Contacts of the strand formed by residues 857 - 863 (chain B) in PDB entry 5M64
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 PRO 857 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836B TRP* 4.2 29.2 - - + +
839B LYS* 3.3 29.1 - - + +
840B LEU* 3.3 19.8 - - + +
855B GLY 4.4 3.6 - - - +
856B ASP* 1.3 90.7 - - - +
858B ILE* 1.3 61.2 + - - +
860B ALA* 4.8 3.1 - - + -
871B ILE* 3.6 39.5 - - + -
872B LYS 4.2 0.4 - - - +
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Residues in contact with ILE 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809B VAL* 5.8 4.5 - - + -
839B LYS* 4.5 13.7 - - - +
840B LEU* 3.2 20.6 - - - +
844B GLY 4.3 0.7 - - - +
846B PRO* 3.8 13.7 - - + +
852B VAL* 3.9 15.5 - - + -
856B ASP 3.1 27.3 + - - +
857B PRO* 1.3 76.1 - - - +
859B CYS* 1.3 66.1 + - + +
860B ALA 3.9 1.1 - - - -
872B LYS 3.2 9.4 + - - +
873B THR* 4.0 1.6 - - - -
874B TYR* 3.6 32.3 - - + +
882B ILE* 5.9 0.4 - - + -
903B ILE* 4.4 20.0 - - + -
905B TYR* 3.7 28.5 - - + +
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Residues in contact with CYS 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809B VAL* 3.6 42.4 - - + -
811B LEU* 5.0 0.7 - - - -
825B PHE* 4.8 15.7 - - - -
844B GLY 4.5 8.5 - - - -
845B LEU* 6.6 0.2 - - - -
858B ILE* 1.3 80.4 - - + +
860B ALA* 1.3 57.5 + - - +
861B TYR* 3.4 30.1 - - - -
871B ILE* 4.6 0.4 - - - -
872B LYS* 3.0 36.1 + - + +
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Residues in contact with ALA 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826B GLY 3.6 9.8 - - - +
827B PHE* 4.2 21.9 - - + -
836B TRP* 5.2 4.0 - - - +
840B LEU* 4.2 22.8 - - + +
844B GLY* 3.7 20.5 + - - -
857B PRO* 4.8 0.9 - - + -
858B ILE 3.9 2.8 + - - +
859B CYS* 1.3 70.8 - - - +
861B TYR* 1.3 59.6 + - - +
869B THR* 5.6 1.3 - - - -
870B LYS 3.4 7.9 - - - +
871B ILE* 3.7 26.7 - - + -
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Residues in contact with TYR 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810B ASP 6.0 0.4 - - - -
811B LEU* 5.2 10.3 - - + -
823B GLN* 3.7 22.0 - - + -
824B HIS 3.4 13.5 - - - +
825B PHE* 4.3 9.4 - - + -
826B GLY 3.2 7.9 - - - +
859B CYS* 3.4 27.8 - - - -
860B ALA* 1.3 73.0 - - - +
862B PHE* 1.3 64.9 + - - +
863B ASP* 3.1 28.9 - - - -
869B THR* 3.3 4.5 - - - -
870B LYS* 3.1 56.6 + - + +
872B LYS* 3.5 40.3 - - + +
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Residues in contact with PHE 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B GLN* 3.4 2.9 - - - -
824B HIS* 2.8 50.2 + + + +
826B GLY 2.8 15.2 + - - +
827B PHE 3.8 9.6 - - - +
828B GLY* 3.6 20.2 - - - -
829B ASN* 4.2 12.6 - - - -
830B ASP* 3.5 16.6 - - - -
861B TYR* 1.3 75.1 - - - +
863B ASP* 1.3 87.5 + - - +
864B ASP* 5.1 0.7 - - - -
867B ASN* 3.5 24.9 - - + -
868B LYS 3.3 31.6 - - - -
869B THR* 3.6 11.7 - - + -
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Residues in contact with ASP 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822B THR 3.8 4.7 - - - +
823B GLN* 3.8 6.9 - - + +
824B HIS* 4.9 0.9 - - - -
861B TYR* 3.1 31.0 - - - -
862B PHE* 1.3 96.6 - - - +
864B ASP* 1.3 61.3 + - - +
865B THR* 4.3 7.9 - - + +
866B LEU* 4.3 8.3 - - + +
867B ASN* 3.3 21.8 - - - +
868B LYS* 2.9 21.3 + - - +
870B LYS* 2.3 41.9 + - - +
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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