Contacts of the helix formed by residues 685 - 698 (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 SER 685 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A ARG 4.2 0.8 + - - -
684A MET* 1.3 72.0 - - - +
686A ALA* 1.3 63.7 + - - +
687A ASP* 2.3 30.1 + - - -
688A ALA* 3.3 19.8 + - - +
689A ILE* 3.4 11.5 + - - +
772A THR* 4.3 5.8 + - - -
773A VAL 3.7 20.3 + - - -
774A HIS* 5.0 6.1 - - - -
775A ILE 5.1 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A LYS* 4.3 13.7 - - - +
684A MET 3.5 3.7 + - - +
685A SER* 1.3 72.5 + - - +
687A ASP* 1.3 60.5 + - - +
689A ILE* 3.4 12.5 + - - +
690A GLU* 3.0 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A SER* 2.3 32.4 + - - -
686A ALA* 1.3 72.7 - - - +
688A ALA* 1.3 65.4 + - - +
690A GLU* 3.4 13.9 - - + +
691A ILE* 3.1 23.0 + - - +
775A ILE* 3.7 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A MET* 6.4 1.3 - - + -
685A SER* 3.3 21.5 - - - +
686A ALA 3.2 0.2 - - - -
687A ASP* 1.3 82.9 + - - +
689A ILE* 1.3 62.5 + - + +
691A ILE* 3.8 0.5 - - - +
692A ALA* 3.2 23.6 + - - +
773A VAL* 4.2 4.5 - - + +
774A HIS 3.8 12.6 - - - +
775A ILE* 3.8 14.1 - - - -
778A VAL* 3.5 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A LYS* 4.3 20.2 - - + +
636A ILE* 3.8 44.4 - - + -
637A ASP* 4.9 16.6 - - + +
640A LEU* 4.6 14.4 - - + -
644A ASN* 5.4 3.4 - - - +
684A MET* 4.9 18.2 - - + +
685A SER 3.4 14.3 + - - +
686A ALA* 3.4 13.1 + - - +
688A ALA* 1.3 74.9 - - + +
690A GLU* 1.3 59.5 + - - +
692A ALA* 3.5 5.5 + - - +
693A SER* 2.8 37.8 + - - +
710A CYS* 5.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A HIS* 4.2 6.1 - - - -
630A GLU* 4.3 5.9 - - - +
633A LYS* 3.3 32.5 - - - +
686A ALA 3.0 14.4 + - - +
687A ASP* 3.4 16.6 - - + +
688A ALA 3.2 0.4 - - - -
689A ILE* 1.3 76.3 - - - +
691A ILE* 1.3 60.2 + - + +
693A SER* 3.0 4.7 + - - -
694A ARG* 2.8 68.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ASP 3.1 7.4 + - - +
688A ALA 3.8 6.3 - - - +
690A GLU* 1.3 78.2 - - + +
692A ALA* 1.3 66.4 + - - +
694A ARG* 3.9 16.8 - - + +
695A LYS* 3.4 32.5 + - + +
775A ILE* 3.7 28.0 - - + -
778A VAL* 4.4 8.1 - - + -
779A MET* 4.2 25.8 - - + -
782A LEU* 3.9 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A LEU* 4.3 1.8 - - - +
636A ILE* 5.1 2.7 - - + -
688A ALA 3.2 20.5 + - - +
689A ILE 3.8 4.0 - - - +
691A ILE* 1.3 76.9 - - - +
693A SER* 1.3 60.5 + - - +
696A VAL* 3.3 30.1 + - - +
706A ALA* 4.7 1.0 - - - +
709A VAL* 3.9 20.8 - - + +
710A CYS* 4.2 13.9 - - - -
778A VAL* 3.7 17.3 - - + -
782A LEU* 4.7 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A HIS* 3.4 26.5 - - - +
632A LEU* 3.5 25.5 - - - +
633A LYS* 3.6 15.2 + - - +
636A ILE* 3.9 8.1 - - - +
689A ILE 2.8 20.3 + - - -
690A GLU 3.0 4.8 + - - -
692A ALA* 1.3 77.8 - - - +
694A ARG* 1.3 64.0 + - - +
695A LYS 3.3 0.4 - - - -
697A ALA* 3.2 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A HIS* 3.5 39.4 + - - -
690A GLU* 2.8 53.9 + - + +
691A ILE* 4.4 17.5 - - + +
693A SER* 1.3 73.3 - - - +
695A LYS* 1.3 58.4 + - - +
697A ALA* 4.5 0.3 - - - +
698A SER* 3.3 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A ILE* 3.4 26.4 + - - +
692A ALA 4.7 0.4 - - - +
693A SER 3.3 0.4 - - - -
694A ARG* 1.3 79.2 - - - +
696A VAL* 1.3 63.8 + - - +
698A SER* 3.7 6.7 + - - -
699A VAL* 3.4 27.1 - - + +
779A MET* 5.2 11.1 - - - +
782A LEU* 3.7 37.2 - - + +
786A LEU* 5.0 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A LEU* 3.9 11.7 - - + -
692A ALA 3.3 21.5 + - - +
695A LYS* 1.3 77.7 - - - +
697A ALA* 1.3 62.3 + - - +
699A VAL* 3.2 14.2 + - - +
700A SER* 3.2 5.1 + - - +
701A GLY 3.2 13.2 + - - -
702A ASP* 3.8 27.1 - - - +
705A ARG* 3.9 37.0 - - + +
706A ALA* 4.0 4.0 - - - +
709A VAL* 4.3 9.9 - - + -
782A LEU* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A TYR 3.7 20.6 - - - +
628A THR* 3.9 1.3 - - - -
629A HIS* 3.7 23.6 - - + +
632A LEU* 3.9 7.2 - - + +
693A SER 3.2 17.6 + - - +
694A ARG 4.9 0.2 - - - +
696A VAL* 1.3 78.6 - - - +
698A SER* 1.3 59.4 + - - +
699A VAL 3.5 0.7 + - - -
700A SER 4.4 1.4 + - - -
701A GLY* 3.7 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ARG 3.3 20.7 + - - -
695A LYS* 4.0 7.9 - - - -
696A VAL 3.2 1.2 - - - -
697A ALA* 1.3 78.3 - - - +
699A VAL* 1.3 62.6 + - - +
----------------------------------------------------------
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