Contacts of the helix formed by residues 3715 - 3731 (chain F) in PDB entry 6X34
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 ASP3715 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2119F ARG* 5.9 0.9 - - - +
3701F PHE* 6.0 0.4 - - + -
3713F ASP* 4.6 8.0 - - + +
3714F GLU* 1.3 82.7 - - - +
3716F TYR* 1.3 62.5 + - - +
3717F LEU* 3.1 17.7 - - + -
3718F TYR* 2.9 35.2 + - + +
3719F MET* 3.6 5.5 + - - +
3788F MET* 4.0 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3716 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2123F SER* 4.8 14.2 - - - -
2126F HIS* 6.2 4.9 - + - -
2127F ARG* 5.9 3.9 - - + -
3714F GLU* 3.5 16.8 - - + +
3715F ASP* 1.3 76.8 - - - +
3717F LEU* 1.3 78.1 + - + +
3719F MET* 3.7 7.1 + - - +
3720F ALA* 3.3 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3717 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2119F ARG* 3.5 57.2 - - + +
2122F PHE* 5.6 4.7 - - + -
2123F SER* 5.3 12.8 - - - +
2126F HIS* 6.2 0.9 - - - -
3700F HIS* 4.5 9.6 - - + +
3701F PHE* 4.2 17.9 - - + -
3715F ASP* 3.1 20.5 - - + -
3716F TYR* 1.3 97.0 - - + +
3718F TYR* 1.3 71.0 + - - +
3720F ALA* 3.7 5.7 - - - +
3721F TYR* 3.4 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3718 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3701F PHE* 3.5 53.1 - + + +
3715F ASP* 2.9 21.3 + - + +
3717F LEU* 1.3 82.3 - - - +
3719F MET* 1.3 56.7 + - - +
3720F ALA 3.2 0.2 + - - -
3721F TYR* 3.5 1.4 + - + +
3722F ALA* 3.0 34.1 + - + +
3773F MET* 4.4 15.1 + - - +
3774F VAL* 5.3 3.5 - - - +
3777F MET* 3.8 25.7 - - + +
3788F MET* 3.7 25.8 - - + -
3791F SER* 6.5 0.2 - - - -
3792F THR* 3.4 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET3719 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3715F ASP 3.6 6.6 + - - +
3716F TYR* 3.7 7.8 + - - +
3717F LEU 3.5 0.2 - - - -
3718F TYR* 1.3 79.3 - - - +
3720F ALA* 1.3 64.0 + - - +
3722F ALA* 3.8 8.4 - - - +
3723F ASP* 3.6 19.2 + - - +
3787F ALA 5.7 0.9 - - - +
3788F MET* 5.7 7.7 - - + +
3791F SER* 4.0 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3720 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2126F HIS* 3.4 36.3 - - + +
3716F TYR* 3.3 18.6 + - + +
3717F LEU* 3.7 9.9 - - - +
3718F TYR 3.1 1.2 - - - -
3719F MET* 1.3 79.1 - - - +
3721F TYR* 1.3 64.4 + - + +
3722F ALA 3.4 0.2 + - - -
3723F ASP* 3.7 2.6 + - - +
3724F ILE* 3.3 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3721 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122F PHE* 2.3 51.1 + + + -
2123F SER* 4.9 1.6 - - - -
2125F LEU* 3.3 20.9 - - + +
2126F HIS* 3.3 29.8 + + + -
3673F LEU* 5.4 3.1 - - + -
3697F LEU* 4.3 23.6 - - + -
3701F PHE* 5.2 15.9 - + + -
3717F LEU* 3.4 24.9 + - + +
3718F TYR 4.4 2.0 - - - +
3720F ALA* 1.3 78.9 - - + +
3722F ALA* 1.3 59.0 - - - +
3724F ILE* 3.8 16.3 - - + +
3725F MET* 2.9 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3722 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3718F TYR* 3.0 29.0 + - + +
3719F MET* 3.9 10.1 - - - +
3720F ALA 3.2 0.6 - - - -
3721F TYR* 1.3 78.2 - - - +
3723F ASP* 1.3 56.9 + - - +
3726F ALA* 3.0 31.5 + - - +
3791F SER* 4.3 26.5 - - - +
3792F THR* 5.8 1.6 - - + -
3795F LEU* 3.5 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3723 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3719F MET 3.6 12.6 + - - +
