Contacts of the helix formed by residues 853 - 872 (chain A) in PDB entry 5PYC
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A PHE* 3.6 33.4 - + + -
844A HIS* 2.9 45.6 + + - -
848A TYR* 3.7 35.0 - + + -
851A ASP* 2.8 19.2 + - + +
852A LYS* 1.3 74.9 - - + +
854A THR* 1.3 65.2 + - - +
855A ARG 3.0 3.3 + - - -
856A LEU* 3.0 31.6 + - + +
771B MET 3.8 21.8 - - - -
772B LEU* 3.7 12.8 - - + -
773B PRO* 3.9 20.2 - - + -
825B GLN* 3.8 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 854 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A HIS* 3.6 12.1 + - - -
845A LYS* 3.8 25.8 + - - +
848A TYR* 4.1 10.8 - - - +
849A ARG 3.9 18.4 + - - +
850A GLU 5.2 0.9 - - - -
851A ASP 3.0 22.5 + - - +
852A LYS* 4.1 4.5 - - - +
853A PHE* 1.3 77.9 - - - +
855A ARG* 1.3 68.4 + - + +
857A GLY* 3.0 14.7 + - - -
858A ILE* 3.5 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 855 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A LYS* 3.0 16.1 + - + +
853A PHE 3.0 1.0 + - - -
854A THR* 1.3 83.1 - - + +
856A LEU* 1.3 63.4 + - - +
858A ILE* 3.1 15.6 + - + +
859A GLN* 2.9 52.8 + - + +
823B ASN 4.6 1.6 + - - -
824B GLU* 3.1 38.8 + - - +
825B GLN* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 856 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LYS* 3.7 37.0 - - + +
794A PHE* 3.5 37.5 - - + -
795A PHE* 4.0 10.5 - - + -
844A HIS* 4.2 7.0 - - + +
853A PHE* 3.0 29.2 + - + +
855A ARG* 1.3 78.0 - - - +
857A GLY* 1.3 56.6 + - - +
859A GLN* 3.4 7.8 + - - +
860A VAL* 3.0 34.3 + - - +
825B GLN* 3.8 37.5 - - + +
828B THR* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 857 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A PHE* 3.7 12.1 - - - -
841A PHE* 3.9 16.4 - - - +
844A HIS* 3.6 20.1 - - - -
845A LYS* 5.3 3.4 - - - -
854A THR 3.0 9.2 + - - -
856A LEU* 1.3 79.4 - - - +
858A ILE* 1.3 55.3 + - - +
861A GLN* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 858 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A LYS* 4.2 29.6 - - + +
854A THR* 3.5 22.2 + - + +
855A ARG* 3.1 18.1 + - + +
857A GLY* 1.3 77.8 - - - +
859A GLN* 1.3 59.9 + - + +
861A GLN* 3.8 4.2 - - - +
862A ASP* 3.0 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 859 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LYS* 2.9 45.0 + - + +
855A ARG* 2.9 65.6 + - + +
856A LEU* 3.7 14.4 - - - +
857A GLY 3.3 0.2 - - - -
858A ILE* 1.3 79.0 - - + +
860A VAL* 1.3 64.0 + - - +
862A ASP* 3.3 9.3 + - - +
863A ILE* 3.2 25.8 + - - +
824B GLU 4.7 1.6 + - - -
825B GLN* 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 860 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A VAL* 3.9 22.9 - - + +
789A ASP* 4.8 5.2 - - + +
791A LYS* 3.6 36.3 - - + +
792A SER* 4.3 5.2 - - - +
795A PHE* 3.7 17.5 - - + -
841A PHE* 3.5 28.5 - - + -
856A LEU 3.0 17.1 + - - +
859A GLN* 1.3 74.3 - - - +
861A GLN* 1.3 64.8 + - - +
863A ILE* 3.1 10.6 + - + +
864A PHE* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 861 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A ARG* 3.9 20.9 + - - +
841A PHE* 3.6 38.3 - - + +
842A HIS* 4.9 0.9 + - - -
845A LYS* 4.5 18.4 + - - +
857A GLY 2.9 21.1 + - - +
858A ILE* 3.8 5.2 - - - +
860A VAL* 1.3 75.6 - - - +
862A ASP* 1.3 59.8 + - - +
864A PHE* 3.2 2.9 + - + +
865A GLU* 2.9 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 862 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A ILE* 3.0 35.2 + - - +
859A GLN* 3.6 11.0 - - - +
860A VAL 3.3 0.2 - - - -
861A GLN* 1.3 78.8 - - - +
