Contacts of the strand formed by residues 725 - 730 (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 ILE 725 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719F PHE* 5.4 2.8 - - - -
720F SER* 2.4 44.1 + - - +
721F ARG* 5.1 4.0 - - + +
723F GLY* 2.8 17.8 + - - +
724F GLU* 1.3 76.2 - - - +
726F LEU* 1.3 68.9 + - - +
737F LEU* 5.0 9.6 - - + -
738F TRP 3.6 3.8 - - - +
739F ASP* 3.6 23.6 - - - +
776F LYS* 5.2 12.3 - - - +
794F ALA* 5.1 13.9 - - + -
795F GLY* 6.2 3.6 - - - +
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Residues in contact with LEU 726 (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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685F ALA* 4.2 13.9 - - + -
693F VAL* 5.0 9.4 - - + -
695F LEU* 6.3 1.8 - - + -
707F LEU* 3.8 18.2 - - + -
717F LEU* 4.8 7.9 - - + -
718F ARG 3.8 15.3 - - - +
719F PHE* 3.6 36.6 - - + -
724F GLU 4.0 1.5 - - - -
725F ILE* 1.3 75.3 - - - +
727F ALA* 1.3 65.4 + - - +
737F LEU* 3.3 14.0 - - - +
738F TRP* 3.2 60.1 + - + -
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Residues in contact with ALA 727 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717F LEU* 3.8 0.3 - - - -
718F ARG* 3.0 40.5 + - + +
720F SER* 5.5 5.6 - - - -
725F ILE 3.7 2.4 + - - +
726F LEU* 1.3 74.2 - - - +
728F SER* 1.3 63.2 + - - +
735F VAL* 6.0 2.2 - - + -
737F LEU* 4.0 16.4 - - + -
769F LEU* 3.3 18.8 - - + +
771F GLY* 5.8 1.6 - - - -
778F THR* 4.2 23.1 - - + +
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Residues in contact with SER 728 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710F HIS* 3.1 27.0 + - - -
714F VAL* 4.5 0.9 - - - +
716F SER* 3.4 7.4 - - - -
717F LEU* 3.4 23.8 - - - +
726F LEU* 5.3 0.9 - - - -
727F ALA* 1.3 77.7 - - - +
729F GLY* 1.3 63.4 + - - +
735F VAL* 3.4 12.9 - - - +
736F ARG 3.1 38.5 + - - -
738F TRP* 4.1 11.4 - - - -
766F GLN* 4.7 0.4 - - - +
769F LEU* 3.9 4.7 - - - +
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Residues in contact with GLY 729 (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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710F HIS* 4.8 2.4 + - - -
714F VAL* 4.0 6.9 - - - +
715F CYS* 3.3 18.7 + - - -
716F SER* 2.8 21.5 + - - +
728F SER* 1.3 80.1 + - - +
730F SER* 1.3 61.8 + - - -
734F THR 3.4 7.2 - - - -
766F GLN* 3.2 20.0 - - - -
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Residues in contact with SER 730 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710F HIS* 3.2 29.7 + - - +
713F THR 3.3 15.9 - - - -
715F CYS* 4.2 6.5 - - - +
729F GLY* 1.3 74.3 - - - -
731F MET* 1.3 65.4 + - - +
732F ASP* 2.3 26.7 + - - -
733F ASN* 3.4 12.6 + - - -
734F THR* 2.4 24.0 + - - +
766F GLN* 3.9 15.2 + - - +
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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
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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