Contacts of the helix formed by residues 829 - 848 (chain A) in PDB entry 5FB0
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 ARG 829 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A LEU 4.0 7.4 - - - +
768A MET* 2.8 44.5 + - - +
769A ARG 3.2 16.8 - - - +
770A GLN* 3.6 26.5 + - + +
771A MET* 3.6 16.9 - - - +
827A TYR* 3.8 6.8 - - - +
828A THR* 1.3 89.6 + - - +
830A VAL* 1.3 66.8 + - - +
831A GLU* 3.1 19.1 - - + +
832A GLY* 3.3 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 830 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A VAL* 3.8 23.6 - - + +
767A LEU* 3.9 6.3 + - + +
769A ARG 3.0 15.3 + - - +
770A GLN 4.9 0.2 - - - +
771A MET* 3.8 12.1 - - - -
775A GLU* 3.9 31.4 - - + -
779A CYS* 3.7 20.6 - - - -
829A ARG* 1.3 72.5 - - - +
831A GLU* 1.3 63.4 + - - +
833A PHE* 3.0 14.6 + - - +
834A VAL* 3.0 27.9 + - + +
868A PHE* 4.9 0.2 - - + -
872A PHE* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 831 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A LEU* 3.4 37.6 + - + +
768A MET* 6.3 3.6 - - - -
829A ARG* 4.1 21.8 - - + +
830A VAL* 1.3 79.4 - - - +
832A GLY* 1.3 59.9 + - - +
834A VAL* 4.2 0.2 - - - +
835A GLN* 2.9 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 832 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A TYR* 3.4 28.1 - - - -
829A ARG 3.3 5.3 + - - +
830A VAL 3.1 1.6 + - - -
831A GLU* 1.3 85.8 - - - +
833A PHE* 1.3 56.5 + - - +
835A GLN* 3.3 7.3 + - - +
836A ASP* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A MET* 3.8 17.7 - - + -
779A CYS* 3.6 40.2 - - + -
782A LEU* 3.5 32.5 - - + -
783A LEU* 3.8 22.0 - - + -
818A VAL* 3.5 25.4 - - + -
822A LEU* 4.1 13.5 - - + -
827A TYR* 3.5 20.1 - + + -
829A ARG 4.1 0.4 + - - -
830A VAL 3.0 7.1 + - - +
832A GLY* 1.3 72.5 - - - +
834A VAL* 1.3 74.2 + - + +
835A GLN 3.1 0.2 + - - -
836A ASP* 3.1 2.8 + - - +
837A MET* 3.0 47.4 + - + +
864A PHE* 4.1 6.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 834 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A LEU* 3.6 23.3 - - + -
782A LEU* 5.3 0.2 - - + -
830A VAL* 3.0 28.2 + - + +
831A GLU 4.2 1.6 - - - +
833A PHE* 1.3 83.7 - - + +
835A GLN* 1.3 55.6 + - - +
837A MET* 3.6 1.4 + - - +
838A ARG* 2.9 65.4 + - - +
864A PHE* 4.1 18.4 - - + -
868A PHE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 835 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A GLU* 2.9 43.1 + - - +
832A GLY* 3.7 7.3 - - - +
833A PHE 3.1 0.2 - - - -
834A VAL* 1.3 75.6 - - - +
836A ASP* 1.3 64.3 + - - +
838A ARG* 3.9 6.0 - - + +
839A LEU* 2.9 28.1 + - - +
842A HIS* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A LYS* 3.7 19.3 + - - -
813A MET* 3.4 28.7 - - + +
817A LYS* 4.8 2.4 + - - -
818A VAL* 3.8 13.7 - - + -
821A SER* 5.3 0.5 + - - -
827A TYR* 2.8 32.2 + - - +
832A GLY 3.0 17.8 + - - +
833A PHE 3.1 2.4 + - - +
835A GLN* 1.3 76.0 - - - +
837A MET* 1.3 67.0 + - - +
839A LEU* 3.1 17.3 + - - +
840A ILE* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A LEU* 3.8 24.5 - - + -
786A VAL* 4.1 12.6 - - + -
815A LEU* 3.9 24.9 - - + -
818A VAL* 4.0 13.0 - - + -
833A PHE* 3.0 39.7 + - + +
834A VAL 3.8 0.2 - - - +
836A ASP* 1.3 78.4 - - - +
838A ARG* 1.3 61.6 + - - +
840A ILE* 3.2 21.0 + - + +
841A PHE* 3.3 26.0 - - + -
864A PHE* 3.4 47.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A GLU* 3.1 36.1 + - - -
767A LEU* 4.2 8.7 - - - +
834A VAL* 2.9 40.4 + - - +
835A GLN* 4.1 6.1 - - + +
837A MET* 1.3 76.9 - - - +
