Contacts of the helix formed by residues 812 - 825 (chain B) in PDB entry 5JO3
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 LYS 812 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B ASP* 3.8 24.2 - - + +
809B LYS* 3.0 33.6 + - + +
811B ASN* 1.3 94.6 - - - +
813B ILE* 1.3 64.5 + - - +
814B PRO 3.5 0.9 - - - -
815B SER* 3.0 19.9 + - - +
816B MET* 3.0 41.9 + - + +
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Residues in contact with ILE 813 (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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779B ALA* 5.9 2.2 - - + +
783B ALA* 4.0 19.7 - - + -
787B PHE* 3.8 27.6 - - + -
810B LYS* 3.1 23.3 + - + +
812B LYS* 1.3 76.7 - - - +
814B PRO* 1.3 73.9 - - + +
816B MET* 3.1 17.6 + - + +
817B GLN* 2.8 33.5 + - + +
853B TRP* 4.0 22.0 - - + -
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Residues in contact with PRO 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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810B LYS 4.5 1.3 - - - +
811B ASN* 3.7 15.3 - - - +
812B LYS 3.8 0.2 - - - -
813B ILE* 1.3 94.4 - - + +
815B SER* 1.3 61.3 + - - +
817B GLN* 3.3 2.6 + - - +
818B VAL* 3.1 27.9 + - - +
853B TRP* 3.7 40.7 - - + +
856B LEU* 4.0 17.5 - - + +
857B ALA* 3.7 18.2 - - - +
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Residues in contact with SER 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B ASN 5.2 0.6 + - - -
812B LYS* 3.0 32.8 + - - -
814B PRO* 1.3 79.7 - - - +
816B MET* 1.3 57.6 + - - +
818B VAL* 3.4 6.3 + - - +
819B GLY* 3.0 24.1 + - - -
857B ALA* 3.9 16.0 - - - +
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Residues in contact with MET 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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787B PHE* 6.0 0.7 - - + -
803B ASP* 4.0 14.8 - - - +
804B LEU* 3.7 45.5 - - + +
809B LYS 5.1 1.1 - - - +
812B LYS* 3.0 41.9 + - + +
813B ILE* 3.7 17.7 - - + +
815B SER* 1.3 77.6 - - - +
817B GLN* 1.3 60.4 + - + +
819B GLY* 3.3 1.8 + - - +
820B PHE* 2.9 30.3 + - - +
903B 6LK 3.5 35.0 - - + +
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Residues in contact with GLN 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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768B ILE* 3.9 6.2 - - - +
775B GLN* 3.4 24.0 - - - +
779B ALA* 3.8 7.3 - - - +
813B ILE* 2.8 28.3 + - + +
814B PRO 3.6 0.9 - - - +
816B MET* 1.3 73.6 - - + +
818B VAL* 1.3 65.0 + - - +
820B PHE* 3.3 3.4 + - - +
821B ILE* 2.9 30.8 + - + +
853B TRP* 3.6 41.3 - - + +
903B 6LK 3.1 52.4 + - - -
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Residues in contact with VAL 818 (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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814B PRO 3.1 15.8 + - - +
815B SER* 3.7 9.2 - - - +
816B MET 3.3 0.2 - - - -
817B GLN* 1.3 74.6 - - - +
819B GLY* 1.3 58.9 + - - +
821B ILE* 3.3 7.5 + - - +
822B ASP* 2.9 31.1 + - - +
850B ARG* 3.5 40.8 - - + +
853B TRP* 3.7 6.5 - - + -
854B GLN* 3.5 48.2 - - + +
857B ALA* 4.8 0.4 - - + -
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Residues in contact with GLY 819 (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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815B SER 3.0 14.8 + - - -
816B MET* 3.3 3.3 + - - -
817B GLN 3.3 0.2 - - - -
818B VAL* 1.3 77.8 - - - +
820B PHE* 1.3 56.0 + - - +
822B ASP* 3.4 6.6 + - - +
823B ALA* 2.8 33.5 + - - +
903B 6LK 5.8 5.4 - - - -
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Residues in contact with PHE 820 (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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725B LEU* 4.1 9.4 - - + -
765B LEU* 3.9 16.6 - - + -
768B ILE* 4.6 9.2 - - + -
816B MET 2.9 17.9 + - - +
817B GLN* 3.7 3.4 - - - +
818B VAL 3.3 0.2 - - - -
819B GLY* 1.3 74.7 - - - +
821B ILE* 1.3 60.8 + - - +
823B ALA* 4.8 2.0 - - - -
824B ILE* 2.9 70.7 + - + +
825B CYS* 3.4 21.5 + - - -
903B 6LK 3.4 91.0 + + + +
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Residues in contact with ILE 821 (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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768B ILE* 3.6 36.3 - - + -
817B GLN 2.9 21.0 + - - +
818B VAL 3.7 4.0 - - - +
820B PHE* 1.3 74.1 - - - +
822B ASP* 1.3 62.4 + - - +
825B CYS* 3.1 8.8 + - - -
826B LEU* 2.9 48.8 + - + +
846B CYS* 3.8 16.4 - - - +
849B ASN* 4.2 2.5 - - + -
850B ARG* 3.8 48.9 - - + +
853B TRP* 4.1 14.4 - - + -
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Residues in contact with ASP 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B VAL* 2.9 19.3 + - - +
819B GLY* 3.8 5.6 - - - +
821B ILE* 1.3 79.1 - - - +
823B ALA* 1.3 61.0 + - + +
824B ILE 3.7 0.2 + - - -
826B LEU* 3.6 21.1 + - - +
827B GLN* 4.1 12.6 + - - +
850B ARG* 2.7 49.6 + - - -
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Residues in contact with ALA 823 (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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732B ARG* 2.8 32.0 + - - +
819B GLY 2.8 21.0 + - - +
820B PHE* 4.8 0.9 - - - -
822B ASP* 1.3 75.3 - - + +
824B ILE* 1.3 68.4 + - + +
827B GLN* 3.6 5.0 + - - +
903B 6LK 6.4 2.0 - - + -
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Residues in contact with ILE 824 (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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725B LEU* 4.1 12.1 - - + -
728B TYR* 2.6 40.4 + - + -
729B ILE* 3.8 35.7 - - + -
732B ARG* 3.8 5.1 + - - +
765B LEU* 3.6 28.9 - - + -
820B PHE* 2.9 41.8 + - + +
823B ALA* 1.3 91.8 - - + +
825B CYS* 1.3 63.0 + - - +
826B LEU 3.9 0.4 - - - -
827B GLN* 5.0 1.8 - - - -
828B LEU* 3.9 3.6 + - - +
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Residues in contact with CYS 825 (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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765B LEU* 4.3 9.0 - - - -
768B ILE* 3.8 20.9 - - - -
820B PHE* 3.5 39.9 - - - -
821B ILE* 3.1 12.4 + - - +
824B ILE* 1.3 80.7 - - - +
826B LEU* 1.3 68.5 + - - +
827B GLN 3.3 2.0 - - - -
828B LEU* 3.1 5.0 + - - +
829B TYR* 3.0 34.9 + - + -
846B CYS* 3.8 19.7 - - - -
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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