Contacts of the helix formed by residues 783 - 790 (chain F) in PDB entry 5TWV
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 783 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782F ALA* 1.3 79.2 - - - +
784F VAL* 1.3 60.9 + - - +
785F GLU* 3.9 9.0 - - - -
786F GLU* 4.0 11.2 - - - +
787F ASN* 2.8 27.6 + - - +
819F ASP 3.5 15.9 - - - -
820F GLN* 5.0 5.4 - - - -
821F THR 3.5 12.3 - - - -
822F GLN* 4.7 1.9 - - - +
823F ILE* 4.8 0.7 - - - -
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Residues in contact with VAL 784 (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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782F ALA 3.9 0.2 + - - -
783F THR* 1.3 73.1 - - - +
785F GLU* 1.3 58.0 + - - +
787F ASN* 3.2 10.2 + - - +
788F ILE* 2.9 28.8 + - - +
799F TYR* 5.8 2.2 - - - +
818F GLY 4.8 3.8 - - - +
819F ASP* 3.7 16.8 + - + +
821F THR* 3.6 11.2 + - - +
823F ILE* 4.6 8.9 - - + +
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Residues in contact with GLU 785 (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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783F THR* 3.2 5.1 - - - -
784F VAL* 1.3 77.8 - - - +
786F GLU* 1.3 57.4 + - - +
788F ILE* 3.0 9.6 + - - +
789F THR* 2.8 26.5 + - - -
794F PHE* 3.9 17.9 - - + -
799F TYR* 5.0 11.0 - - + -
819F ASP* 3.8 28.6 + - + +
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Residues in contact with GLU 786 (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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782F ALA* 3.9 24.7 - - + -
783F THR* 3.3 10.7 + - - +
785F GLU* 1.3 75.4 - - - +
787F ASN* 1.3 64.3 + - - +
788F ILE 3.2 0.2 - - - -
789F THR* 4.2 7.6 - - - +
790F PHE* 3.3 21.0 + - - -
794F PHE* 4.6 9.1 - - + -
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Residues in contact with ASN 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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780F LEU* 5.4 17.3 - - + +
782F ALA* 4.7 2.4 - - + +
783F THR 2.8 14.9 + - - +
784F VAL* 3.2 14.1 + - - +
786F GLU* 1.3 75.7 - - - +
788F ILE* 1.3 59.2 - - - +
790F PHE* 4.5 8.8 - - - +
823F ILE* 6.1 2.5 - - + -
838F ILE* 4.9 14.5 - - + +
842F ARG* 3.8 18.9 - - - +
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Residues in contact with ILE 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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784F VAL 2.9 12.0 + - - +
785F GLU* 3.0 12.1 + - - +
787F ASN* 1.3 77.7 - - - +
789F THR* 1.3 65.5 + - - +
790F PHE* 3.6 3.5 + - - +
799F TYR* 4.7 17.5 - - + -
838F ILE 5.7 0.9 - - - -
841F ALA* 5.4 9.2 - - + +
842F ARG* 4.3 12.1 - - - +
845F TYR* 3.2 31.5 - - + +
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Residues in contact with THR 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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785F GLU 2.8 10.9 + - - -
786F GLU* 3.6 4.7 + - - -
788F ILE* 1.3 75.8 - - - +
790F PHE* 1.3 67.8 + - - +
791F GLU 4.6 2.2 - - - -
792F SER* 2.5 38.4 + - - -
793F PRO 5.5 0.4 - - - -
794F PHE* 3.6 38.8 - - - -
845F TYR* 3.8 11.8 - - - -
846F GLN* 5.9 1.4 - - - +
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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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770F VAL 5.9 1.6 - - - -
786F GLU 3.3 13.7 + - - -
787F ASN* 4.5 10.3 - - - +
788F ILE 4.2 6.3 - - - +
789F THR* 1.3 79.8 - - - +
791F GLU* 1.3 69.6 + - + +
792F SER* 4.5 0.7 - - - -
842F ARG* 5.3 14.1 - - + +
846F GLN* 5.4 13.5 - - + -
1213F THR* 4.0 26.0 - - - -
1216F ALA* 5.1 4.5 - - + -
1217F PHE* 3.9 34.1 - - + -
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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