Contacts of the helix formed by residues 851 - 868 (chain B) in PDB entry 5V4R
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 ASN 851 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845B PHE* 4.5 2.2 - - - -
846B LEU* 3.7 6.9 - - - +
849B HIS 3.4 5.8 + - - +
850B PHE* 1.3 83.1 - - - +
852B LYS* 1.3 65.0 + - - +
853B LYS* 3.3 10.7 + - - +
854B MET* 2.8 66.0 + - - +
855B TYR* 3.1 19.4 + - - +
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Residues in contact with LYS 852 (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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850B PHE* 4.0 19.1 - - + -
851B ASN* 1.3 72.4 - - - +
853B LYS* 1.3 66.1 + - - +
855B TYR* 3.2 5.0 + - + -
856B GLU* 2.9 70.2 + - + +
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Residues in contact with LYS 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851B ASN* 3.3 8.8 + - - +
852B LYS* 1.3 82.0 - - - +
854B MET* 1.3 63.5 + - + +
856B GLU* 3.6 3.4 + - - +
857B GLU* 3.3 22.7 + - - +
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Residues in contact with MET 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B PHE* 3.8 27.6 - - + -
810B GLN* 5.4 2.2 - - - +
813B TYR* 3.5 45.8 - - + +
841B PHE* 4.3 0.7 - - + -
842B TRP* 3.9 24.7 - - + +
845B PHE* 3.8 22.4 - - + -
846B LEU* 3.9 8.3 - - + -
851B ASN* 2.8 42.4 + - - +
853B LYS* 1.3 72.8 - - + +
855B TYR* 1.3 58.6 + - - +
857B GLU* 3.3 5.8 + - - +
858B PHE* 2.8 32.0 + - - +
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Residues in contact with TYR 855 (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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846B LEU* 3.8 16.1 - - + +
850B PHE* 3.6 19.1 - + + -
851B ASN 3.1 18.3 + - - +
852B LYS* 3.8 3.6 - - + +
854B MET* 1.3 77.0 - - - +
856B GLU* 1.3 81.2 + - + +
858B PHE* 3.3 2.8 - + - +
859B LYS* 2.9 37.1 + - + +
877B LEU* 4.2 9.4 - - + -
880B TYR* 3.9 22.0 - + - -
881B TYR* 2.7 41.8 + + - -
893B ILE* 3.7 19.0 - - + +
896B ASP* 2.6 34.8 + - - +
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Residues in contact with GLU 856 (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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852B LYS* 2.9 60.0 + - + +
853B LYS* 4.1 3.4 - - - +
855B TYR* 1.3 92.8 - - - +
857B GLU* 1.3 56.7 + - - +
859B LYS* 3.5 18.5 + - - +
860B GLN* 3.0 30.0 + - - +
896B ASP* 4.9 2.3 - - - +
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Residues in contact with GLU 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B TYR* 4.4 1.7 + - - -
817B ARG* 2.7 46.0 + - - -
821B LEU* 3.7 10.8 - - - +
842B TRP* 3.6 25.9 - - + -
853B LYS 3.3 16.2 + - - +
854B MET* 3.8 3.9 - - - +
856B GLU* 1.3 76.3 - - - +
858B PHE* 1.3 65.3 + - - +
860B GLN* 4.4 4.5 - - + -
861B LEU* 2.9 39.6 + - + +
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Residues in contact with PHE 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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839B PHE* 3.8 26.0 - + - -
842B TRP* 3.5 31.9 - + + -
843B SER* 3.9 17.7 - - - -
846B LEU* 3.6 20.0 - - + -
854B MET 2.8 22.2 + - - +
855B TYR* 3.3 8.1 - + - +
857B GLU* 1.3 72.4 - - - +
859B LYS* 1.3 57.0 + - - +
861B LEU* 4.0 0.2 - - - -
862B ALA* 2.9 26.9 + - + +
873B GLY 3.7 17.7 - - - -
876B CYS* 3.6 10.5 - - + -
877B LEU* 3.4 47.1 - - + -
880B TYR* 4.1 8.5 - + + -
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Residues in contact with LYS 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B TYR* 2.9 38.1 + - + +
856B GLU* 3.9 20.5 + - - +
858B PHE* 1.3 73.5 - - - +
860B GLN* 1.3 63.9 + - - +
862B ALA* 3.4 1.2 + - - +
863B LEU* 3.0 44.0 + - + +
877B LEU* 4.0 26.9 - - + -
881B TYR* 3.6 8.3 - - - +
896B ASP* 2.9 30.2 + - - +
899B GLU* 5.3 4.0 + - - -
900B GLU* 3.9 17.2 + - - +
