Contacts of the helix formed by residues 857 - 877 (chain B) in PDB entry 5XA0
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 857 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B PHE 3.4 11.3 + - - +
855B SER 2.7 4.9 + - - -
856B ASP* 1.3 72.7 - - - +
858B GLU* 1.3 51.1 - - + +
861B LYS* 2.2 40.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B LYS* 2.8 38.2 - - + +
855B SER* 2.7 11.2 + - - +
857B LYS* 1.3 74.4 - - + +
859B LYS* 1.3 58.4 + - - +
862B LEU* 2.9 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 859 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B ASP* 6.3 3.1 - - + -
852B PHE* 5.5 2.9 - - + -
855B SER* 2.6 35.6 + - - +
856B ASP* 4.2 1.1 - - - +
858B GLU* 1.3 70.7 - - - +
860B ASN* 1.3 60.5 + - - +
862B LEU* 3.4 5.0 + - - +
863B THR* 2.8 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 860 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B ASP* 2.3 52.9 + - + +
859B LYS* 1.3 73.2 - - - +
861B LYS* 1.3 67.0 + - - +
863B THR* 3.6 6.5 - - - -
864B PHE* 2.8 23.2 + - - +
969B ASP* 6.3 2.2 - - + -
973B LYS* 5.5 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 861 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B LYS 3.7 6.3 - - - +
725B GLU* 2.6 32.6 - - + +
856B ASP 2.8 8.9 + - - -
857B LYS 2.2 30.1 - - - +
858B GLU 3.7 1.1 - - - +
860B ASN* 1.3 77.2 - - - +
862B LEU* 1.3 57.7 + - - +
864B PHE* 2.8 18.7 + - - +
865B GLU 3.1 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 862 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B GLN 5.0 2.0 - - - +
724B LYS* 4.0 4.5 - - - -
725B GLU* 3.0 23.4 - - - +
728B ASP* 4.1 1.9 - - - +
858B GLU 2.9 23.9 + - - +
859B LYS* 3.8 5.6 - - - +
861B LYS* 1.3 69.8 - - - +
863B THR* 1.3 56.1 + - - +
865B GLU 4.0 0.2 - - - -
866B VAL* 2.8 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 863 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B TYR* 6.5 0.9 - - - -
859B LYS 2.8 18.5 + - - -
860B ASN* 3.8 6.7 - - - -
861B LYS 3.0 0.2 - - - -
862B LEU* 1.3 76.1 - - - +
864B PHE* 1.3 61.3 + - - +
865B GLU 3.3 0.4 - - - -
866B VAL* 4.5 1.1 - - - -
867B VAL* 2.3 48.1 + - - +
973B LYS* 6.4 2.5 - - - -
976B GLU* 3.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 864 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B ASN 2.8 17.9 + - - +
861B LYS* 3.5 5.4 - - - +
863B THR* 1.3 77.8 - - - +
865B GLU* 1.3 50.0 + - - +
868B ASN* 2.3 42.0 + - - +
972B LEU* 6.0 6.7 - - + +
973B LYS* 6.0 5.8 - - - +
976B GLU* 4.6 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 865 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B GLU 3.6 25.8 - - - +
728B ASP* 3.0 19.4 - - + +
729B ILE* 3.3 22.9 + - + +
861B LYS 3.1 6.3 + - - +
862B LEU 4.3 0.9 - - - +
864B PHE* 1.3 76.4 - - - +
866B VAL* 1.3 61.8 + - - +
868B ASN* 3.7 2.3 - - - +
869B LEU* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 866 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B ASP* 2.7 20.5 - - + +
836B THR* 6.4 2.5 - - - -
862B LEU* 2.8 23.9 + - + +
863B THR* 4.5 1.1 - - - -
865B GLU* 1.3 68.3 - - - +
867B VAL* 1.3 67.1 + - - +
869B LEU* 3.0 7.2 + - - +
870B ALA* 2.8 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 867 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B THR* 2.3 41.4 + - - +
866B VAL* 1.3 74.8 - - - +
868B ASN* 1.3 63.5 + - - +
870B ALA* 2.7 24.1 + - - +
871B ARG* 3.4 4.2 + - - +
976B GLU* 3.4 29.5 - - + +
