Contacts of the helix formed by residues 871 - 876 (chain B) in PDB entry 6MZL
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 PRO 871 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B ASP* 1.3 86.7 - - + +
872B ALA* 1.3 55.5 + - + +
873B LEU 3.2 2.9 - - - -
874B PHE* 2.8 19.3 + - + +
875B LYS* 2.6 36.4 + - + -
894B VAL* 4.5 15.0 - - + -
897B TYR* 3.4 43.7 - - + +
906B GLU* 4.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 872 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B ASP* 3.3 6.4 - - + +
871B PRO* 1.3 82.3 - - + +
873B LEU* 1.3 57.5 + - - +
875B LYS* 3.6 11.9 - - + +
876B SER* 2.9 27.4 + - - -
201K GLN* 3.9 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 873 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B LEU* 5.9 1.6 - - + -
858B ILE* 4.7 15.5 - - + -
862B GLN* 5.5 3.8 - - - +
867B VAL* 5.4 3.4 - - + -
870B ASP 4.7 6.7 + - - +
871B PRO 3.2 1.1 - - - -
872B ALA* 1.3 74.5 - - - +
874B PHE* 1.3 71.3 + - + +
876B SER* 2.4 30.8 + - - +
877B TYR* 3.0 19.6 + - + +
201K GLN* 4.3 23.8 - - + +
202K SER 3.4 27.8 - - - +
203K LEU* 3.7 24.7 - - + +
213K LEU* 5.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 874 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B LEU* 3.5 43.1 - - + -
858B ILE* 3.8 17.5 - - + -
859B ARG* 3.3 49.8 - - + -
862B GLN* 4.5 15.9 - - - -
870B ASP 4.9 1.3 - - - -
871B PRO* 2.8 19.3 + - + +
873B LEU* 1.3 81.9 - - + +
875B LYS* 1.3 51.9 + - - +
877B TYR* 2.9 8.3 + - - +
878B ALA* 2.8 32.6 + - - +
890B ALA* 3.5 21.5 - - + +
893B ALA* 3.9 20.6 - - + -
894B VAL* 4.9 9.6 - - + -
897B TYR* 5.9 1.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 875 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B PRO* 2.6 24.6 + - + +
872B ALA* 3.6 13.9 - - - +
874B PHE* 1.3 72.1 - - - +
876B SER* 1.3 60.4 + - - +
878B ALA* 3.2 17.6 + - - +
879B GLU* 3.6 11.4 - - - +
894B VAL* 5.6 4.1 - - + +
906B GLU* 3.3 37.7 - - - +
909B TRP* 3.2 51.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 876 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872B ALA 2.9 16.1 + - - -
873B LEU* 2.4 32.2 + - - +
875B LYS* 1.3 76.3 - - - +
877B TYR* 1.3 70.0 + - - +
879B GLU* 3.1 36.8 - - - +
882B HIS* 3.6 0.7 + - - -
201K GLN* 3.6 19.6 + - - -
215K ALA* 6.2 0.4 - - - -
216K ALA* 3.4 13.2 + - - +
----------------------------------------------------------
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