Contacts of the helix formed by residues 7039 - 7044 (chain A) in PDB entry 6W4H
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 SER7039 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6832A ALA* 5.0 2.8 - - - +
6833A THR 3.1 28.2 + - - -
6834A LEU* 4.7 1.1 - - - -
6835A PRO* 4.4 5.6 - - - -
6847A GLN* 4.3 0.7 - - - +
6995A VAL* 3.9 13.0 - - - -
7038A SER* 1.3 71.2 - - - +
7040A TYR* 1.3 72.0 + - - +
7041A SER 3.3 2.7 - - - -
7042A LEU* 2.9 37.6 + - - +
7043A PHE* 3.6 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR7040 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6798A ALA 4.1 12.6 + - - -
6802A ALA* 3.2 39.0 - - + +
6803A TRP* 3.5 45.6 - + + +
7036A GLN* 4.1 8.3 + - - -
7037A LEU 6.0 0.2 - - - -
7038A SER* 3.2 14.1 + - - +
7039A SER* 1.3 82.7 - - - +
7041A SER* 1.3 62.2 + - - +
7042A LEU 3.1 1.4 + - - -
7043A PHE* 3.2 26.6 + + - +
7044A ASP* 4.4 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER7041 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6802A ALA 4.9 0.2 + - - -
6803A TRP 4.2 9.2 + - - -
6804A GLN 3.9 8.6 + - - -
6805A PRO* 3.5 19.2 - - - +
6847A GLN* 3.1 23.9 + - - +
6850A GLN* 2.7 47.0 + - - -
7039A SER 3.2 0.8 + - - -
7040A TYR* 1.3 76.7 - - - +
7042A LEU* 1.3 60.0 + - - +
7043A PHE 3.2 1.3 + - - -
7044A ASP* 3.5 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU7042 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6834A LEU* 4.6 0.4 - - + -
6835A PRO* 3.7 29.4 - - + -
6843A ALA* 3.6 44.0 - - + +
6846A THR* 4.0 7.6 - - + -
6847A GLN* 3.7 19.3 - - + +
6850A GLN* 4.6 2.0 - - - +
6995A VAL* 3.9 4.3 - - + -
7039A SER* 2.9 28.9 + - - +
7041A SER* 1.3 78.5 - - - +
7043A PHE* 1.3 59.6 + - - +
7044A ASP 3.3 0.7 + - - -
7045A MET* 3.7 18.2 - - - +
4298B LEU* 3.6 40.4 - - + +
4299B CYS 5.6 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE7043 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6833A THR 5.9 0.2 - - - -
6835A PRO* 3.8 36.3 - - + -
7039A SER* 3.6 30.3 - - - -
7040A TYR* 3.2 16.4 + + - +
7042A LEU* 1.3 79.4 - - - +
7044A ASP* 1.3 57.2 + - - +
7045A MET* 4.0 1.8 + - - -
4299B CYS 5.6 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP7044 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6850A GLN* 3.7 8.1 + - - -
7040A TYR 4.4 1.4 + - - +
7041A SER* 3.5 16.9 + - - +
7042A LEU 3.3 0.6 - - - -
7043A PHE* 1.3 77.9 - - - +
7045A MET* 1.3 60.2 + - - +
7046A SER* 2.7 33.5 + - - -
7047A LYS* 5.0 2.2 + - - +
----------------------------------------------------------
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