Contacts of the helix formed by residues 893 - 914 (chain A) in PDB entry 3W5D
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 ALA 893 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A TRP* 3.7 21.1 - - + -
889A GLU 4.1 1.4 + - - -
890A ILE* 3.1 25.7 + - + +
891A PHE 3.5 0.8 - - - -
892A GLU* 1.3 78.7 - - - +
894A PRO* 1.3 67.2 - - + +
895A GLU* 3.2 15.5 - - - +
896A PRO* 2.9 26.2 - - + +
897A MET* 4.4 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 894 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A GLU 3.4 4.4 - - - +
893A ALA* 1.3 83.0 - - + +
895A GLU* 1.3 71.8 + - - +
896A PRO 3.5 0.2 - - - -
897A MET* 3.7 8.5 + - + +
898A THR* 2.6 33.6 + - - -
958A LYS* 3.7 22.7 - - + +
959A LEU 4.0 13.2 - - - +
960A LYS* 3.7 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 895 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A TRP* 3.3 40.1 - - + +
861A ASP* 5.2 5.7 - - + +
893A ALA* 3.6 9.5 - - - +
894A PRO* 1.3 94.9 - - - +
896A PRO* 1.4 67.4 - - + +
898A THR* 3.2 8.2 + - - -
899A MET* 2.9 26.2 + - - +
960A LYS* 4.6 18.5 - - + +
961A ALA 5.6 2.7 - - - +
962A LEU* 4.3 3.4 - - + +
966A GLN* 4.5 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A ALA* 3.8 26.6 - - + +
855A TRP* 3.6 19.7 - - + -
856A PHE* 3.5 43.1 - - + -
891A PHE 5.3 1.1 - - - +
893A ALA 2.9 30.7 - - - +
895A GLU* 1.4 85.2 - - + +
897A MET* 1.3 63.5 + - + +
899A MET* 2.9 17.1 + - + +
900A ALA 2.9 11.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
785A GLU* 3.9 16.4 - - + +
786A ALA* 3.5 23.4 - - - +
787A LEU* 4.5 0.2 - - - +
788A ILE* 4.2 18.4 - - + -
791A GLN* 3.9 26.0 - - - +
892A GLU* 4.3 22.7 - - + +
893A ALA 4.5 6.1 - - - +
894A PRO* 3.8 9.9 - - + +
896A PRO* 1.3 79.9 - - + +
898A THR* 1.3 53.7 + - - +
900A ALA* 3.1 3.6 + - - +
901A LEU* 2.8 36.7 + - - +
958A LYS* 4.2 33.9 - - + +
959A LEU* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A PRO 2.6 22.6 + - - -
895A GLU 3.2 6.0 + - - -
897A MET* 1.3 77.0 - - - +
899A MET* 1.3 59.7 + - - +
901A LEU* 4.1 1.8 - - - -
902A SER* 2.7 35.2 + - - +
944A HIS* 5.9 0.7 - - + -
948A LEU* 3.7 21.8 - - + -
959A LEU* 3.2 15.8 - - + +
960A LYS 3.0 39.0 + - - +
962A LEU* 3.7 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A ALA* 3.4 31.0 - - + +
854A TRP* 3.7 23.1 - - + -
855A TRP* 4.2 15.0 - - + -
895A GLU 2.9 15.5 + - - +
896A PRO 2.9 10.6 + - - +
898A THR* 1.3 76.7 - - - +
900A ALA* 1.3 60.0 + - - +
902A SER* 3.9 1.6 - - - -
903A VAL* 3.0 33.8 + - + +
962A LEU* 3.9 15.0 - - + -
966A GLN* 3.7 45.8 - - - +
969A MET* 4.2 10.5 - - + -
970A VAL* 3.7 13.7 - - + +
973A ILE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A ALA* 3.5 26.2 - - + +
787A LEU* 3.9 7.4 - - + -
848A THR* 3.3 37.7 - - - +
851A ALA* 4.0 3.9 - - - +
852A ALA* 4.5 1.8 - - + -
896A PRO 2.9 11.2 + - - +
897A MET 3.5 6.5 - - - +
899A MET* 1.3 76.0 - - - +