977B ILE* 4.6 2.7 - - - +
980B PHE* 4.6 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 868 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B THR 3.4 0.2 + - - -
864B PHE* 2.3 32.6 + - - +
865B GLU* 3.7 3.8 - - - +
867B VAL* 1.3 79.8 - - - +
869B LEU* 1.3 61.9 + - - +
870B ALA 3.1 0.2 + - - -
871B ARG* 3.4 15.5 + - - +
872B ASN* 4.2 3.3 + - - +
976B GLU* 3.8 13.7 - - + +
979B GLN* 5.2 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 869 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B ASP* 4.1 5.8 - - + +
729B ILE* 5.7 0.2 - - - -
732B TYR* 3.2 34.3 - - + +
865B GLU 2.8 21.7 + - - +
866B VAL* 3.4 6.1 - - - +
868B ASN* 1.3 73.0 - - - +
870B ALA* 1.3 62.2 + - - +
871B ARG 3.4 0.2 - - - -
872B ASN* 3.8 7.0 + - - +
873B LEU* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 870 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866B VAL 2.8 11.4 + - - +
867B VAL* 2.7 24.8 + - - +
869B LEU* 1.3 71.9 - - - +
871B ARG* 1.3 62.2 + - - +
873B LEU* 3.1 6.6 + - - +
874B ILE* 2.9 27.0 + - - +
980B PHE* 4.6 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 871 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B VAL 3.4 2.2 + - - +
868B ASN 3.4 9.0 + - - +
870B ALA* 1.3 79.5 - - - +
872B ASN* 1.3 63.3 + - - +
874B ILE* 3.6 6.2 + - - +
875B TYR* 3.7 3.8 + - - +
979B GLN* 3.2 48.0 - - + +
980B PHE* 3.3 12.4 - - - +
983B ASN* 3.4 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 872 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868B ASN 4.2 2.7 + - - +
869B LEU* 3.8 8.6 + - - +
871B ARG* 1.3 74.7 - - - +
873B LEU* 1.4 68.4 + - - +
875B TYR* 2.9 18.9 + - - +
876B PHE* 3.1 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 873 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B LEU 3.1 18.7 + - - +
870B ALA* 3.1 8.7 + - - +
872B ASN* 1.4 77.6 - - - +
874B ILE* 1.3 63.0 + - - +
876B PHE* 4.2 4.7 - - - +
877B GLY* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 874 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B ALA 2.9 16.1 + - - +
871B ARG* 3.9 6.7 - - - +
872B ASN 3.1 0.4 - - - -
873B LEU* 1.3 76.5 - - - +
875B TYR* 1.3 62.2 + - - +
877B GLY 3.3 16.1 - - - +
878B PHE* 3.6 15.0 - - - +
980B PHE* 5.2 0.7 - - - +
983B ASN 5.7 0.9 - - - -
984B VAL* 4.1 31.9 - - + +
988B TYR* 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 875 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B ALA* 3.9 9.0 - - - +
742B ARG* 4.4 19.8 - - - +
743B MET* 4.5 12.8 + - + +
871B ARG 3.7 7.6 + - - +
872B ASN* 2.9 10.1 + - - +
874B ILE* 1.3 80.9 - - - +
876B PHE* 1.3 63.1 + - - +
877B GLY* 3.6 0.7 + - - -
878B PHE* 5.1 1.7 + - - +
983B ASN* 4.8 14.3 - - + +
988B TYR* 5.8 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 876 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739B LEU* 5.4 12.3 - - + -
740B PHE 5.7 0.4 - - - +
741B ALA* 3.0 41.0 + - - +
825B SER* 5.3 2.6 - - - -
872B ASN 3.1 13.9 + - - +
873B LEU* 4.2 5.4 - - - +
875B TYR* 1.3 77.3 - - - +
877B GLY* 1.3 57.2 + - - +
878B PHE 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 877 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B SER* 3.5 25.5 + - - -
826B LYS* 4.7 6.5 - - - +
873B LEU 3.0 16.3 + - - +
874B ILE* 3.3 10.5 - - - +
876B PHE* 1.3 77.9 - - - +
878B PHE* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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