7.8 + - - +
723A TYR 2.9 16.0 + - - +
724A SER* 4.0 8.5 - - - +
726A PHE* 1.3 78.6 - - - +
728A GLU* 1.3 66.8 + - - +
730A ILE* 3.2 9.9 + - + +
731A LEU* 3.1 57.7 + - + +
759A ILE* 4.9 4.0 - - + -
763A GLU* 2.9 29.0 + - + -
988A ARG* 3.7 17.8 - - - +
991A LEU* 3.8 21.6 - - + +
995A LEU* 3.4 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A SER 3.3 17.0 + - - +
725A GLU* 3.4 5.1 + - - +
727A LYS* 1.3 81.1 - - - +
729A LEU* 1.3 65.9 + - - +
731A LEU* 3.5 26.0 + - - +
732A GLN* 3.4 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A GLU 3.3 9.0 + - - +
726A PHE* 3.2 11.9 + - - +
728A GLU* 1.3 78.0 - - - +
730A ILE* 1.3 63.2 + - + +
732A GLN* 3.3 31.9 + - - +
737A VAL* 4.0 10.2 + - + +
1022A VAL* 3.9 22.8 - - + +
1025A LYS* 3.7 33.2 - - + +
1026A LEU* 3.5 49.1 - - + +
1029A ILE* 3.6 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A PHE* 3.1 46.8 + - + +
727A LYS* 3.2 13.2 + - + +
729A LEU* 1.3 78.0 - - + +
731A LEU* 1.3 63.4 + - + +
732A GLN 3.3 5.0 + - - +
735A LEU* 4.2 5.9 - - - +
737A VAL* 4.4 19.7 - - + +
738A VAL* 4.3 12.8 - - + +
756A LEU* 4.6 2.2 - - + -
759A ILE* 4.9 5.4 - - + -
760A PHE* 3.5 31.7 - - + -
995A LEU* 4.3 9.0 - - + -
998A LEU* 3.4 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A LYS* 3.1 46.5 + - + +
728A GLU* 3.5 22.9 + - - +
729A LEU 3.3 0.2 - - - -
730A ILE* 1.3 76.6 - - + +
732A GLN* 1.3 65.6 + - - +
733A LYS 3.5 1.2 + - - -
759A ILE* 4.1 21.5 - - + -
760A PHE* 4.0 30.5 - - + -
763A GLU* 3.8 22.9 - - + +
765A LEU* 4.2 16.3 - - + +
768A LEU* 3.7 16.8 - - - +
----------------------------------------------------------
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