901A LEU* 1.3 57.9 + - - +
903A VAL* 3.1 5.4 + - - +
904A LEU* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A LEU* 3.6 16.4 - - + +
791A GLN* 4.1 30.5 - - + +
794A TRP* 6.2 1.1 - - + -
795A VAL* 4.1 24.5 - - + -
897A MET 2.8 21.5 + - - +
898A THR* 4.4 3.4 - - + +
900A ALA* 1.3 72.9 - - - +
902A SER* 1.3 56.3 + - - +
904A LEU* 3.2 8.6 + - + +
905A VAL* 2.9 30.0 + - + +
944A HIS* 3.7 18.8 - - + -
947A ILE* 4.1 8.5 - - + -
957A PHE* 6.0 0.4 - - + -
959A LEU* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A THR* 2.7 29.3 + - - +
899A MET 3.9 2.7 - - - -
901A LEU* 1.3 73.4 - - - +
903A VAL* 1.3 59.1 + - - +
905A VAL* 3.9 1.7 - - - +
906A THR* 2.6 36.9 + - - -
944A HIS* 2.9 27.8 + - - -
948A LEU* 4.7 0.7 - - - +
962A LEU* 3.8 9.2 - - - +
967A TRP* 3.9 16.9 - - - -
970A VAL* 3.7 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A ALA* 3.8 32.8 - - + +
848A THR* 3.9 7.9 - - + -
851A ALA* 3.4 20.4 - - + -
899A MET 3.0 19.1 + - - +
900A ALA 3.3 7.6 - - - +
902A SER* 1.3 72.8 - - - +
904A LEU* 1.3 57.7 + - - +
906A THR 3.2 0.3 + - - -
907A ILE* 2.7 40.4 + - + +
970A VAL* 4.1 14.1 - - + -
973A ILE* 3.4 23.8 - - + -
974A SER* 3.3 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A SER* 4.9 2.2 - - - +
770A GLY 5.6 0.4 - - - -
771A GLU* 4.3 26.2 - - + +
787A LEU* 4.3 18.6 - - + -
792A LEU* 4.9 3.1 - - + -
795A VAL* 3.8 38.1 - - + -
844A VAL* 4.1 23.6 - - + -
848A THR* 3.7 13.2 - - + +
900A ALA 2.8 15.3 + - - +
901A LEU* 3.4 15.3 - - + +
903A VAL* 1.3 75.0 - - - +
905A VAL* 1.3 64.0 + - - +
907A ILE* 3.0 3.8 + - - +
908A GLU* 2.8 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A TRP* 6.2 0.7 - - + -
795A VAL* 3.9 17.9 - - + -
799A THR* 3.8 31.9 - - + +
800A ASP* 5.7 0.2 - - - -
901A LEU* 2.9 24.7 + - + +
902A SER* 3.9 3.8 - - - +
904A LEU* 1.3 73.7 - - - +
906A THR* 1.3 63.2 + - - +
908A GLU* 3.4 2.6 + - - -
909A MET* 3.1 27.4 + - + +
940A SER 5.1 0.9 - - - +
941A MET* 3.7 26.2 - - + -
944A HIS* 3.7 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A SER 2.6 23.4 + - - -
905A VAL* 1.3 73.0 - - - +
907A ILE* 1.3 67.2 + - - +
909A MET* 3.3 9.7 + - + +
910A CYS* 3.1 26.9 + - - -
941A MET* 4.4 10.2 - - + +
967A TRP* 3.8 12.8 - - - -
970A VAL* 3.5 11.1 - - + +
971A LEU* 4.1 22.9 - - + -
974A SER* 3.3 24.7 - - - +
975A LEU* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A TYR* 3.8 19.7 - - + -
844A VAL* 3.5 36.6 - - + -
847A ALA* 3.8 29.6 - - + -
903A VAL* 2.7 23.3 + - + +
904A LEU* 3.6 4.9 - - - +
906A THR* 1.3 72.9 - - - +
908A GLU* 1.3 56.4 + - - +
910A CYS* 2.8 10.4 + - - +
911A ASN* 2.6 33.4 + - + -
973A ILE 4.1 1.1 - - - +
974A SER* 3.4 28.5 - - - +
977A VAL* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A TYR* 2.9 36.9 + - - +
766A SER* 5.0 0.9 + - - +
767A SER* 3.3 41.1 + - - +
795A VAL* 5.3 0.2 - - + -
800A ASP* 3.4 23.1 - - - +
