Contacts of the helix formed by residues 853 - 872 (chain B) in PDB entry 5PXU
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 PHE 853 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B PHE* 3.6 42.0 - + + -
844B HIS* 3.0 26.3 + + - -
848B TYR* 3.5 52.5 - + + -
851B ASP* 2.9 18.6 + - - +
852B LYS* 1.3 74.5 - - + +
854B THR* 1.3 67.0 + - - +
855B ARG 2.9 3.0 + - - -
856B LEU* 3.0 40.5 + - + +
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Residues in contact with THR 854 (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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844B HIS* 3.6 11.0 - - - -
845B LYS* 3.6 33.6 + - - +
848B TYR* 3.9 10.4 - - - +
849B ARG 3.8 16.1 + - - +
850B GLU 5.6 0.7 - - - +
851B ASP 3.0 18.8 + - - +
852B LYS* 4.5 3.1 - - - +
853B PHE* 1.3 77.0 - - - +
855B ARG* 1.3 68.0 + - + +
857B GLY* 3.0 15.1 + - - -
858B ILE* 3.5 22.5 + - + +
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Residues in contact with ARG 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B LYS* 5.4 1.6 - - - +
852B LYS* 3.0 17.2 + - - +
853B PHE 2.9 1.2 + - - -
854B THR* 1.3 82.8 - - + +
856B LEU* 1.3 67.3 + - + +
858B ILE* 3.3 15.0 + - + +
859B GLN* 2.9 57.4 + - + +
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Residues in contact with LEU 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B LYS* 3.6 47.6 - - + +
794B PHE* 3.6 18.8 - - + -
795B PHE* 4.0 11.4 - - + -
844B HIS* 4.3 4.9 - - + +
852B LYS 4.9 2.5 - - - +
853B PHE* 3.0 48.5 + - + +
855B ARG* 1.3 80.5 - - + +
857B GLY* 1.3 56.5 - - - +
859B GLN* 3.2 8.0 + - - +
860B VAL* 3.0 35.2 + - - +
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Residues in contact with GLY 857 (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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795B PHE* 3.6 12.8 - - - -
841B PHE* 3.6 13.4 - - - -
844B HIS* 3.5 21.3 + - - -
845B LYS* 6.5 0.2 - - - -
854B THR 3.0 9.4 + - - -
856B LEU* 1.3 77.1 - - - +
858B ILE* 1.3 57.0 + - - +
861B GLN* 3.0 32.0 + - - +
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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
----------------------------------------------------------
845B LYS* 5.9 9.6 - - + -
854B THR* 3.5 26.6 + - + +
855B ARG* 3.3 18.9 + - + +
857B GLY* 1.3 76.9 - - - +
859B GLN* 1.3 62.3 + - + +
861B GLN* 4.0 4.6 - - - +
862B ASP* 2.8 41.2 + - - +
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Residues in contact with GLN 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B LYS* 2.8 43.4 + - + +
855B ARG* 2.9 62.9 + - + +
856B LEU* 3.2 18.2 + - - +
858B ILE* 1.3 79.8 - - + +
860B VAL* 1.3 61.8 + - - +
862B ASP* 3.4 7.1 + - - +
863B ILE* 3.4 23.9 + - - +
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Residues in contact with VAL 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B VAL* 3.8 22.0 - - + +
789B ASP* 4.8 5.4 - - + +
791B LYS* 3.6 34.8 - - + -
792B SER* 4.4 5.6 - - - +
795B PHE* 3.7 19.3 - - + -
841B PHE* 3.5 27.6 - - + -
856B LEU 3.0 15.7 + - - +
859B GLN* 1.3 73.7 - - - +
861B GLN* 1.3 66.8 + - - +
863B ILE* 3.2 12.1 + - + +
864B PHE* 3.0 20.3 + - - +
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Residues in contact with GLN 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B ARG* 3.9 20.0 - - - +
841B PHE* 3.3 42.0 - - + +
842B HIS 4.9 0.7 + - - -
857B GLY 3.0 21.6 + - - +
858B ILE* 4.0 4.9 - - - +
860B VAL* 1.3 75.9 - - - +
862B ASP* 1.3 58.2 + - - +
864B PHE* 3.1 4.3 + - + +
865B GLU* 2.8 55.8 + - + +
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Residues in contact with ASP 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858B ILE* 2.8 39.0 + - - +
859B GLN* 3.8 7.0 - - - +
860B VAL 3.2 0.2 - - - -
861B GLN* 1.3 75.0 - - - +
863B ILE* 1.3 61.5 + - + +
865B GLU* 3.9 7.1 - - - +
866B LYS* 2.9 54.2 + - + +
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Residues in contact with ILE 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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785B LYS 4.1 17.0 - - - +
786B VAL* 4.3 11.4 - - + -
789B ASP* 3.8 28.7 - - + +
859B GLN 3.4 15.5 + - - +
860B VAL* 3.2 13.4 + - + +
