Contacts of the helix formed by residues 786 - 796 (chain F) in PDB entry 1XFV
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 GLU 786 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700F TYR* 4.9 5.0 + - - -
723F PHE* 4.0 25.4 - - + -
727F GLN* 3.4 24.5 - - - +
782F PHE* 3.7 28.0 - - - +
784F GLU 4.3 0.6 + - - -
785F ASN* 1.4 71.4 - - - +
787F THR* 1.3 68.9 + - - +
789F ASN* 3.6 20.2 + - - +
790F PHE* 3.7 7.3 + - + +
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Residues in contact with THR 787 (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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785F ASN* 3.1 28.6 + - + +
786F GLU* 1.3 85.8 - - - +
788F ASP* 1.3 72.9 + - - +
790F PHE* 3.4 12.3 + - - +
791F GLU* 3.9 8.7 + - - +
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Residues in contact with ASP 788 (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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785F ASN* 3.0 22.7 + - - +
787F THR* 1.3 80.9 + - - +
789F ASN* 1.3 56.0 + - - +
790F PHE 2.9 2.9 - - - -
791F GLU* 2.8 25.6 + - + +
792F VAL* 2.4 54.1 + - + +
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Residues in contact with ASN 789 (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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723F PHE* 4.2 7.3 - - - -
780F LEU* 3.3 24.9 - - - +
781F ASN* 2.6 43.9 + - + +
782F PHE* 3.8 7.7 - - - +
785F ASN* 4.0 4.6 + - - +
786F GLU* 3.6 38.0 + - + +
787F THR 3.1 0.2 - - - -
788F ASP* 1.3 83.1 + - - +
790F PHE* 1.3 57.1 + - - +
792F VAL* 3.1 10.9 - - - +
793F PHE* 2.9 24.4 + - - +
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Residues in contact with PHE 790 (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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716F LYS* 5.9 1.8 - - + -
719F LYS* 5.5 2.7 - - + -
720F ILE* 3.4 39.5 - - + -
723F PHE* 3.8 33.8 - + + -
786F GLU 3.7 5.8 + - - +
787F THR 3.4 9.9 + - - +
788F ASP 2.9 0.6 - - - -
789F ASN* 1.3 77.0 - - - +
791F GLU* 1.4 68.9 + - + +
792F VAL 3.0 1.3 - - - -
793F PHE* 2.8 49.4 + + - +
794F GLN* 2.9 13.2 + - + +
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Residues in contact with GLU 791 (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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787F THR* 4.1 5.5 - - - +
788F ASP* 2.8 32.5 + - + +
790F PHE* 1.4 76.0 - - + +
792F VAL* 1.3 67.7 + - - +
794F GLN* 2.9 28.5 + - - +
795F LYS* 3.3 5.4 + - - +
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Residues in contact with VAL 792 (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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779F GLN 4.5 12.3 - - - +
780F LEU* 4.7 4.0 - - + -
788F ASP* 2.4 59.3 + - + +
789F ASN* 3.1 13.9 - - - +
791F GLU* 1.3 69.9 - - - +
793F PHE* 1.3 65.2 + - - +
794F GLN 2.9 1.4 + - - -
795F LYS* 2.9 7.8 + - - +
796F ILE* 2.8 44.6 + - + +
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Residues in contact with PHE 793 (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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719F LYS* 3.9 30.1 - - + -
722F ILE* 3.7 27.6 - - + -
723F PHE* 3.9 20.4 - + + -
726F ILE* 5.2 0.7 - - + -
764F LEU* 5.9 0.2 - - + -
776F LEU* 3.7 41.5 - - + -
780F LEU* 4.6 4.5 - - + -
789F ASN 2.9 9.9 + - - +
790F PHE* 2.8 43.2 + + + +
792F VAL* 1.3 79.7 - - - +
794F GLN* 1.3 64.7 + - - +
796F ILE* 3.1 18.8 - - + +
797F ILE* 3.4 20.6 - - + +
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Residues in contact with GLN 794 (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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719F LYS* 5.0 15.0 - - - +
790F PHE* 2.9 9.8 + - + +
791F GLU* 2.9 17.1 + - - +
792F VAL 2.9 1.0 + - - -
793F PHE* 1.3 77.3 - - + +
795F LYS* 1.3 80.5 + - - +
797F ILE* 2.5 52.8 + - + +
798F ASP* 4.4 8.7 - - - +
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Residues in contact with LYS 795 (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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791F GLU 3.3 4.0 + - - +
792F VAL* 2.9 12.0 + - - +
794F GLN* 1.3 90.2 - - - +
796F ILE* 1.3 56.6 + - + +
797F ILE 2.5 17.1 + - - -
798F ASP* 2.8 35.2 + - - +
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Residues in contact with ILE 796 (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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771F ILE* 3.9 19.9 - - + +
776F LEU* 4.0 30.3 - - + +
779F GLN* 3.8 38.1 - - + +
780F LEU* 4.7 5.2 - - + -
792F VAL* 2.8 51.7 + - + +
793F PHE* 3.1 16.4 - - + +
794F GLN 3.0 0.2 + - - -
795F LYS* 1.3 76.7 - - + +
797F ILE* 1.3 60.0 + - + +
798F ASP 3.9 1.0 + - - -
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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