Contacts of the helix formed by residues 833 - 850 (chain A) in PDB entry 3DPK
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 THR 833 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ILE* 5.7 5.2 - - + -
775A ILE* 3.9 13.2 - - - +
825A GLU* 4.5 3.9 + - + -
831A VAL* 4.0 18.8 - - + -
832A TYR* 1.3 80.0 - - - +
834A VAL* 1.3 65.0 + - - +
835A GLN* 2.7 28.8 + - - +
836A SER* 2.7 41.8 + - - -
837A ASP* 3.1 9.7 + - - -
897A PRO* 5.4 0.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
553A ILE* 5.3 8.0 - - + +
770A ALA* 3.8 39.3 - - + +
773A ASN* 5.7 1.8 - - - +
774A CYS 4.6 5.8 - - - +
775A ILE* 3.8 18.4 - - + +
833A THR* 1.3 74.4 - - - +
835A GLN* 1.3 67.7 + - + +
837A ASP* 2.9 26.8 + - - +
838A VAL* 3.0 15.1 + - + +
902A THR* 6.1 2.2 - - - -
903A PHE* 3.9 19.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
833A THR* 2.7 33.1 + - - +
834A VAL* 1.3 85.6 - - + +
836A SER* 1.3 60.5 + - - +
838A VAL* 3.2 21.6 + - + +
839A TRP 3.2 6.6 + - - -
897A PRO* 3.9 39.7 - - + +
898A THR* 5.3 6.1 - - - -
900A ARG* 3.0 21.7 + - + +
901A PRO 5.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A ARG* 5.8 0.2 - - - +
823A ALA* 4.0 5.7 + - - +
825A GLU* 3.6 17.0 + - - -
826A SER* 3.4 23.7 + - - -
831A VAL 4.4 0.4 - - - -
832A TYR* 3.6 12.6 - - - +
833A THR* 2.7 40.5 + - - -
835A GLN* 1.3 73.0 - - - +
837A ASP* 1.3 66.5 + - - +
839A TRP* 3.2 14.0 + - - +
840A SER* 3.3 15.1 + - - -
900A ARG* 3.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A MET* 3.7 24.3 - - + +
774A CYS 4.5 1.2 - - - +
775A ILE* 3.5 12.5 - - - +
776A HIS* 2.9 27.7 + - - +
777A ARG* 3.0 28.3 + - - +
779A VAL* 4.3 7.7 - - + +
832A TYR* 5.9 0.2 - - - -
833A THR 3.1 6.3 + - - +
834A VAL* 2.9 15.3 + - - +
836A SER* 1.3 84.6 + - - +
838A VAL* 1.3 55.9 + - - +
840A SER* 3.2 9.2 + - - -
841A TYR* 2.9 27.2 + - - +
903A PHE* 3.7 6.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL* 3.0 19.3 + - + +
835A GLN* 3.3 15.0 - - + +
836A SER 3.2 0.4 - - - -
837A ASP* 1.3 73.8 - - - +
839A TRP* 1.3 66.2 + - - +
841A TYR* 3.2 3.8 + - - +
842A GLY 3.1 16.6 + - - -
892A CYS* 3.4 24.8 - - - +
900A ARG* 4.0 15.9 - - + -
901A PRO* 3.5 31.4 - - + +
902A THR* 4.7 1.3 - - - -
903A PHE* 3.6 34.5 - - + +
906A ILE* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A LYS 5.2 0.8 + - - -
821A TRP 3.6 18.1 + - - -
822A MET 3.2 11.7 + - - -
823A ALA* 3.6 20.9 - - + -
824A PRO* 3.5 34.1 - - + -
835A GLN 3.2 2.6 + - - -
836A SER 3.2 10.4 + - - +
838A VAL* 1.3 77.9 - - - +
840A SER* 1.3 60.9 + - - +
842A GLY 3.2 9.4 + - - -
843A ILE* 3.3 23.2 + - + +
856A TYR* 4.3 15.3 + - - -
869A VAL* 5.0 13.9 - - + -
873A TYR 5.4 6.7 - - - -
874A GLN* 6.1 0.9 - - + -
892A CYS 3.4 14.8 + - - +
893A TRP* 3.1 58.7 + + + -
894A ALA 3.9 5.4 - - - -
895A LEU* 4.7 8.5 - - + -
900A ARG* 3.7 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A ARG 5.9 2.0 - - - -
779A VAL* 3.7 35.7 + - - +
821A TRP* 2.6 28.3 + - - +
822A MET* 4.3 4.3 - - - +
836A SER 3.3 10.4 + - - -
837A ASP* 3.2 12.3 + - - -
839A TRP* 1.3 74.5 - - - +
841A TYR* 1.3 65.4 + - - +
843A ILE* 3.1 7.1 + - - +
844A LEU* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A SER* 2.6 27.7 + - - -
762A VAL* 3.8 31.2 - - + -
763A ALA* 3.6 19.2 - - + +
766A MET* 4.7 2.7 - - + -
779A VAL* 3.9 10.5 - - + +
837A ASP 2.9 13.2 + - - +
838A VAL 3.4 8.3 - - - +
840A SER* 1.3 78.0 - - - +
842A GLY* 1.3 57.9 + - - +
844A LEU* 3.1 12.9 + - + +
845A LEU* 2.9 57.6 + - + +
888A ILE* 4.7 0.2 - - + -
892A CYS* 4.2 4.5 - - - -
903A PHE* 3.7 21.1 - + + -