839A LEU* 1.3 57.8 + - - +
841A PHE* 3.2 12.2 + - + +
842A HIS* 2.9 49.1 + - + +
861A GLN* 5.8 3.4 - - - +
864A PHE* 4.2 4.0 - - + -
865A GLU* 3.0 41.9 + - - +
868A PHE* 3.9 7.7 - - - -
869A ARG* 4.0 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A LYS* 3.7 51.1 - - + +
813A MET* 4.1 11.7 - - + -
835A GLN 2.9 20.1 + - - +
836A ASP* 3.1 12.0 + - - +
838A ARG* 1.3 73.1 - - - +
840A ILE* 1.3 65.6 + - - +
842A HIS* 4.1 15.0 - - + -
843A ASN* 3.0 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A PHE* 3.9 33.7 - - + -
813A MET* 3.5 31.2 - - + +
814A TRP 3.8 25.4 - - - +
815A LEU* 4.0 21.3 - - + +
818A VAL* 4.5 1.6 - - + -
836A ASP 3.1 15.1 + - - +
837A MET* 3.4 20.6 - - + +
838A ARG 3.2 0.4 - - - -
839A LEU* 1.3 77.4 - - - +
841A PHE* 1.3 68.1 + - + +
843A ASN* 3.3 3.6 + - - +
844A HIS* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A VAL* 6.0 0.7 - - + -
795A PHE* 5.5 5.8 - + - -
837A MET* 3.3 31.4 - - + -
838A ARG* 3.2 13.1 + - + +
840A ILE* 1.3 85.6 - - + +
842A HIS* 1.3 66.9 + - - +
844A HIS* 3.6 6.6 - - + +
845A LYS* 2.9 34.0 + - - +
857A GLY* 4.2 10.1 - - - +
860A VAL* 4.0 18.2 - - + -
861A GLN* 3.7 64.2 - - + +
864A PHE* 3.7 38.1 - + + -
865A GLU* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A ARG* 2.9 40.9 + - + +
839A LEU* 3.7 16.2 - - + +
841A PHE* 1.3 79.4 - - - +
843A ASN* 1.3 66.6 + - - +
845A LYS* 3.3 12.2 + - - +
846A GLU* 3.0 22.8 + - - +
861A GLN* 5.2 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A TYR* 4.4 16.1 + - - +
809A PRO* 4.3 15.5 - - + +
810A GLN 5.4 0.3 + - - -
811A LYS 2.9 30.1 + - - +
812A PRO* 4.2 6.1 - - - +
813A MET 4.3 5.4 + - - +
839A LEU* 3.0 36.1 + - - +
840A ILE* 3.9 4.1 - - - +
842A HIS* 1.3 77.5 - - - +
844A HIS* 1.3 62.9 + - - +
846A GLU* 3.0 20.7 + - - +
847A PHE* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A PHE* 3.4 30.6 - + - -
795A PHE* 3.6 20.7 - + + -
801A TYR* 5.4 1.8 + - - -
840A ILE 3.0 17.4 + - - +
841A PHE* 3.2 7.8 + - - +
843A ASN* 1.3 76.4 - - - +
845A LYS* 1.3 65.2 + - + +
846A GLU 3.1 1.0 + - - -
847A PHE* 5.6 0.7 - - - -
848A TYR* 3.2 56.9 + + + +
853A PHE* 2.8 32.0 + - + -
854A THR* 4.1 7.7 + - - -
857A GLY* 3.8 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 845 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A PHE* 2.9 22.8 + - - +
842A HIS* 3.7 11.7 + - - +
844A HIS* 1.3 79.1 - - + +
846A GLU* 1.3 59.6 + - - +
848A TYR 4.6 7.5 - - - +
854A THR* 6.1 5.4 - - + -
857A GLY 5.7 1.6 - - - -
858A ILE* 4.7 20.6 - - + +
861A GLN* 2.6 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A PRO* 4.8 2.8 - - - +
810A GLN 5.5 2.0 + - - -
842A HIS 3.0 11.9 + - - +
843A ASN* 3.0 26.9 + - - +
845A LYS* 1.3 81.2 - - - +
847A PHE* 1.3 82.8 + - + +
848A TYR 3.8 0.4 - - - -
849A ARG* 6.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A TYR* 3.8 34.3 - + + -
808A GLY 3.2 44.9 - - - -
809A PRO* 3.6 25.6 - - + -
843A ASN 3.0 12.2 + - - +
846A GLU* 1.3 107.2 - - + +
848A TYR* 1.3 66.4 + - + +
849A ARG* 4.1 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A PHE* 4.1 21.3 - + - -
799A PRO* 6.5 0.2 - - + -
800A TYR* 4.5 22.2 - - - +
801A TYR* 4.2 24.9 - + - -
844A HIS* 3.2 48.9 + + + +
845A LYS* 4.6 7.8 - - - +
847A PHE* 1.3 87.6 - - + +
849A ARG* 1.3 62.9 + - - +
850A GLU* 3.7 9.0 - - + +
853A PHE* 4.1 20.6 - + + -
854A THR* 3.5 12.0 + - - +
----------------------------------------------------------
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