844A VAL* 4.0 26.3 - - - +
904A LEU* 2.8 33.8 + - + +
905A VAL* 3.9 4.3 - - - +
907A ILE* 1.3 69.4 - - - +
909A MET* 1.3 61.7 + - + +
911A ASN* 3.8 12.8 + - - +
912A ALA* 2.8 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A TYR* 4.2 0.2 - - - +
799A THR* 3.4 42.6 - - + +
800A ASP* 4.0 7.2 - - - +
803A PRO* 4.0 10.5 - - + -
905A VAL 3.1 19.8 + - - +
906A THR* 3.6 8.3 - - + +
908A GLU* 1.3 78.6 - - - +
910A CYS* 1.3 61.7 - - - +
912A ALA* 3.4 16.2 + - - +
913A LEU* 3.5 7.2 + - - +
937A ILE* 3.6 49.3 - - + +
940A SER* 3.9 18.8 - - - -
941A MET* 3.9 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 910 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A THR* 3.1 21.6 + - - -
907A ILE 2.8 11.1 + - - +
909A MET* 1.3 76.4 - - - +
911A ASN* 1.3 57.3 + - - +
913A LEU* 3.0 25.9 + - - +
914A ASN* 3.2 15.7 + - - -
974A SER* 4.3 16.2 - - - -
975A LEU* 4.4 18.4 - - - -
977A VAL* 3.5 15.9 - - + -
978A ILE* 3.8 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 911 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A TYR* 3.8 14.5 - - + +
766A SER* 4.1 19.8 + - - -
837A TYR* 5.2 7.1 - - - -
840A ILE* 3.9 24.9 - - - +
844A VAL* 6.0 0.2 - - - -
907A ILE* 2.6 22.1 + - + +
908A GLU* 3.8 21.7 + - - +
910A CYS* 1.3 70.9 - - - +
912A ALA* 1.3 56.2 + - - +
913A LEU 3.2 0.2 - - - -
914A ASN* 3.3 23.8 + - - +
915A SER* 2.8 35.5 + - - -
977A VAL* 3.9 7.6 - - + +
981A ASP* 4.7 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 912 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A TYR* 3.5 20.8 - - + +
803A PRO* 3.9 19.7 - - + -
807A LEU* 3.7 4.3 - - + +
908A GLU 2.8 13.6 + - - +
909A MET* 3.4 14.1 - - - +
910A CYS 3.2 0.2 - - - -
911A ASN* 1.3 76.2 - - - +
913A LEU* 1.3 61.0 + - - +
915A SER* 3.3 15.7 + - - -
916A LEU 3.7 1.6 + - - -
933A LEU* 3.5 26.2 - - + +
937A ILE* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 913 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A MET 3.5 13.7 + - - +
910A CYS* 3.0 11.7 + - - +
912A ALA* 1.3 74.8 - - - +
914A ASN* 1.3 56.2 + - - +
915A SER 2.9 9.3 + - - -
916A LEU* 3.3 14.0 + - + +
922A LEU* 3.5 31.5 - - + +
927A PRO* 3.9 36.1 - - + -
933A LEU* 4.0 19.5 - - + -
934A LEU* 4.3 9.4 - - + -
937A ILE* 4.1 14.4 - - + -
978A ILE* 4.7 14.8 - - + -
985A LYS* 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 914 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A GLN* 5.0 0.2 + - - -
836A ARG* 4.6 2.6 + - - -
910A CYS 3.2 16.9 + - - -
911A ASN* 3.3 30.4 + - - +
913A LEU* 1.3 74.1 - - - +
915A SER* 1.3 57.7 + - - +
916A LEU 3.5 0.4 - - - -
917A SER 3.4 6.2 - - - +
922A LEU* 4.2 5.7 - - - +
977A VAL* 3.7 19.8 + - - +
978A ILE* 3.8 27.5 - - - +
981A ASP* 3.2 28.7 - - - +
982A GLU* 4.1 8.0 - - - +
985A LYS* 3.3 28.5 + - - +
----------------------------------------------------------
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