Contacts of the helix formed by residues 791 - 803 (chain r) in PDB entry 6FF7
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 ARG 791 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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790r THR* 1.3 75.0 - - - +
792r VAL* 1.3 65.9 + - + +
793r ASP 3.5 0.4 - - - -
794r ARG* 3.6 16.8 - - - +
795r THR* 4.2 2.6 + - - -
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Residues in contact with VAL 792 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790r THR* 4.6 0.2 - - - -
791r ARG* 1.3 75.6 - - + +
793r ASP* 1.3 57.9 + - - +
794r ARG 3.0 5.2 - - - -
795r THR* 2.9 25.7 + - - +
796r LEU* 2.9 11.4 + - - +
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Residues in contact with ASP 793 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770r LYS* 5.1 15.7 - - + -
771r ASN* 5.1 6.3 - - + +
772r LEU* 5.7 3.4 - - + +
790r THR* 3.8 20.7 - - - -
791r ARG 3.5 0.8 - - - -
792r VAL* 1.3 74.8 - - - +
794r ARG* 1.3 60.2 + - - +
796r LEU* 3.6 14.6 - - + -
797r VAL* 2.9 27.0 + - - +
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Residues in contact with ARG 794 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785r HIS* 5.8 6.1 - - + +
786r HIS 4.7 17.7 - - - +
787r ALA* 6.1 1.1 - - - -
790r THR* 4.6 7.9 - - - +
791r ARG 3.6 15.0 + - - +
792r VAL 3.0 0.6 - - - -
793r ASP* 1.3 76.0 - - - +
795r THR* 1.3 59.4 + - - +
797r VAL* 3.2 6.5 + - - +
798r GLU* 2.9 29.2 + - - +
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Residues in contact with THR 795 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791r ARG 4.2 1.7 + - - -
792r VAL* 2.9 13.8 + - - -
794r ARG* 1.3 78.0 - - - +
796r LEU* 1.3 58.0 + - - +
798r GLU* 3.4 7.4 + - - +
799r ASP* 3.0 29.8 + - - +
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Residues in contact with LEU 796 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792r VAL 2.9 7.7 + - - +
793r ASP* 3.8 20.4 - - + +
794r ARG 3.2 0.2 - - - -
795r THR* 1.3 77.7 - - - +
797r VAL* 1.3 57.8 + - - +
799r ASP* 4.0 7.1 - - - +
800r LEU* 3.5 18.0 + - - +
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Residues in contact with VAL 797 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783r ALA* 5.9 5.8 - - + -
784r ILE 4.7 14.8 - - - +
785r HIS* 5.0 9.0 - - + -
793r ASP 2.9 17.7 + - - +
794r ARG* 3.7 6.5 - - - +
796r LEU* 1.3 77.0 - - - +
798r GLU* 1.3 59.6 + - - +
799r ASP 3.2 0.2 - - - -
800r LEU* 3.0 10.0 + - - +
801r PHE* 2.9 27.9 + - - +
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Residues in contact with GLU 798 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794r ARG 2.9 17.2 + - - +
795r THR* 3.7 9.2 - - - +
797r VAL* 1.3 75.2 - - - +
799r ASP* 1.3 62.8 + - - +
801r PHE* 3.2 6.7 + - - +
802r ALA* 3.0 26.2 + - - +
819r VAL* 6.2 3.6 - - + -
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Residues in contact with ASP 799 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795r THR 3.0 17.4 + - - +
796r LEU* 4.0 9.0 - - - +
798r GLU* 1.3 76.0 - - - +
800r LEU* 1.3 62.1 + - - +
802r ALA* 3.6 5.8 + - - +
803r ASP* 3.4 24.1 + - - +
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Residues in contact with LEU 800 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796r LEU 3.5 12.5 + - - +
797r VAL* 3.0 14.1 + - - +
799r ASP* 1.3 80.4 - - - +
801r PHE* 1.3 57.2 + - - +
803r ASP* 3.9 3.1 + - - +
804r LYS 3.6 1.9 + - - -
805r HIS* 3.1 36.6 + - + +
806r ILE* 3.8 11.0 + - + -
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Residues in contact with PHE 801 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797r VAL 2.9 13.5 + - - +
798r GLU* 3.2 6.9 + - - +
800r LEU* 1.3 77.2 - - - +
802r ALA* 1.3 65.8 + - - +
803r ASP 3.2 0.2 - - - -
804r LYS* 3.1 14.4 + - - +
806r ILE* 4.6 18.4 - - + +
809r LEU* 5.5 10.1 - - + -
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Residues in contact with ALA 802 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798r GLU 3.0 16.8 + - - +
799r ASP* 4.0 6.7 - - - +
800r LEU 3.5 0.2 - - - -
801r PHE* 1.3 77.1 - - - +
803r ASP* 1.3 58.2 + - - +
804r LYS* 3.3 5.7 + - - +
821r LEU* 5.6 7.0 - - + -
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Residues in contact with ASP 803 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799r ASP 3.4 14.7 + - - +
800r LEU* 4.5 3.8 - - - +
801r PHE 3.2 0.8 - - - -
802r ALA* 1.3 75.8 - - + +
804r LYS* 1.3 69.3 + - - +
805r HIS* 3.4 5.4 + - + +
681v PRO* 4.8 17.6 - - + +
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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