Contacts of the helix formed by residues 787 - 799 (chain A) in PDB entry 5FLZ
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 SER 787 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A LEU* 5.1 4.0 - - - +
774A ILE 3.9 0.5 + - - -
777A LYS* 3.3 28.9 - - - +
778A CYS* 3.8 7.2 - - - -
781A ASN* 3.1 27.1 - - - +
786A LEU* 1.4 81.2 - - - +
788A THR* 1.3 61.3 + - - +
790A LYS* 3.4 35.7 + - - +
791A PHE* 3.9 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A LYS* 3.8 19.8 - - + +
786A LEU* 3.6 20.2 - - - +
787A SER* 1.3 72.1 - - - +
789A GLU* 1.4 55.0 - - + +
791A PHE* 3.2 8.4 + - - +
792A ASP* 2.7 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A ASN 4.0 2.4 - - - +
773A SER* 2.8 44.3 + - - +
774A ILE* 3.2 23.4 - - + +
777A LYS* 3.9 22.0 - - + +
787A SER* 3.2 1.4 + - - -
788A THR* 1.4 82.2 - - + +
790A LYS* 1.4 60.2 + - - +
792A ASP* 3.6 10.6 - - + +
793A PHE* 2.8 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A LEU 5.5 1.2 + - - -
695A LEU* 4.0 37.2 - - + +
696A GLN* 5.0 4.4 - - - +
698A GLN* 3.8 20.1 + - - +
699A ILE* 3.7 25.6 - - + +
774A ILE* 3.7 21.2 - - + +
778A CYS* 3.4 30.4 - - - +
781A ASN* 4.3 7.1 - - - +
787A SER* 3.4 26.0 + - - +
789A GLU* 1.4 76.1 - - - +
791A PHE* 1.4 61.6 + - - +
793A PHE* 3.2 6.5 + - - +
794A TYR* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A LEU* 4.3 25.7 - - + +
786A LEU* 5.2 10.8 - - + -
787A SER 3.9 10.4 + - - +
788A THR* 3.2 11.3 + - - +
790A LYS* 1.4 74.0 - - - +
792A ASP* 1.4 62.0 + - - +
794A TYR* 3.2 32.1 + + - -
795A ASP* 2.8 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A THR* 2.7 50.0 + - - +
789A GLU* 3.6 10.8 + - + +
791A PHE* 1.4 63.1 - - - +
793A PHE* 1.3 57.4 + - + +
795A ASP* 3.3 11.3 + - - +
796A SER* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A GLN* 5.5 3.1 - - - +
770A ASN* 3.3 47.6 - - + -
774A ILE* 5.0 7.4 - - + -
789A GLU* 2.8 39.0 + - + +
790A LYS* 3.2 10.5 + - - +
792A ASP* 1.3 72.5 - - + +
794A TYR* 1.4 63.8 + - - +
796A SER* 3.2 10.1 + - - -
797A SER* 3.1 32.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
695A LEU* 5.3 6.5 - - + -
698A GLN* 3.3 31.9 - - - +
790A LYS 3.1 8.5 + - - +
791A PHE* 3.2 47.1 + + - -
793A PHE* 1.4 76.4 - - - +
795A ASP* 1.3 81.2 + - - +
797A SER* 3.2 7.8 + - - -
798A SER* 2.9 41.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A PHE* 2.8 40.5 + - - +
792A ASP* 3.6 12.3 - - - +
794A TYR* 1.3 98.8 + - - +
796A SER* 1.4 54.4 + - - +
798A SER* 2.9 12.0 + - - -
799A VAL* 2.6 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A ASP* 2.9 25.3 + - - +
793A PHE* 3.2 13.6 + - - -
795A ASP* 1.4 74.8 - - - +
797A SER* 1.3 64.6 + - - +
799A VAL* 3.3 6.4 + - - -
800A ASP* 3.0 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A PHE* 3.1 18.0 + - - -
794A TYR* 3.4 11.0 - - - -
796A SER* 1.3 83.2 - - - +
798A SER* 1.3 63.3 + - - +
799A VAL* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A TYR* 2.9 41.3 + - - -
795A ASP* 3.1 11.8 + - - -
797A SER* 1.3 77.7 - - - +
799A VAL* 1.3 76.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A ASP* 2.6 22.8 + - - +
796A SER* 3.0 5.0 + - - -
797A SER 4.4 0.2 - - - -
798A SER* 1.3 91.4 - - - +
800A ASP* 1.4 68.8 + - - +
----------------------------------------------------------
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