Contacts of the strand formed by residues 813 - 817 (chain B) in PDB entry 5J67
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 TYR 813 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723B PHE* 4.6 3.6 - + + -
753B ILE* 4.1 12.1 - - + -
754B LYS* 3.2 35.5 + - - +
756B PHE* 3.4 22.9 - + - -
765B VAL* 3.6 30.1 - - + -
766B ILE 3.8 4.0 - - - +
767B PRO* 3.8 24.7 - - + -
768B LEU* 3.7 4.9 - - - -
811B ASN* 3.1 41.3 + - - -
812B LEU* 1.3 71.8 - - - +
814B ARG* 1.3 59.5 - - - +
815B VAL* 3.8 6.2 + - + +
858B LEU* 3.6 1.8 - - - +
859B TYR* 2.8 37.3 + - + +
951B PRO* 3.6 28.5 - - + -
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Residues in contact with ARG 814 (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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764B LEU 3.5 3.6 - - - +
765B VAL* 3.7 0.3 - - - -
766B ILE* 2.9 42.3 + - + +
768B LEU* 3.3 24.5 - - + +
813B TYR* 1.3 70.8 - - - +
815B VAL* 1.3 58.0 + - - +
816B LYS* 4.0 22.0 + - - +
856B GLU* 3.6 27.7 + - + +
857B ALA 3.6 7.0 + - - -
858B LEU* 3.9 27.9 - - - +
955B GLU* 4.9 2.4 + - - -
957B ASN* 3.3 28.8 + - - +
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Residues in contact with VAL 815 (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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723B PHE* 3.8 30.3 - - + +
726B MET* 3.3 32.7 - - + +
763B LEU* 4.6 10.1 - - + -
764B LEU 3.6 5.2 - - - +
765B VAL* 4.4 11.2 - - + -
813B TYR 4.0 7.2 - - - +
814B ARG* 1.3 78.0 - - - +
816B LYS* 1.3 68.7 + - - +
856B GLU* 3.5 0.7 - - - -
857B ALA 2.7 41.7 + - - +
859B TYR* 3.5 27.8 - - + -
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Residues in contact with LYS 816 (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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726B MET* 4.2 2.2 - - - -
763B LEU* 3.5 3.3 - - - +
764B LEU* 2.7 50.2 + - + +
766B ILE* 3.5 29.9 - - - +
814B ARG* 4.0 16.9 + - - +
815B VAL* 1.3 77.2 - - - +
817B LEU* 1.3 58.8 + - - +
818B SER* 4.2 2.2 - - - -
855B ALA 3.4 8.5 - - - +
856B GLU* 3.4 39.5 - - + +
958B ARG* 6.0 3.1 - - - +
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Residues in contact with LEU 817 (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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726B MET* 3.5 35.2 - - + +
727B LEU* 4.2 2.0 - - + -
743B PHE* 3.6 27.1 - - + -
762B GLY 3.6 3.6 - - - +
763B LEU* 4.1 7.2 - - + +
816B LYS* 1.3 75.1 - - - +
818B SER* 1.3 64.6 + - - +
820B ILE* 3.9 26.2 - - + -
853B TYR* 4.3 11.9 - - + -
854B ILE 3.2 22.0 - - - +
855B ALA* 3.4 16.1 + - + +
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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