Contacts of the strand formed by residues 778 - 782 (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 THR 778 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720F SER* 5.7 3.3 - - - -
727F ALA* 4.2 18.9 - - + +
735F VAL* 6.2 1.1 - - + -
737F LEU* 5.4 2.8 - - - +
769F LEU* 3.8 28.9 - - + -
770F LEU 4.0 7.0 - - - +
771F GLY* 4.7 3.7 - - - -
777F SER* 1.3 83.2 + - - +
779F PRO* 1.3 60.9 - - - +
780F VAL* 4.2 4.5 - - + -
790F LEU 3.9 0.2 - - - +
791F VAL* 3.4 0.6 - - - -
792F LEU* 2.6 67.6 + - + +
793F ALA* 5.4 3.0 - - - -
794F ALA* 5.6 3.6 - - - +
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Residues in contact with PRO 779 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477F ASP* 5.0 8.0 - - - +
480F ASP* 5.1 9.6 - - - +
769F LEU* 3.9 1.4 - - - +
770F LEU* 3.4 35.0 + - + +
772F THR* 3.2 20.6 - - + +
777F SER* 5.3 0.4 - - - -
778F THR* 1.3 86.6 - - - +
780F VAL* 1.3 61.0 + - - +
781F VAL* 5.7 0.8 - - - +
789F ASN* 3.4 24.2 - - - +
790F LEU 3.3 5.4 - - - +
791F VAL* 3.8 25.4 - - + -
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Residues in contact with VAL 780 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735F VAL* 5.2 4.3 - - + -
766F GLN* 3.5 37.5 - - + +
768F LEU 3.8 16.4 - - - +
769F LEU* 3.7 22.2 - - + +
778F THR* 4.2 3.8 - - + -
779F PRO* 1.3 77.9 - - - +
781F VAL* 1.3 64.6 + - - +
782F HIS* 3.2 17.0 - - + +
789F ASN* 2.9 6.8 - - - +
790F LEU 2.7 33.8 + - - +
792F LEU* 4.0 27.8 - - + -
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Residues in contact with VAL 781 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F ALA* 3.7 40.4 - - + +
477F ASP* 5.3 11.7 - - - +
483F SER* 5.8 6.7 - - - -
485F ILE* 5.3 6.5 - - + -
765F SER 3.6 0.2 - - - +
766F GLN* 3.3 27.5 - - - +
767F GLU* 3.7 12.4 + - - +
768F LEU 4.0 14.7 + - - +
769F LEU* 6.0 0.4 - - - -
779F PRO 5.7 0.7 - - - +
780F VAL* 1.3 79.4 - - - +
782F HIS* 1.3 64.5 + - - +
783F LEU* 4.3 10.1 - - + -
787F ARG* 6.1 2.9 - - - -
788F ARG 5.7 0.4 - - - -
789F ASN* 4.5 19.7 - - + +
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Residues in contact with HIS 782 (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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735F VAL* 5.3 0.7 - - + -
761F LEU* 3.5 29.5 - - + +
764F ASN* 3.4 31.3 + - - +
765F SER 3.3 4.5 - - - -
766F GLN* 3.2 31.4 - - + +
780F VAL* 3.2 41.5 + - + +
781F VAL* 1.3 74.7 - - - +
783F LEU* 1.3 65.2 + - - +
784F HIS 4.1 0.9 - - - -
786F THR 2.8 23.8 - - - +
787F ARG 4.4 0.2 - - - -
788F ARG* 3.4 24.2 + - + +
790F LEU* 3.5 22.7 + - + +
792F LEU* 6.0 1.7 - - + +
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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
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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