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Residues in contact with GLN 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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856B GLU 3.0 18.6 + - - +
857B GLU* 3.8 6.1 - - + +
859B LYS* 1.3 78.2 - - - +
861B LEU* 1.3 62.4 + - + +
863B LEU* 3.3 10.2 + - - +
864B GLU* 2.9 63.5 + - - +
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Residues in contact with LEU 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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821B LEU* 3.7 29.6 - - + -
824B ARG* 3.8 16.2 - - - +
835B MET* 3.7 17.0 - - + -
839B PHE* 3.8 15.5 - - + -
842B TRP* 4.1 4.3 - - + -
857B GLU* 2.9 36.7 + - + +
860B GLN* 1.3 76.9 - - + +
862B ALA* 1.3 67.9 + - - +
864B GLU* 3.2 27.9 + - - +
865B ASP* 3.0 28.2 + - - +
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Residues in contact with ALA 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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839B PHE* 3.6 13.1 - - + -
858B PHE* 2.9 21.0 + - + +
859B LYS* 3.8 5.6 - - - +
861B LEU* 1.3 76.1 - - - +
863B LEU* 1.3 58.2 + - - +
865B ASP* 3.5 3.0 + - - +
866B ALA* 3.0 27.9 + - - +
873B GLY* 3.4 32.1 - - - +
874B LEU* 3.7 11.2 + - + +
877B LEU* 4.5 9.6 - - + -
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Residues in contact with LEU 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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859B LYS* 3.0 38.7 + - + +
860B GLN* 3.7 9.4 - - - +
862B ALA* 1.3 73.2 - - - +
864B GLU* 1.3 60.8 + - - +
866B ALA* 3.3 4.2 + - + +
867B LYS* 2.9 29.8 + - - +
874B LEU* 4.0 24.9 - - + -
877B LEU* 5.4 0.4 - - + -
900B GLU* 3.5 24.0 - - + +
903B LYS* 3.7 24.2 - - - +
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Residues in contact with GLU 864 (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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824B ARG* 3.1 22.9 + - - +
829B ILE* 4.3 19.0 - - + +
860B GLN* 2.9 44.4 + - - +
861B LEU* 3.2 23.3 + - - +
863B LEU* 1.3 75.7 - - - +
865B ASP* 1.3 63.5 + - - +
867B LYS* 3.3 18.1 + - - +
868B GLU* 3.6 7.1 + - - +
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Residues in contact with ASP 865 (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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824B ARG* 2.7 43.3 + - - -
829B ILE* 3.2 17.7 - - - +
830B GLY* 4.1 11.9 + - - -
835B MET* 5.1 1.0 - - - +
836B ASN* 4.9 4.2 - - - +
839B PHE* 3.3 24.6 - - + -
861B LEU 3.0 14.2 + - - +
862B ALA* 3.8 4.5 - - - +
864B GLU* 1.3 74.9 - - - +
866B ALA* 1.3 63.5 + - - +
868B GLU* 2.9 15.8 + - - +
869B GLY 3.3 0.2 + - - -
870B TYR* 3.1 33.1 + - + +
873B GLY 5.1 4.0 + - - +
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Residues in contact with ALA 866 (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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862B ALA 3.0 17.6 + - - +
863B LEU* 3.3 8.2 + - + +
865B ASP* 1.3 75.4 - - - +
867B LYS* 1.3 62.6 + - - +
869B GLY* 2.9 14.3 + - - -
870B TYR 3.2 14.7 + - - +
871B ARG* 4.5 10.7 + - - +
874B LEU* 3.8 30.3 - - + -
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Residues in contact with LYS 867 (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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863B LEU 2.9 14.4 + - - +
864B GLU* 3.4 13.5 - - - +
865B ASP 3.2 0.6 - - - -
866B ALA* 1.3 76.3 - - - +
868B GLU* 1.3 62.7 + - + +
869B GLY 3.7 0.2 + - - -
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Residues in contact with GLU 868 (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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829B ILE* 3.7 33.4 - - + +
864B GLU 3.6 7.4 + - - +
865B ASP 2.9 9.7 + - - +
867B LYS* 1.3 81.6 - - + +
869B GLY* 1.3 59.6 + - - +
870B TYR* 3.5 30.7 + - + -
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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