Contacts of the helix formed by residues 890 - 905 (chain A) in PDB entry 1TXD
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 ASN 890 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A ARG 3.9 1.9 + - - -
830A LYS* 3.0 33.5 + - - +
831A ILE 4.3 1.6 + - - -
833A SER* 3.6 27.7 + - - +
886A THR 3.3 15.9 + - - +
887A PHE 3.4 5.8 - - - +
888A CYS 3.2 0.2 - - - -
889A SER* 1.3 82.1 + - - +
891A GLN* 1.3 50.9 + - - +
892A PRO* 3.4 1.6 - - - -
893A PHE* 2.9 27.7 + - - +
894A ALA* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 891 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A PHE* 3.5 6.6 + - + +
888A CYS* 3.3 20.7 + - - +
889A SER 3.3 0.2 - - - -
890A ASN* 1.3 76.2 - - - +
892A PRO* 1.3 62.8 - - + +
894A ALA* 3.0 7.2 + - - +
895A LEU* 2.9 46.4 + - + +
930A ILE* 4.1 14.6 - - + +
931A PRO* 3.3 45.1 - - - +
934A MET* 4.9 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 892 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A CYS 4.2 1.8 - - - +
889A SER 3.3 18.2 - - - +
890A ASN 3.4 1.6 - - - -
891A GLN* 1.3 94.7 - - + +
893A PHE* 1.3 65.5 + - + +
895A LEU* 4.2 6.6 - - + +
896A GLU* 3.3 24.1 + - - +
978A VAL* 5.2 3.1 - - + +
981A ALA 4.7 1.6 - - - -
982A GLU* 3.7 37.2 - - + +
985A GLN* 3.8 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 893 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A LYS* 3.8 27.7 - - + +
889A SER 4.0 7.6 - - - -
890A ASN* 2.9 28.5 + - - +
892A PRO* 1.3 79.6 - - + +
894A ALA* 1.3 62.9 + - - +
896A GLU* 3.4 3.9 + - - +
897A MET* 3.1 23.9 + - - +
981A ALA* 3.9 28.3 - - + -
984A LYS* 4.0 14.4 - - + -
985A GLN* 3.5 42.0 - - + -
988A GLU* 3.4 32.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 894 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A LYS 3.2 17.0 - - - +
831A ILE* 2.9 32.2 - - + +
890A ASN* 2.8 17.7 + - - +
891A GLN* 3.0 7.5 + - - +
893A PHE* 1.3 75.8 - - - +
895A LEU* 1.3 64.0 + - + +
897A MET* 3.2 3.0 + - - +
898A ILE* 3.0 32.6 + - + +
930A ILE* 5.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 895 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A GLN* 2.9 37.6 + - + +
892A PRO* 4.2 5.6 - - + +
894A ALA* 1.3 78.4 - - - +
896A GLU* 1.3 62.4 + - - +
898A ILE* 3.8 16.2 + - + +
899A LYS* 3.3 25.5 + - - +
927A LYS* 3.7 47.0 - - + +
930A ILE* 4.2 18.4 - - + -
931A PRO* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A PRO 3.3 16.6 + - - +
893A PHE* 4.0 3.4 - - - +
894A ALA 3.2 0.2 - - - -
895A LEU* 1.3 79.5 - - - +
897A MET* 1.3 59.0 + - - +
899A LYS* 3.4 21.9 + - - +
900A SER* 3.0 37.0 + - - -
985A GLN* 3.9 21.2 + - - +
989A ASP* 4.4 13.0 - - - +
992A ARG* 4.8 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A SER* 5.6 1.3 - - - +
827A GLU* 4.3 18.4 - - + +
830A LYS* 4.1 32.8 - - + -
831A ILE* 3.4 25.8 - - + -
893A PHE 3.1 16.9 + - - +
894A ALA 3.2 4.5 + - - +
896A GLU* 1.3 77.3 - - - +
898A ILE* 1.3 59.2 + - - +
900A SER* 3.2 15.5 + - - -
901A ARG* 2.9 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A ILE* 3.6 25.1 - - + +
894A ALA 3.0 24.5 + - - +
895A LEU* 3.8 15.5 - - + +
896A GLU 3.4 0.2 - - - -
897A MET* 1.3 76.8 - - - +
899A LYS* 1.4 58.4 + - + +
901A ARG 3.3 0.2 + - - -
902A GLN* 2.9 51.7 + - - +
908A PHE* 3.7 15.5 - - + -
912A VAL* 5.3 1.6 - - + -
926A LEU* 3.7 33.9 - - + -
927A LYS* 4.9 7.6 - - + +
930A ILE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A LEU 3.3 15.3 + - - +
896A GLU* 3.7 25.1 + - - +
898A ILE* 1.4 77.1 - - + +
900A SER* 1.3 57.2 + - - +
902A GLN* 3.3 16.5 + - - +
903A LYS* 3.0 30.0 + - - +
927A LYS* 6.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A GLU* 3.0 26.8 + - - +
897A MET* 3.2 25.6 + - - -
899A LYS* 1.3 76.5 - - - +
901A ARG* 1.3 64.8 + - - +
903A LYS* 3.3 11.3 + - - +
904A LYS* 3.1 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A LEU* 4.1 17.1 - - + +
827A GLU* 3.2 31.7 + - + -
831A ILE* 4.6 2.5 - - + -
897A MET* 2.9 42.8 + - + +
900A SER* 1.3 76.6 + - - +
902A GLN* 1.3 59.6 + - - +
904A LYS* 3.8 30.5 - - - +
905A ASP* 2.8 55.3 + - - +
908A PHE* 3.4 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A ILE* 2.9 36.3 + - - +
899A LYS* 3.3 16.9 + - - +
901A ARG* 1.3 77.4 - - - +
903A LYS* 1.3 61.7 + - - +
904A LYS 3.6 0.3 + - - -
905A ASP 4.1 4.0 + - - +
906A SER* 5.0 0.3 + - - -
908A PHE* 4.0 15.5 - - + -
909A GLN* 3.7 43.0 - - + +
912A VAL* 3.4 29.5 - - - +
916A GLU* 5.0 2.0 + - - -
925A GLN* 5.5 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A LYS 3.0 17.8 + - - +
900A SER* 3.6 11.2 - - - +
901A ARG 3.1 0.2 - - - -
902A GLN* 1.3 79.3 - - - +
904A LYS* 1.3 73.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A SER* 3.1 35.3 + - - +
901A ARG* 3.8 28.6 - - - +
903A LYS* 1.3 95.2 - - - +
905A ASP* 1.3 60.1 + - - +
906A SER 4.1 1.8 + - - -
992A ARG* 6.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A ILE* 3.6 28.8 - - - +
823A LEU* 5.5 0.3 - - - +
901A ARG* 2.8 40.0 + - - +
902A GLN 4.5 3.6 - - - -
903A LYS 3.8 0.8 - - - -
904A LYS* 1.3 77.8 - - - +
906A SER* 1.3 65.2 + - - +
907A ARG* 2.9 24.6 + - - +
908A PHE* 2.8 20.2 + - + +
909A GLN* 3.0 10.0 + - - +
----------------------------------------------------------
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