Contacts of the helix formed by residues 858 - 869 (chain A) in PDB entry 4FYT
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 ASP 858 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ARG* 2.9 26.2 + - - -
816A PHE* 5.9 1.2 - - - -
822A VAL* 6.0 0.3 - - - +
826A ASP* 4.8 4.1 - - - +
829A ARG* 3.6 39.2 + - - +
854A ILE* 3.8 9.2 - - + -
855A ARG* 2.8 18.9 + - - +
857A GLN* 1.3 98.5 + - - +
859A ALA* 1.3 61.6 + - - +
860A THR 3.5 2.0 - - - -
861A SER* 3.6 7.3 + - - -
862A THR* 2.8 30.4 + - - -
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Residues in contact with ALA 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848A THR* 3.4 26.7 - - - +
854A ILE* 4.3 4.5 - - - -
855A ARG 3.4 4.7 + - - +
856A LYS* 3.2 19.1 + - - +
857A GLN 3.6 0.2 - - - -
858A ASP* 1.3 77.1 - - - +
860A THR* 1.3 60.0 + - + +
862A THR* 3.1 5.9 + - - -
863A ILE* 3.0 33.4 + - + +
891A TYR* 3.6 27.6 - - + -
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Residues in contact with THR 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856A LYS 4.8 0.8 + - - -
857A GLN 5.4 1.1 + - - -
858A ASP 3.5 0.2 - - - -
859A ALA* 1.3 74.1 - - - +
861A SER* 1.3 60.5 + - - +
863A ILE* 3.3 14.1 + - + +
864A ILE* 2.9 37.8 + - - +
887A LEU* 5.1 0.7 - - + -
891A TYR* 3.9 39.8 + - + +
897A SER* 4.1 20.7 + - - -
898A PHE* 5.8 1.8 - - + -
901A LEU* 4.4 28.9 - - + -
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Residues in contact with SER 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A ARG* 3.2 19.8 + - - -
857A GLN 5.2 3.1 + - - -
858A ASP* 3.7 15.8 - - - -
859A ALA 3.3 0.4 - - - -
860A THR* 1.3 80.8 + - - +
862A THR* 1.3 60.5 + - - +
864A ILE* 3.4 12.5 + - - +
865A SER* 3.1 25.1 + - - -
4B ASP* 6.0 3.1 - - - -
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Residues in contact with THR 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A ARG* 2.9 30.9 + - + +
844A TYR* 3.5 36.6 - - + +
848A THR* 3.5 24.2 - - + -
854A ILE* 4.1 4.7 - - + +
858A ASP 2.8 23.1 + - - -
859A ALA* 3.1 4.7 + - - -
861A SER* 1.3 74.3 - - - +
863A ILE* 1.3 65.3 + - - +
865A SER* 3.1 8.6 + - - -
866A ILE* 3.1 22.1 + - - +
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Residues in contact with ILE 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A LEU* 3.9 16.2 - - + -
848A THR* 3.5 24.0 - - - +
849A LEU* 4.3 16.6 - - + -
859A ALA* 3.0 19.2 + - + +
860A THR* 3.3 21.5 + - + +
862A THR* 1.3 77.2 - - - +
864A ILE* 1.3 55.8 + - - +
866A ILE* 3.2 10.7 + - - +
867A THR* 3.0 26.2 + - - -
876A VAL* 3.6 26.6 - - + +
879A PHE* 4.6 12.1 - - + -
880A VAL* 5.5 0.4 - - + -
887A LEU* 4.6 7.2 - - + -
891A TYR* 5.7 0.7 - - + -
901A LEU* 3.9 15.7 - - + -
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Residues in contact with ILE 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860A THR* 2.9 23.3 + - - +
861A SER* 3.6 12.3 - - - +
863A ILE* 1.3 73.6 - - - +
865A SER* 1.3 65.7 + - - +
867A THR* 3.2 8.9 + - - +
868A ASN* 3.0 42.0 + - - +
897A SER 5.2 1.1 - - - +
900A ASN* 3.7 37.0 - - + +
901A LEU* 3.8 17.0 - - + +
904A ALA* 3.7 24.2 - - + -
907A ARG* 4.6 2.9 - - - +
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Residues in contact with SER 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A ARG* 5.2 1.9 + - - -
830A ALA* 4.3 21.5 - - - +
833A ALA* 3.6 23.7 - - - +
861A SER* 3.1 16.0 + - - -
862A THR* 3.1 12.2 + - - -
864A ILE* 1.3 75.7 - - - +
866A ILE* 1.3 62.6 + - - +
868A ASN* 3.5 18.1 + - - +
869A ASN* 3.6 8.7 + - - +
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Residues in contact with ILE 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A ALA* 3.9 20.6 - - + -
841A LEU* 4.4 13.9 - - + +
844A TYR* 3.8 23.8 - - + -
845A LEU* 3.8 33.2 - - + +
848A THR* 4.2 10.5 - - + -
862A THR 3.1 14.6 + - - +
863A ILE* 3.2 6.9 + - - +
865A SER* 1.3 77.9 - - - +
867A THR* 1.3 62.6 + - - +
869A ASN* 3.1 19.2 + - - +
872A GLY* 3.3 11.3 - - - -
875A LEU* 3.9 19.5 - - + -
876A VAL* 3.6 16.8 - - + -
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Residues in contact with THR 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863A ILE 3.0 11.1 + - - +
864A ILE* 3.4 12.1 - - - +
866A ILE* 1.3 76.2 - - - +
868A ASN* 1.3 61.8 + - - +
869A ASN 3.4 3.8 + - - +
872A GLY 4.0 3.6 - - - -
873A GLN* 3.6 18.9 + - - +
876A VAL* 3.6 32.2 - - + +
901A LEU* 5.9 1.6 - - + -
904A ALA* 3.7 35.7 - - + +
905A VAL* 3.8 15.4 - - + +
908A ARG* 2.9 21.8 + - - -
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Residues in contact with ASN 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A LYS* 4.8 8.0 + - - -
707A LEU* 5.8 2.6 - - - +
864A ILE* 3.0 30.0 + - - +
865A SER* 3.6 10.9 - - - +
866A ILE 3.2 0.2 - - - -
867A THR* 1.3 80.7 - - - +
869A ASN* 1.3 59.8 + - - +
870A VAL 3.6 0.2 + - - -
904A ALA* 4.2 1.6 - - - +
907A ARG* 2.8 36.8 + - - +
908A ARG* 2.9 23.2 + - - +
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Residues in contact with ASN 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A LYS* 6.1 0.2 - - - +
833A ALA 2.9 25.1 + - - +
834A CYS* 3.6 10.1 + - - +
835A SER 2.7 28.8 + - - -
836A LYS* 4.8 1.7 - - - +
841A LEU* 3.7 10.2 - - + +
865A SER 3.6 3.6 + - - +
866A ILE 3.1 13.3 + - - +
867A THR 3.4 3.5 - - - +
868A ASN* 1.3 77.2 - - - +
870A VAL* 1.3 62.3 + - - +
871A ILE* 3.0 18.2 + - - +
872A GLY* 2.7 23.9 + - - +
873A GLN 3.2 8.8 + - - -
908A ARG* 3.9 0.4 - - - -
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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