906A ILE* 3.8 33.7 - - + -
910A LEU* 3.7 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A VAL 3.1 10.1 + - - -
839A TRP 3.2 5.9 + - - -
841A TYR* 1.3 75.7 - - - +
843A ILE* 1.3 61.5 + - - +
845A LEU* 3.2 11.5 + - - +
846A TRP 3.1 16.6 + - - -
889A MET* 3.8 5.5 - - - +
892A CYS* 3.8 18.6 - - - -
893A TRP* 3.4 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A LYS 3.9 15.9 - - - +
821A TRP* 3.5 31.4 - - + +
839A TRP* 3.3 26.6 + - + +
840A SER 3.1 8.0 + - - +
842A GLY* 1.3 71.9 - - - +
844A LEU* 1.3 64.1 + - - +
846A TRP* 3.2 5.9 + - - +
847A GLU* 3.0 20.4 + - - +
855A PRO* 3.9 21.8 - - + -
856A TYR* 3.8 17.3 - - - +
875A MET* 3.6 22.4 - - + -
893A TRP* 3.3 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A LEU* 4.3 4.9 - - + -
762A VAL* 3.6 35.7 - - + -
779A VAL* 4.1 18.4 - - + -
780A ALA* 3.8 2.9 - - - -
781A ALA* 3.4 39.9 - - + +
784A VAL* 4.2 8.3 - - + -
821A TRP* 4.7 0.4 - - - -
840A SER 3.0 12.1 + - - +
841A TYR* 3.3 17.7 - - + +
843A ILE* 1.3 72.5 - - - +
845A LEU* 1.3 60.5 + - + +
847A GLU* 3.1 13.8 + - - +
848A ILE* 2.9 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 845 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A SER* 3.6 28.0 - - - +
841A TYR* 2.9 45.6 + - + +
842A GLY* 3.2 11.4 + - - +
844A LEU* 1.3 77.2 - - + +
846A TRP* 1.3 62.1 + - - +
848A ILE* 4.4 5.6 - - + -
849A PHE* 2.9 37.7 + - + +
885A ILE* 4.4 8.7 - - + +
888A ILE* 3.7 35.4 - - + -
889A MET* 3.8 24.5 - - + +
910A LEU* 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A GLY 3.1 9.3 + - - +
843A ILE 3.2 8.5 + - - +
845A LEU* 1.3 80.1 - - - +
847A GLU* 1.3 62.4 + - + +
849A PHE 3.8 0.3 - - - -
850A SER* 2.9 40.0 + - - -
853A LEU* 3.5 48.9 - - + -
854A ASN 3.6 15.3 - - - -
855A PRO* 3.6 8.7 - - + -
857A PRO* 3.8 19.7 - - + -
875A MET* 3.3 45.2 - - + +
876A ALA 2.9 27.4 + - - -
878A PRO* 3.6 22.1 - - + +
886A TYR* 5.3 0.4 - + - -
889A MET* 3.8 16.3 - - - -
893A TRP* 4.2 4.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A LEU* 4.1 14.4 - - - +
675A LEU* 3.6 2.5 - - + +
781A ALA* 3.0 39.8 + - + +
782A ARG* 4.8 0.9 + - - -
821A TRP* 2.8 42.2 + - - -
843A ILE 3.0 13.5 + - - +
844A LEU* 3.1 15.2 + - - +
846A TRP* 1.3 79.5 - - + +
848A ILE* 1.3 58.4 + - - +
850A SER* 3.2 8.4 + - - -
852A GLY* 2.7 34.3 + - - -
853A LEU 4.1 15.1 - - - +
855A PRO* 4.3 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A LEU* 4.0 29.2 - - + -
675A LEU* 3.7 12.3 - - + +
755A LEU* 3.8 32.1 - - + +
758A PHE* 4.3 13.9 - - + +
759A SER* 4.0 19.3 - - - +
762A VAL* 5.7 0.7 - - + -
844A LEU* 2.9 34.7 + - + +
845A LEU* 3.6 10.1 - - + +
847A GLU* 1.3 75.4 - - - +
849A PHE* 1.3 77.9 + - + +
851A LEU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A SER* 5.0 2.9 - - - -
755A LEU* 3.7 33.7 - - + -
756A LEU* 4.0 18.8 - - + -
759A SER* 3.2 27.1 - - - -
845A LEU* 2.9 32.0 + - + +
848A ILE* 1.3 80.9 - - + +
850A SER* 1.3 57.0 + - - +
851A LEU 3.4 0.4 - - - -
878A PRO* 3.3 10.2 - - + +
880A PHE* 3.1 50.9 + - - +
881A ALA* 3.7 24.5 - - + -
882A PRO* 4.1 15.0 - - + -
885A ILE* 3.4 28.5 - - + -
889A MET* 4.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 850 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A TRP* 2.9 30.8 + - - -
847A GLU* 3.2 6.6 + - - -
849A PHE* 1.3 77.3 - - - +
851A LEU* 1.3 69.7 + - - +
852A GLY 3.4 0.2 + - - -
853A LEU* 3.1 54.2 + - - +
878A PRO* 3.9 12.8 - - - -
879A ALA* 5.0 2.0 - - - +
880A PHE* 4.8 5.9 - - - -
----------------------------------------------------------
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