Contacts of the helix formed by residues 3694 - 3706 (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 LEU3694 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670F ILE* 3.9 30.3 - - + +
3673F LEU* 3.8 28.4 + - + -
3674F SER* 3.6 33.4 + - - +
3692F ASP* 3.2 3.7 - - + +
3693F PRO* 1.3 77.3 - - - +
3695F HIS* 1.3 61.7 + - - +
3696F GLN 3.3 0.4 - - - -
3697F LEU* 3.4 29.3 + - + +
3698F VAL* 4.2 7.1 + - - +
3725F MET* 5.8 5.8 - - + -
3764F ARG* 4.4 18.2 - - + +
3765F LEU* 4.7 13.9 - - + -
3768F ARG* 5.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS3695 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3691F PRO* 4.3 19.3 - - + -
3692F ASP* 2.9 29.4 + - + +
3694F LEU* 1.3 80.2 - - - +
3696F GLN* 1.3 60.0 + - - +
3697F LEU 3.4 0.2 - - - -
3698F VAL* 3.7 3.2 + - - +
3699F LEU* 3.3 55.5 + - + +
3767F ASN 5.4 0.9 - - - -
3768F ARG* 3.6 24.6 - - + +
3769F GLY* 3.8 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3696 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2107F ALA* 4.2 17.6 + - - +
2110F ASP 5.0 1.0 + - - -
2111F PHE* 3.8 33.6 - - + +
2112F VAL* 5.1 14.6 - - + -
2118F VAL* 4.8 7.3 - - + +
2122F PHE* 4.3 13.7 - - + -
3691F PRO* 3.6 26.6 + - + +
3692F ASP 3.0 26.8 + - - +
3693F PRO* 3.1 19.0 - - - +
3694F LEU 3.3 0.8 - - - -
3695F HIS* 1.3 77.4 - - - +
3697F LEU* 1.3 60.3 + - - +
3699F LEU* 3.2 6.4 + - + +
3700F HIS* 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3697 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122F PHE* 3.5 35.2 - - + -
3673F LEU* 3.9 20.6 - - + -
3693F PRO 3.4 16.4 - - - +
3694F LEU* 3.4 35.4 - - + +
3695F HIS 3.4 0.2 - - - -
3696F GLN* 1.3 76.5 - - - +
3698F VAL* 1.3 63.6 + - - +
3700F HIS* 3.3 7.1 + - - +
3701F PHE* 3.1 34.7 - - + -
3721F TYR* 4.3 28.7 - - + -
3725F MET* 5.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3698 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3694F LEU 4.2 4.9 + - - +
3695F HIS 3.7 10.1 + - - +
3696F GLN 3.3 0.4 - - - -
3697F LEU* 1.3 79.4 - - - +
3699F LEU* 1.3 62.6 + - + +
3700F HIS 3.7 0.2 + - - -
3701F PHE* 4.2 2.4 + - - +
3702F SER* 3.8 15.6 + - - -
3768F ARG* 4.9 4.0 - - + -
3769F GLY* 3.5 41.6 - - - +
3770F ALA* 4.0 9.6 - - + +
3773F MET* 4.3 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3699 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2111F PHE* 4.7 22.0 - - + -
3695F HIS* 3.3 51.8 + - + +
3696F GLN* 3.2 6.8 + - - +
3697F LEU 3.2 0.6 - - - -
3698F VAL* 1.3 78.6 - - + +
3700F HIS* 1.3 61.6 + - - +
3702F SER* 2.5 28.5 + - - +
3703F ARG* 3.8 21.6 + - - +
3769F GLY* 5.5 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS3700 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2115F PRO* 3.3 38.0 - - + +
2118F VAL* 3.5 17.9 - - + +
2119F ARG* 3.4 42.2 + - + +
2122F PHE* 4.6 15.9 - + + -
3696F GLN 2.8 17.0 + - - +
3697F LEU* 3.3 10.3 + - - +
3699F LEU* 1.3 78.4 - - - +
3701F PHE* 1.3 85.0 + + - +
3702F SER 3.3 0.5 + - - -
3703F ARG* 3.5 18.6 + - - +
3704F THR* 3.8 12.2 + - + +
3717F LEU* 4.5 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3701 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122F PHE* 6.1 2.7 - + - -
3697F LEU* 3.1 35.8 + - + +
3698F VAL* 4.2 4.0 + - - +
3699F LEU 3.5 0.2 - - - -
3700F HIS* 1.3 90.3 - + - +
3702F SER* 1.3 62.0 + - - +
3703F ARG 3.3 0.2 - - - -
3704F THR* 2.7 30.4 + - + +
3705F ALA* 3.2 12.8 + - - +
3715F ASP* 6.0 0.7 - - + -
3717F LEU* 4.2 24.5 - - + -
3718F TYR* 3.5 66.9 - + + +
3721F TYR* 5.2 14.1 - + + -
3725F MET* 6.3 2.7 - - + -
3773F MET* 5.4 7.9 - - + -
3777F MET* 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3702 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461F HIS* 5.3 1.6 - - - -
462F GLU* 6.1 1.6 - - - -
3698F VAL 3.9 10.2 + - - -
3699F LEU* 2.5 39.6 + - - +
3701F PHE* 1.3 77.1 - - - +
3703F ARG* 1.3 61.3 + - - +
3705F ALA* 3.5 2.7 + - - -
3706F LEU* 3.4 28.2 + - - +
3773F MET* 5.7 6.0 - - - +
3776F GLN* 4.1 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3703 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461F HIS* 3.4 55.9 + - + +
2111F PHE* 5.0 20.0 - - - -
2113F GLN* 5.9 4.1 - - - +
2114F SER 6.3 0.4 - - - -
2115F PRO* 4.9 25.2 - - + +
3699F LEU* 3.8 23.6 + - - +
3700F HIS* 3.5 11.7 + - - +
3701F PHE 3.3 0.6 - - - -
3702F SER* 1.3 78.0 + - - +
3704F THR* 1.3 55.8 + - + +
3706F LEU 3.5 1.5 + - - -
3707F THR* 2.3 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR3704 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2119F ARG* 3.4 28.9 - - - +
3700F HIS* 3.8 17.7 - - + +
3701F PHE* 2.7 36.0 + - + +
3703F ARG* 1.3 78.9 - - + +
3705F ALA* 1.3 60.8 + - - +
3707F THR* 3.2 14.8 + - - -
3777F MET* 5.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3705 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3701F PHE 3.2 12.4 + - - +
3702F SER* 3.5 3.8 + - - +
3703F ARG 3.2 0.2 - - - -
3704F THR* 1.3 81.9 + - - +
3706F LEU* 1.3 74.8 + - + +
3707F THR 3.5 1.3 + - - -
3708F GLU 4.9 4.2 - - - +
3773F MET 6.0 0.2 - - - +
3776F GLN* 4.4 20.6 - - + +
3777F MET* 4.5 15.9 - - + -
3780F ALA* 3.9 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3706 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461F HIS* 4.5 5.5 + - + +
462F GLU* 5.3 16.6 - - + +
465F GLN* 3.5 27.8 - - + +
3702F SER 3.4 13.5 + - - +
3703F ARG* 3.6 4.3 - - - -
3704F THR 3.4 0.2 - - - -
3705F ALA* 1.3 87.4 - - + +
3707F THR* 1.3 62.5 + - - +
3708F GLU 3.8 2.5 - - - -
3776F GLN* 3.4 43.3 - - + +
3814F TYR* 5.4 2.9 - - - +
----------------------------------------------------------
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