3720F ALA 3.7 2.9 + - - +
3721F TYR 3.4 0.2 - - - -
3722F ALA* 1.3 78.5 - - - +
3724F ILE* 1.3 63.3 + - + +
3726F ALA* 4.4 3.5 - - - +
3727F LYS* 3.2 26.7 + - - +
3794F LYS* 6.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3724 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2126F HIS* 3.7 23.8 - - + +
3665F PHE* 3.6 28.9 - - + -
3666F GLU* 3.2 40.6 - - + +
3669F MET* 4.4 15.3 - - + -
3670F ILE* 4.8 7.0 - - + -
3720F ALA 3.3 20.6 - - - +
3721F TYR* 3.5 17.8 + - + +
3722F ALA 3.3 0.4 - - - -
3723F ASP* 1.3 78.8 - - + +
3725F MET* 1.3 59.9 + - - +
3728F SER* 3.0 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET3725 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670F ILE* 4.4 19.3 - - + +
3694F LEU* 5.8 7.0 - - + -
3697F LEU* 5.1 19.7 - - + -
3698F VAL* 6.1 0.9 - - - +
3701F PHE* 6.3 2.5 - - + -
3721F TYR* 2.9 28.0 + - + +
3722F ALA* 6.1 0.2 - - - -
3724F ILE* 1.3 77.8 - - - +
3726F ALA* 1.3 60.1 + - - +
3728F SER* 2.7 18.1 + - - +
3729F CYS* 3.5 11.8 + - - +
3765F LEU* 3.6 41.9 - - + +
3770F ALA* 5.2 6.7 - - - -
3795F LEU* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3726 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3722F ALA 3.0 19.1 + - - +
3723F ASP* 4.4 3.6 - - - +
3725F MET* 1.3 75.8 - - - +
3727F LYS* 1.3 66.4 + - - +
3729F CYS* 3.4 0.7 + - - -
3730F HIS* 3.3 13.3 + - - +
3765F LEU* 6.0 0.2 - - - -
3794F LYS* 4.2 15.7 - - + +
3795F LEU* 3.8 32.3 - - + +
3798F SER* 3.2 25.6 + - - -
3799F ILE* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3727 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3666F GLU* 3.9 16.2 - - + -
3723F ASP 3.2 20.6 + - - +
3726F ALA* 1.3 76.5 - - - +
3728F SER* 1.3 57.6 + - - +
3730F HIS* 4.8 2.7 - - - +
3731F LEU* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3728 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3666F GLU* 3.2 30.2 - - - +
3667F ASP* 4.5 7.7 - - - +
3670F ILE* 3.6 17.4 - - - +
3724F ILE 3.0 9.1 + - - -
3725F MET* 2.7 26.5 + - - +
3727F LYS* 1.3 77.8 - - - +
3729F CYS* 1.3 60.7 + - - +
3731F LEU 3.8 12.8 - - - -
3761F GLN* 3.5 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS3729 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3725F MET 4.0 7.9 - - - +
3726F ALA* 3.4 3.4 + - - +
3727F LYS 3.3 0.4 - - - -
3728F SER* 1.3 84.1 + - - +
3730F HIS* 1.3 60.3 + - - +
3731F LEU 4.9 0.5 - - - +
3758F LEU* 4.6 12.6 - - - +
3761F GLN* 3.4 27.0 - - - +
3762F GLN* 4.0 25.8 - - - -
3765F LEU* 4.7 4.3 - - + -
3798F SER* 3.2 35.9 - - - +
3799F ILE* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS3730 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3726F ALA 3.3 12.8 + - - +
3727F LYS* 4.4 2.9 - - - +
3729F CYS* 1.3 83.0 - - - +
3731F LEU* 1.3 62.0 + - + +
3758F LEU* 5.2 11.5 - - - +
3798F SER* 4.2 13.0 - - - +
3801F ASN* 5.0 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3731 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3667F ASP* 6.0 4.3 - - - -
3727F LYS* 2.9 23.0 + - + +
3728F SER* 3.8 14.2 - - - +
3729F CYS 4.9 0.9 - - - +
3730F HIS* 1.3 81.2 - - + +
3761F GLN* 5.2 5.5 - - - +
----------------------------------------------------------
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