863A ILE* 1.3 61.7 + - + +
865A GLU* 4.0 5.8 - - - +
866A LYS* 3.0 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A LYS 4.0 17.9 - - - +
786A VAL* 4.4 9.4 - - + -
789A ASP* 3.8 31.9 - - + +
859A GLN 3.2 13.8 + - - +
860A VAL* 3.1 12.4 + - + +
862A ASP* 1.3 73.8 - - + +
864A PHE* 1.3 68.4 + - - +
866A LYS* 4.0 9.6 - - + +
867A ASN* 3.0 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 864 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A LEU* 3.6 39.8 - - + +
786A VAL* 3.9 15.3 - - + +
833A PHE* 4.3 0.7 - + - -
834A VAL* 4.3 19.7 - - + -
837A MET* 3.6 44.2 - - + -
838A ARG* 4.0 20.0 - - + -
841A PHE* 4.0 17.0 - + + -
860A VAL 3.0 12.6 + - - +
861A GLN* 3.4 7.9 - - + +
863A ILE* 1.3 78.8 - - - +
865A GLU* 1.3 85.3 + - + +
867A ASN 3.4 0.2 + - - -
868A PHE* 2.8 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 865 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A ARG* 2.8 45.6 + - - -
861A GLN* 2.9 48.9 + - + +
862A ASP* 4.0 6.3 - - - +
863A ILE 3.4 0.2 - - - -
864A PHE* 1.3 82.0 - - - +
866A LYS* 1.3 66.8 + - - +
868A PHE* 3.3 8.6 + - - +
869A ARG* 3.0 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 866 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A ASP* 3.0 32.8 + - + +
863A ILE* 4.0 11.2 - - + +
865A GLU* 1.3 77.9 - - - +
867A ASN* 1.3 62.5 + - - +
869A ARG* 3.4 26.5 + - - +
870A ASN* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A LEU* 3.6 18.2 - - + -
785A LYS* 3.5 42.6 + - + +
786A VAL* 6.0 0.4 - - + -
863A ILE* 3.0 41.5 + - - +
864A PHE* 4.9 0.2 - - - -
866A LYS* 1.3 80.3 - - - +
868A PHE* 1.4 58.4 + - - +
870A ASN* 4.4 7.2 - - - +
871A ILE* 2.8 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A GLU* 3.7 29.6 - - + -
766A VAL* 4.0 21.1 - - + -
767A LEU* 4.0 15.7 - - + -
782A LEU* 3.6 22.4 - - + +
830A VAL* 4.7 0.7 - - + -
834A VAL* 3.8 23.6 - - + -
838A ARG* 4.3 3.6 - - - -
864A PHE* 2.8 27.3 + + + +
865A GLU* 3.3 20.2 + - - +
867A ASN* 1.4 71.4 - - - +
869A ARG* 1.3 71.0 + - + +
872A PHE* 3.1 53.7 + + - +
874A ILE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A GLU* 3.0 43.1 + - - +
866A LYS* 3.6 33.1 - - - +
868A PHE* 1.3 81.4 - - + +
870A ASN* 1.3 56.9 + - - +
873A ALA* 3.0 8.3 + - - -
874A ILE* 2.9 57.1 + - + +
875A GLN 6.0 0.2 - - - -
876A GLU* 5.0 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 870 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A GLN* 5.4 7.6 + - - -
781A PHE* 5.7 1.4 - - - -
866A LYS 3.1 17.7 + - - +
867A ASN* 3.8 9.9 - - - +
868A PHE 3.3 0.2 - - - -
869A ARG* 1.3 76.3 - - - +
871A ILE* 1.3 74.4 + - + +
873A ALA* 3.2 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ILE* 5.1 5.5 - - + +
751A GLN* 5.2 9.7 + - - +
778A LYS* 3.6 53.8 - - + +
781A PHE* 3.4 38.8 - - + -
782A LEU* 3.7 26.7 - - + -
785A LYS* 4.4 4.3 - - + -
867A ASN* 2.8 35.0 + - + +
868A PHE* 4.2 1.6 - - - +
870A ASN* 1.3 83.4 - - - +
872A PHE* 1.3 67.8 + - + +
873A ALA* 3.7 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A HIS* 3.5 14.1 + - - +
766A VAL* 3.5 30.9 - - + +
769A ARG* 3.9 8.6 + - - +
775A GLU* 3.2 26.7 - - - -
778A LYS* 3.5 37.5 - - + +
779A CYS* 4.1 21.5 - - - -
782A LEU* 4.1 14.6 - - + -
830A VAL* 4.3 8.5 - - + -
834A VAL* 5.8 0.2 - - + -
868A PHE* 3.1 41.0 + + + +
869A ARG 3.9 0.2 - - - -
871A ILE* 1.3 84.2 - - + +
873A ALA* 1.3 72.7 + - - +
874A ILE* 3.3 10.1 + - + +
----------------------------------------------------------
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