Contacts of the strand formed by residues 766 - 769 (chain F) 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 GLN 766 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715F CYS* 3.3 26.3 - - - +
716F SER* 3.4 11.4 + - - +
728F SER 4.7 0.2 - - - +
729F GLY* 3.2 29.4 - - - -
730F SER 4.6 14.5 + - - +
731F MET* 5.5 0.6 - - - +
733F ASN* 5.8 0.4 - - - -
734F THR 4.4 3.8 + - - -
735F VAL* 3.3 26.7 - - - +
761F LEU* 3.4 8.9 - - + +
764F ASN 4.2 2.7 - - - +
765F SER* 1.3 79.5 - - - +
767F GLU* 1.3 64.4 + - - +
768F LEU 4.7 0.4 - - - +
769F LEU* 5.8 0.2 - - - +
780F VAL* 3.5 15.0 - - + +
781F VAL 3.3 8.7 - - - +
782F HIS* 3.2 34.8 - - - +
62H LYS* 4.3 2.1 - - - +
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Residues in contact with GLU 767 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472F GLY 3.1 31.5 - - - +
473F LEU 3.1 20.9 - - - +
474F THR* 3.2 27.8 - - - -
475F ALA* 3.2 12.2 + - + +
715F CYS 3.5 7.3 - - - +
716F SER* 4.5 0.7 - - - -
765F SER* 5.0 4.9 - - - +
766F GLN* 1.3 75.1 - - - +
768F LEU* 1.3 68.6 + - + +
781F VAL* 3.7 10.9 + - + +
783F LEU* 3.3 34.4 - - + +
62H LYS* 2.4 38.2 + - + +
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Residues in contact with LEU 768 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474F THR* 3.4 26.0 - - - +
475F ALA 3.7 16.3 + - - +
476F VAL* 3.7 26.0 - - + -
592F GLN* 5.9 2.9 - - - +
634F ARG* 6.2 3.6 - - - +
715F CYS 5.0 4.0 - - - +
716F SER* 3.6 14.3 - - - +
718F ARG* 5.3 8.7 - - - +
766F GLN 4.7 0.2 - - - -
767F GLU* 1.3 93.3 + - - +
769F LEU* 1.3 69.9 + - - +
780F VAL* 3.8 16.1 - - - +
781F VAL* 4.0 11.9 + - - +
62H LYS* 4.3 5.8 - - - +
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Residues in contact with LEU 769 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476F VAL* 6.2 0.3 - - - +
477F ASP* 5.0 2.5 - - - +
716F SER* 3.6 25.8 - - - +
717F LEU 3.9 7.3 + - - +
718F ARG* 3.4 38.8 + - + -
727F ALA* 3.3 37.0 - - + +
728F SER* 3.9 4.0 - - - +
735F VAL* 6.3 1.8 - - + -
766F GLN* 5.8 0.2 - - - +
768F LEU* 1.3 83.3 - - - +
770F LEU* 1.3 67.6 + - - +
778F THR* 3.8 17.0 - - + -
779F PRO 3.9 4.0 - - - +
780F VAL* 3.7 35.0 - - + +
781F VAL* 5.7 1.3 - - - +
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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) + - + + + + + -
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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