Contacts of the helix formed by residues 811 - 815 (chain B) in PDB entry 1L8A
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 VAL 811 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B PHE* 3.4 44.6 - - + +
764B LEU* 4.0 11.4 - - + -
765B ALA* 3.7 14.8 - - + +
788B ILE* 4.0 12.6 - - + -
808B ALA 3.1 19.3 - - - +
810B GLN* 1.3 78.7 - - + +
812B ARG* 1.3 67.7 + - - +
813B THR 3.3 2.5 - - - -
814B TYR* 2.9 25.0 + - + -
815B VAL* 3.1 19.1 + - + +
820B TYR* 3.4 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A ARG* 3.7 28.8 + - + +
813A THR* 3.1 40.7 + - - +
809B GLU* 3.0 17.3 + - - +
810B GLN 3.4 1.0 - - - -
811B VAL* 1.3 76.9 - - - +
813B THR* 1.3 65.4 + - - +
814B TYR 2.8 1.7 + - - -
815B VAL* 2.9 21.7 + - - +
817B ALA 2.8 29.1 + - - -
818B ASP 3.5 16.0 + - - -
820B TYR* 3.2 51.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A GLU* 4.0 16.3 + - - +
812A ARG* 3.5 33.6 - - - +
820A TYR* 4.7 13.7 + - - +
772B GLU* 5.2 6.3 - - + -
810B GLN 5.1 0.4 + - - -
811B VAL 3.2 0.8 + - - -
812B ARG* 1.3 77.4 - - - +
814B TYR* 1.3 89.2 + - + +
815B VAL 4.6 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A GLU* 3.0 24.6 + - - -
764B LEU 4.7 0.9 - - - -
765B ALA* 3.8 17.9 - - - -
768B GLY* 3.3 31.0 - - - -
769B GLN* 3.0 30.4 - - + +
772B GLU* 3.9 14.9 - - + +
786B PRO* 3.9 18.7 - - + +
788B ILE* 3.5 25.6 - - + +
789B ALA* 3.8 9.7 - - - +
810B GLN 4.0 11.0 - - - -
811B VAL* 2.9 20.4 + - + +
812B ARG 2.8 0.2 + - - -
813B THR* 1.3 97.4 - - + +
815B VAL* 1.3 65.4 + - - +
816B PRO* 3.2 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B ILE* 4.2 11.4 - - + -
792B MET* 3.6 27.8 - - + -
811B VAL* 3.3 33.9 - - + +
812B ARG* 2.9 13.7 + - - +
813B THR 4.6 2.4 - - - +
814B TYR* 1.3 76.9 - - - +
816B PRO* 1.3 63.9 - - + +
817B ALA* 2.9 30.0 + - + +
820B TYR* 4.0 35.0 - - + -
----------------------------------------------------------
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