Contacts of the helix formed by residues 788 - 796 (chain A) in PDB entry 5WRZ
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 ASP 788 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A HIS* 3.6 25.0 - - - +
661A MET* 4.7 2.8 - - + +
662A LYS* 2.9 32.0 - - - +
663A SER* 3.3 26.7 - - - +
670A GLN* 5.0 1.0 - - - +
787A LYS* 1.3 72.3 - - - +
789A PRO* 1.3 71.8 - - - +
790A ILE* 2.9 36.1 + - - +
791A ASP* 2.9 24.5 + - - +
792A VAL* 3.2 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A HIS* 3.8 17.7 - - + +
787A LYS 3.4 8.4 - - - +
788A ASP* 1.3 90.0 - - - +
790A ILE* 1.3 61.3 + - + +
792A VAL* 3.6 12.5 - - + +
793A ASN* 2.8 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A SER* 4.4 2.7 - - - +
665A LEU* 4.1 10.1 - - + -
670A GLN* 3.9 47.1 - - + +
673A ILE* 3.8 19.6 - - + +
674A LYS* 3.8 36.3 - - + +
788A ASP* 2.9 21.5 + - - +
789A PRO* 1.3 81.6 - - + +
791A ASP* 1.3 59.0 + - - +
793A ASN* 6.0 1.8 - - - +
794A TYR* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A MET* 6.1 0.9 - - - +
663A SER* 3.1 41.5 + - - -
664A LYS 4.4 1.8 + - - -
665A LEU* 3.5 16.5 - - - +
787A LYS* 5.7 3.6 - - + -
788A ASP* 2.9 16.8 + - - +
790A ILE* 1.3 80.8 - - - +
792A VAL* 1.3 64.7 + - + +
794A TYR* 3.6 5.8 - - - +
795A GLU* 3.3 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A SER 4.7 11.2 - - - +
784A ASP* 5.2 6.1 - - + +
787A LYS* 3.8 31.9 - - + +
788A ASP 3.2 11.8 + - - +
789A PRO* 3.1 14.7 + - + +
791A ASP* 1.3 78.3 - - + +
793A ASN* 1.3 68.1 + - - +
795A GLU* 3.3 14.5 + - - +
796A LYS* 3.4 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A ILE* 3.9 9.1 - - + +
677A PHE* 3.4 42.3 - - + +
778A LEU* 3.9 28.2 - - - +
789A PRO* 2.8 27.3 + - - +
790A ILE* 5.5 1.6 - - - +
792A VAL* 1.3 83.0 - - - +
794A TYR* 1.3 64.9 + - - +
796A LYS* 3.2 26.6 + - - +
797A LEU* 3.7 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LEU* 4.0 27.1 - - + +
669A VAL* 3.9 21.1 - - + -
673A ILE* 3.9 27.9 - - + +
790A ILE 3.0 19.7 + - - +
791A ASP* 3.6 5.8 - - - +
793A ASN* 1.3 74.1 - - - +
795A GLU* 1.3 82.7 + - - +
797A LEU* 2.9 29.1 + - - +
798A LYS 4.1 1.2 + - - -
799A THR 3.5 14.1 + - - +
800A ASP* 3.7 9.0 + - - -
801A ILE* 3.0 47.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A ASP* 3.3 16.4 + - + +
792A VAL* 3.5 10.1 - - - +
793A ASN 3.2 0.6 - - - -
794A TYR* 1.3 102.8 - - - +
796A LYS* 1.3 62.7 + - + +
797A LEU 3.2 1.0 + - - -
798A LYS* 3.2 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A PHE* 4.6 4.7 - - + -
777A LEU* 3.4 59.5 + - + +
778A LEU* 4.7 4.6 + - - +
780A GLY 4.1 2.2 + - - -
781A GLY* 3.9 23.2 - - - -
782A SER 4.6 4.8 + - - +
792A VAL* 3.6 33.8 - - - +
793A ASN* 3.2 24.0 + - - +
795A GLU* 1.3 76.9 - - + +
797A LEU* 1.3 61.5 + - - +
798A LYS* 3.3 11.2 + - - +
874A SER* 4.2 6.6 - - - -
----------------------------------------------------------
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