Contacts of the helix formed by residues 4726 - 4735 (chain B) 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 HIS4726 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4679B LEU 4.9 4.5 - - - -
4680B GLU 4.3 10.0 + - - -
4681B PHE* 4.1 24.7 + - - -
4682B ASP* 4.6 3.2 + - - -
4686B ILE* 4.1 33.0 - - + +
4687B THR* 4.3 15.5 - - + +
4688B GLU* 6.4 0.2 - - + -
4722B VAL* 3.1 13.9 + - + +
4725B LYS* 1.3 91.9 + - + +
4727B GLY* 1.3 60.3 + - - +
4728B ASP 3.5 2.0 - - - -
4729B ILE* 3.7 24.4 + - + +
4730B TYR* 4.5 3.3 + - - +
4735B ILE* 3.8 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4722B VAL 3.5 4.0 + - - -
4723B LEU 3.3 20.4 + - - -
4724B ASP 4.3 0.2 - - - -
4725B LYS 3.4 2.6 - - - -
4726B HIS* 1.3 77.4 - - - +
4728B ASP* 1.3 59.7 + - - +
4729B ILE 3.2 2.9 - - - -
4730B TYR 4.4 0.2 - - - -
4731B GLY* 3.1 35.4 + - - +
4732B ARG* 3.7 1.9 + - - -
4735B ILE* 3.7 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP4728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4723B LEU 4.6 0.6 + - - -
4724B ASP 5.0 5.4 + - - +
4725B LYS 4.6 4.2 + - - +
4726B HIS 3.5 0.6 - - - -
4727B GLY* 1.3 76.1 - - - +
4729B ILE* 1.3 69.1 + - + +
4731B GLY* 4.0 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE4729 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4687B THR* 3.7 28.5 - - + +
4725B LYS 4.1 7.0 - - - +
4726B HIS* 3.7 34.3 - - + +
4727B GLY 3.2 0.4 - - - -
4728B ASP* 1.3 84.2 - - + +
4730B TYR* 1.3 75.5 + - + +
4731B GLY 3.3 0.8 + - - -
4071D ALA* 5.8 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR4730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4686B ILE* 4.7 3.6 - - + -
4687B THR* 3.6 46.8 + - + -
4726B HIS 4.5 3.7 + - - +
4727B GLY 3.9 2.2 + - - -
4729B ILE* 1.3 94.3 - - + +
4731B GLY* 1.3 63.5 + - - +
4734B ARG* 3.3 71.8 + - + +
4735B ILE* 5.0 5.6 - - + +
4070D GLU* 4.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4727B GLY 3.1 18.6 + - - +
4728B ASP* 4.0 4.8 + - - -
4729B ILE 3.3 4.6 + - - -
4730B TYR* 1.3 81.4 - - - +
4732B ARG* 1.3 62.7 + - - -
4733B GLU* 3.1 7.6 + - - -
4735B ILE* 3.3 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4723B LEU* 6.0 3.2 - - + +
4727B GLY* 3.7 3.9 + - - +
4731B GLY* 1.3 70.6 - - - -
4733B GLU* 1.3 57.6 + - - +
4735B ILE* 4.0 10.6 - - - +
4736B ALA* 3.5 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4731B GLY* 3.1 1.4 - - - -
4732B ARG* 1.3 78.5 - - - +
4734B ARG* 1.3 68.2 + - + +
4735B ILE 3.4 0.2 - - - -
4736B ALA* 3.5 5.1 + - - +
4737B GLU* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4730B TYR* 3.3 64.2 + - + +
4731B GLY 3.8 1.6 + - - -
4733B GLU* 1.3 79.9 - - + +
4735B ILE* 1.3 63.2 + - - +
4736B ALA 3.4 0.5 + - - -
4737B GLU* 3.4 19.4 + - - +
4070D GLU* 4.1 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE4735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4686B ILE* 4.1 17.7 - - + -
4722B VAL* 3.5 40.6 - - + +
4723B LEU* 3.7 30.2 - - + +
4726B HIS 3.8 8.5 - - - +
4727B GLY* 3.7 20.4 - - - -
4730B TYR* 4.7 5.8 + - + +
4731B GLY 3.3 18.7 + - - +
4732B ARG* 4.0 11.7 - - - +
4734B ARG* 1.3 77.0 - - - +
4736B ALA* 1.3 66.8 + - - +
4737B GLU 3.6 3.5 + - - -
----------------------------------------------------------
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