Contacts of the helix formed by residues 774 - 787 (chain A) in PDB entry 5ZR1
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 HIS 774 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A SER* 5.0 3.8 - - - -
688A ALA* 3.8 2.8 - - - +
772A THR* 3.5 31.4 + - + +
773A VAL* 1.3 77.9 - - - +
775A ILE* 1.3 67.7 + - + +
776A THR* 3.2 16.0 + - + +
777A HIS* 3.3 44.1 + + - +
778A VAL* 3.6 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A SER* 5.1 2.8 - - - -
687A ASP* 3.7 41.1 - - + +
688A ALA* 3.8 10.4 - - - +
691A ILE* 3.7 23.1 - - + -
774A HIS* 1.3 77.8 - - + +
776A THR* 1.3 63.4 + - + +
778A VAL* 3.5 1.3 + - + -
779A MET* 3.1 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A HIS* 3.8 17.9 - - + -
775A ILE* 1.3 83.7 - - + +
777A HIS* 1.3 71.7 + - + +
779A MET* 4.0 6.2 - - - +
780A LYS* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A ALA* 3.7 9.3 - - - +
716A ILE* 3.6 28.3 - - + +
717A ALA* 3.6 28.8 - - + -
720A HIS* 4.4 14.5 + + - +
772A THR 4.7 2.7 - - - -
773A VAL* 3.9 19.3 - - + -
774A HIS* 3.3 45.9 + + + +
775A ILE 3.3 0.4 - - - -
776A THR* 1.3 84.4 - - + +
778A VAL* 1.3 59.9 + - - +
780A LYS* 3.5 5.4 + - + +
781A ALA* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A MET* 6.0 2.2 - - + -
688A ALA* 3.5 45.1 - - + +
691A ILE* 4.4 9.0 - - + -
692A ALA* 3.7 20.0 - - + -
709A VAL* 4.7 6.4 - - + +
710A CYS* 5.6 5.8 - - - -
713A ALA* 3.7 22.4 - - + -
773A VAL* 4.1 8.1 - - + -
774A HIS 3.7 6.1 - - - +
775A ILE 3.5 6.4 + - - +
776A THR 3.4 0.2 - - - -
777A HIS* 1.3 75.2 - - - +
779A MET* 1.3 60.3 + - - +
781A ALA* 3.2 2.8 + - - +
782A LEU* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A ILE* 4.2 29.2 - - + -
695A LYS* 5.2 9.9 - - - +
775A ILE* 3.1 34.0 + - + +
776A THR* 4.3 5.8 - - - +
778A VAL* 1.3 77.2 - - - +
780A LYS* 1.3 56.8 + - - +
782A LEU* 3.9 12.2 - - + +
783A ASN* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ILE* 4.1 24.2 - - + +
719A LYS* 6.0 1.4 - - - +
720A HIS* 4.1 24.6 + - + -
776A THR* 3.2 21.9 + - - +
777A HIS* 3.8 4.5 - - + +
778A VAL 3.3 0.2 - - - -
779A MET* 1.3 76.8 - - - +
781A ALA* 1.3 61.5 + - - +
782A LEU 3.5 0.2 + - - -
783A ASN* 4.4 4.9 - - - +
784A GLU* 3.7 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A VAL* 3.7 18.7 - - + +
712A ARG* 3.7 17.3 - - + +
713A ALA* 3.6 25.8 - - - +
716A ILE* 3.7 8.9 - - + +
777A HIS 3.1 18.4 + - - +
778A VAL 3.2 4.9 + - - +
780A LYS* 1.3 77.4 - - - +
782A LEU* 1.3 59.9 + - - +
784A GLU* 3.6 15.8 - - - +
785A THR* 4.0 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A ILE* 3.9 15.5 - - + +
692A ALA* 4.7 4.9 - - - +
695A LYS* 3.7 50.0 - - + +
696A VAL* 4.5 12.8 - - + -
709A VAL* 3.8 21.8 - - + -
778A VAL* 2.9 17.6 + - + +
779A MET* 3.9 19.3 - - + +
780A LYS 3.2 0.2 - - - -
781A ALA* 1.3 77.7 - - - +
783A ASN* 1.3 63.1 + - - +
784A GLU 3.4 0.7 - - - -
785A THR* 3.3 16.7 + - - +
786A LEU* 3.4 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A MET* 2.8 23.6 + - + +
780A LYS* 4.4 5.2 - - - +
781A ALA 3.6 0.2 - - - -
782A LEU* 1.3 77.8 - - - +
784A GLU* 1.3 58.2 + - - +
786A LEU* 3.3 5.4 + - - +
787A ASN* 2.9 68.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 784 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ARG* 2.5 54.4 + - - +
716A ILE* 5.1 1.9 - - - +
780A LYS* 3.7 18.5 + - - +
781A ALA* 3.6 11.0 - - - +
783A ASN* 1.3 78.6 - - - +
785A THR* 1.3 67.2 + - + +
787A ASN* 4.3 15.3 - - - +
270D GLN 5.6 0.8 - - - +
271D ARG* 5.3 3.3 - - - +
272D VAL 5.7 1.0 - - - +
274D TYR* 5.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A ARG* 4.9 10.3 + - - -
709A VAL* 5.5 2.7 - - + +
712A ARG* 6.1 1.3 - - + -
781A ALA 4.0 14.0 + - - +
782A LEU* 3.3 17.7 + - - +
784A GLU* 1.3 85.7 - - + +
786A LEU* 1.3 71.0 + - - +
787A ASN 3.7 3.0 - - - +
257D LEU* 5.2 11.1 - - - +
270D GLN* 3.7 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A LYS* 5.0 16.4 - - + +
699A VAL* 5.3 15.7 - - + -
705A ARG* 5.1 9.9 - - - +
782A LEU* 3.4 34.7 + - + +
783A ASN* 3.3 8.1 + - - +
785A THR* 1.3 91.5 - - - +
787A ASN* 1.3 66.4 + - - +
788A SER 3.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ASN* 2.9 53.0 + - - +
784A GLU* 4.3 12.5 - - - +
785A THR 3.7 2.6 - - - +
786A LEU* 1.3 83.2 + - - +
788A SER* 1.3 66.1 + - - +
789A HIS 4.4 0.2 + - - -
274D TYR* 5.4 3.3 + - - -
----------------------------------------------------------
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