862B ASP* 1.3 73.1 - - + +
864B PHE* 1.3 68.8 + - - +
866B LYS* 4.8 9.0 - - + -
867B ASN* 2.8 45.1 + - - +
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Residues in contact with PHE 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B LEU* 3.5 40.8 - - + +
786B VAL* 3.8 15.9 - - + -
833B PHE* 4.2 1.3 - + - -
834B VAL* 4.2 19.1 - - + -
837B MET* 3.8 44.4 - - + -
838B ARG* 4.2 19.3 - - + -
841B PHE* 4.2 14.6 - + + -
860B VAL 3.0 12.7 + - - +
861B GLN* 3.4 8.7 - - + +
863B ILE* 1.3 76.4 - - - +
865B GLU* 1.3 91.0 + - + +
868B PHE* 2.9 36.4 + - + +
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Residues in contact with GLU 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B ARG* 2.9 44.8 + - - -
861B GLN* 2.8 45.7 + - + +
862B ASP* 4.0 7.4 - - - +
863B ILE 3.2 0.2 - - - -
864B PHE* 1.3 86.7 - - + +
866B LYS* 1.3 62.1 + - - +
868B PHE* 3.3 12.5 + - - +
869B ARG* 3.1 47.3 + - - +
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Residues in contact with LYS 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B ASP* 2.9 38.3 + - + +
863B ILE* 4.0 11.0 - - + +
865B GLU* 1.3 76.9 - - - +
867B ASN* 1.3 60.9 + - - +
869B ARG* 3.7 25.3 + - - +
870B ASN* 3.0 27.2 + - - +
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Residues in contact with ASN 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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782B LEU* 3.6 19.1 - - + -
785B LYS* 2.8 45.9 + - + +
863B ILE* 2.8 44.2 + - - +
864B PHE* 5.1 0.2 - - - +
866B LYS* 1.3 76.4 - - - +
868B PHE* 1.3 59.5 + - - +
870B ASN* 4.2 8.1 - - - +
871B ILE* 2.8 43.1 + - + +
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Residues in contact with PHE 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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763B GLU* 3.9 29.6 - - + -
766B VAL* 3.9 19.7 - - + -
767B LEU* 4.0 22.2 - - + -
782B LEU* 3.5 24.5 - - + +
830B VAL* 4.4 1.8 - - + -
834B VAL* 3.9 16.2 - - + -
838B ARG* 4.0 6.5 - - - -
864B PHE* 2.9 26.0 + + + +
865B GLU* 3.3 22.0 + - - +
867B ASN* 1.3 75.3 - - - +
869B ARG* 1.3 69.0 + - + +
872B PHE* 3.1 54.8 + + + +
874B ILE* 4.4 10.1 - - + -
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Residues in contact with ARG 869 (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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865B GLU* 3.1 40.8 + - - +
866B LYS* 3.8 30.4 - - - +
868B PHE* 1.3 79.8 - - + +
870B ASN* 1.3 63.6 + - - +
873B ALA* 3.0 19.1 + - - -
874B ILE* 3.1 48.1 + - + +
875B GLN 4.8 7.0 - - - -
876B GLU* 6.2 1.1 - - - +
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Residues in contact with ASN 870 (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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751B GLN* 5.1 9.4 + - - -
758B GLN* 6.0 0.5 - - - +
866B LYS 3.0 20.5 + - - +
867B ASN* 3.7 9.2 - - - +
869B ARG* 1.3 80.4 - - - +
871B ILE* 1.3 72.5 + - + +
873B ALA* 3.4 9.2 + - - +
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Residues in contact with ILE 871 (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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747B ILE* 5.2 4.7 - - + -
751B GLN* 4.7 14.4 + - - +
778B LYS* 3.8 50.1 + - + +
781B PHE* 3.5 36.3 - - + -
782B LEU* 3.7 28.9 - - + +
785B LYS* 4.5 2.9 - - + -
867B ASN* 2.8 35.1 + - + +
868B PHE* 5.0 0.2 - - - -
870B ASN* 1.3 83.0 - - - +
872B PHE* 1.3 68.2 + - + +
873B ALA* 3.4 1.4 + - - +
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Residues in contact with PHE 872 (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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761B HIS* 4.0 7.6 + - - -
766B VAL* 3.4 40.2 - - + +
769B ARG* 4.2 14.1 + - - +
775B GLU* 3.4 26.5 - - - -
778B LYS* 3.7 27.6 - - + +
779B CYS* 4.0 21.5 - - - -
782B LEU* 4.2 12.6 - - + -
830B VAL* 4.0 17.3 - - + -
868B PHE* 3.1 41.1 + + + +
871B ILE* 1.3 90.9 - - + +
873B ALA* 1.3 69.6 + - - +
874B ILE* 3.3 6.8 + - + -
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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
------------------------------------------------------------
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