Contacts of the helix formed by residues 906 - 924 (chain j) in PDB entry 5JPQ
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 SER 906 (chain j).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905j GLY* 1.4 65.0 - - - -
907j GLN* 1.3 60.2 + - - -
908j VAL* 3.1 6.2 - - - +
909j LEU* 3.3 20.2 + - - +
910j ALA* 3.5 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 907 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903j LEU* 4.0 17.9 - - + +
904j PRO* 4.4 7.2 - - + -
905j GLY 2.5 16.7 + - - +
906j SER* 1.3 68.4 - - - +
908j VAL* 1.3 59.9 + - - +
909j LEU 3.2 0.7 - - - -
910j ALA* 3.1 11.8 + - + +
911j ILE* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 908 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880j GLN* 4.3 29.3 - - + +
894j ILE* 5.6 9.4 - - + +
897j LEU 6.4 0.2 - - - -
898j ALA* 5.6 6.7 - - + +
903j LEU* 4.3 13.0 - - + +
905j GLY* 4.0 4.8 - - - -
906j SER 3.1 7.6 - - - +
907j GLN* 1.3 77.6 - - - +
909j LEU* 1.3 63.3 + - - +
911j ILE* 2.9 8.1 + - - +
912j PHE* 2.8 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 909 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880j GLN* 5.3 2.9 - - - +
906j SER* 3.3 15.1 + - - +
907j GLN 3.2 0.4 - - - -
908j VAL* 1.3 78.6 - - - +
910j ALA* 1.3 64.3 + - - +
912j PHE* 3.1 8.6 + - - +
913j MET* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 910 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906j SER 3.5 4.4 + - - +
907j GLN* 3.1 18.9 + - + +
909j LEU* 1.3 79.5 - - - +
911j ILE* 1.3 57.3 + - - +
913j MET* 3.2 9.6 + - - +
914j LYS* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 911 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880j GLN 5.7 0.7 - - - +
883j ILE* 4.6 12.2 - - + +
901j LEU* 6.4 1.8 - - + -
907j GLN 2.8 12.6 + - - +
908j VAL* 2.9 10.0 + - - +
910j ALA* 1.3 74.7 - - - +
912j PHE* 1.3 59.1 + - - +
914j LYS* 3.0 8.4 + - - +
915j ILE* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 912 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879j LEU* 3.1 36.3 + - - +
880j GLN* 4.2 3.1 - - - +
883j ILE* 4.5 3.7 - - - +
884j LEU* 5.2 3.0 - - - +
908j VAL 2.8 11.8 + - - +
909j LEU* 3.1 11.9 + - - +
911j ILE* 1.3 74.9 - - - +
913j MET* 1.3 63.0 + - - +
915j ILE* 3.2 8.3 + - - +
916j MET* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 913 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844j TYR* 3.9 22.2 - - - +
845j ALA* 3.8 13.8 - - - +
847j GLY 5.4 1.8 - - - +
909j LEU 2.9 12.1 + - - +
910j ALA* 3.3 11.9 - - - +
912j PHE* 1.3 75.7 - - - +
914j LYS* 1.3 63.6 + - - +
916j MET* 3.2 8.7 + - - +
917j ARG* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 914 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910j ALA 2.9 13.4 + - - +
911j ILE* 3.0 11.4 + - - +
913j MET* 1.3 76.5 - - - +
915j ILE* 1.3 62.1 + - - +
917j ARG* 3.1 9.3 + - - +
918j LYS* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 915 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875j LYS 4.7 0.9 - - - +
876j LEU* 4.6 22.2 - - + +
877j SER 6.0 0.7 - - - -
883j ILE* 4.5 13.9 - - + -
884j LEU* 4.7 6.5 - - + -
911j ILE 2.8 15.9 + - - +
912j PHE* 3.5 8.7 - - - +
914j LYS* 1.3 77.3 - - - +
916j MET* 1.3 60.4 + - - +
918j LYS* 3.2 8.0 + - - +
919j VAL* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 916 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841j LEU* 5.0 5.6 - - + +
844j TYR* 5.3 5.6 - - + -
845j ALA* 4.1 15.4 - - + +
877j SER 5.5 5.4 - - - -
884j LEU* 5.9 0.8 - - - +
912j PHE 3.0 12.7 + - - +
913j MET* 3.4 11.7 - - - +
915j ILE* 1.3 73.1 - - - +
917j ARG* 1.3 65.7 + - - +
919j VAL* 3.3 7.2 + - - +
920j THR* 3.1 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 917 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845j ALA* 3.7 20.4 - - + +
913j MET 3.0 12.3 + - - +
914j LYS* 3.4 12.3 - - - +
916j MET* 1.3 75.6 - - - +
918j LYS* 1.3 64.9 + - - +
920j THR* 3.3 5.2 + - - -
921j GLN* 3.0 23.0 + - - +
928j SER* 5.6 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 918 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914j LYS 3.0 12.7 + - - +
915j ILE* 3.2 11.4 + - - +
917j ARG* 1.3 76.8 - - - +
919j VAL* 1.3 62.9 + - - +
921j GLN* 3.1 7.7 + - - +
922j HIS* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 919 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864j LEU* 5.7 8.7 - - + +
868j GLY* 5.2 13.5 - - - -
870j LEU* 5.1 16.2 - - + -
876j LEU* 5.5 4.9 - - + -
877j SER 5.8 3.8 - - - +
915j ILE 3.0 13.1 + - - +
916j MET* 3.9 8.5 - - - +
917j ARG 3.3 0.2 - - - -
918j LYS* 1.3 75.8 - - - +
920j THR* 1.3 63.5 + - - +
922j HIS* 3.1 9.5 + - - +
923j PHE* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 920 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841j LEU* 5.9 8.1 - - - -
842j GLU* 6.5 1.1 - - - -
845j ALA* 6.0 2.0 - - - -
916j MET 3.1 16.7 + - - -
917j ARG* 3.8 6.3 - - - -
918j LYS 3.2 0.4 - - - -
919j VAL* 1.3 75.8 - - - +
921j GLN* 1.3 63.0 + - - +
923j PHE* 3.1 9.9 + - - +
924j GLY 2.9 25.0 + - - +
928j SER* 4.3 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 921 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917j ARG 3.0 12.9 + - - +
918j LYS* 3.1 11.0 + - - +
920j THR* 1.3 75.4 - - - +
922j HIS* 1.3 64.0 + - - +
924j GLY 4.1 6.3 - - - -
925j ALA* 3.2 31.7 + - + +
928j SER* 4.5 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 922 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870j LEU* 6.0 5.2 - - + +
918j LYS 3.0 11.4 + - - +
919j VAL* 3.1 11.4 + - - +
921j GLN* 1.3 77.6 - - - +
923j PHE* 1.3 64.2 + - - +
924j GLY* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 923 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919j VAL 3.0 12.7 + - - +
920j THR* 3.4 10.8 - - - +
922j HIS* 1.3 80.0 - - - +
924j GLY* 1.4 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 924 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920j THR 2.9 14.9 + - - +
921j GLN 3.4 2.2 - - - -
922j HIS 4.6 0.2 - - - -
923j PHE* 1.4 80.6 - - - +
925j ALA* 1.3 65.0 + - - +
926j LEU 3.4 2.5 - - - -
927j VAL* 3.6 11.1 + - - +
928j SER* 3.2 18.5 + - - -
----------------------------------------------------------
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