Contacts of the helix formed by residues 770 - 794 (chain i) 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 ASN 770 (chain i).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721i ASP* 5.8 2.0 - - + +
767i GLN* 4.3 1.8 + - - +
768i ASP 3.2 0.6 + - - -
769i GLY* 1.3 79.4 - - - +
771i ASP* 1.3 57.9 + - - +
772i PRO 3.5 1.6 - - - -
773i SER* 3.0 11.8 - - - -
774i TRP* 2.7 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 771 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721i ASP* 2.7 55.6 - - + +
722i TYR* 3.9 9.7 - - + +
763i ILE* 6.0 0.3 - - - +
765i PRO* 4.6 2.5 - - - +
766i LEU 4.9 0.4 - - - +
767i GLN 3.3 5.9 + - - +
770i ASN* 1.3 75.6 - - - +
772i PRO* 1.3 65.9 - - - +
774i TRP* 3.0 6.2 + - - +
775i LEU* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 772 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765i PRO* 3.8 24.0 - - + -
767i GLN 3.2 7.9 - - - -
768i ASP* 4.1 21.2 - - + +
770i ASN 3.5 0.4 - - - -
771i ASP* 1.3 76.1 - - - +
773i SER* 1.3 51.9 + - - +
775i LEU* 3.3 4.4 + - + +
776i GLY* 2.8 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 773 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768i ASP 4.5 3.4 + - - -
769i GLY 4.7 4.0 - - - -
770i ASN* 3.0 23.0 + - - -
772i PRO* 1.3 76.0 - - - +
774i TRP* 1.3 63.1 + - - +
776i GLY* 4.6 0.4 - - - +
777i ALA* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 774 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624i ASP* 6.2 3.6 - - + -
627i PHE* 5.7 10.3 - - + -
770i ASN 2.7 19.1 + - - +
771i ASP* 3.0 5.8 + - - +
773i SER* 1.3 74.2 - - - +
775i LEU* 1.4 58.5 + - - +
777i ALA* 3.8 4.6 - - - +
778i PHE* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 775 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743i VAL* 4.9 16.3 - - + +
744i PRO 5.2 0.7 - - - +
745i VAL* 5.5 4.3 - - - -
763i ILE* 4.6 22.4 - - + +
765i PRO* 5.1 6.7 - - + -
771i ASP 3.0 12.7 + - - +
772i PRO* 3.5 11.0 - - + +
774i TRP* 1.4 77.9 - - - +
776i GLY* 1.3 58.2 + - - +
778i PHE* 3.8 4.6 - - - +
779i ALA* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 776 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772i PRO 2.8 19.4 + - - -
773i SER* 4.0 0.9 - - - -
775i LEU* 1.3 74.0 - - - +
777i ALA* 1.3 58.1 + - - +
779i ALA* 3.1 7.6 + - - +
780i ALA* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 777 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773i SER 2.9 19.8 + - - +
774i TRP* 3.8 4.7 - - - +
776i GLY* 1.3 75.7 - - - +
778i PHE* 1.3 63.7 + - - +
780i ALA* 3.2 7.7 + - - +
781i ASP* 2.9 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 778 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622i PHE* 4.9 17.3 - - + -
745i VAL* 4.0 28.7 - - + +
774i TRP 2.9 17.4 + - - +
775i LEU* 3.8 4.3 - - - +
777i ALA* 1.3 76.3 - - - +
779i ALA* 1.3 64.8 + - - +
781i ASP* 2.8 19.8 + - - +
782i PHE* 2.8 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 779 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743i VAL* 5.5 7.0 - - + -
744i PRO 3.9 23.1 - - - +
775i LEU 2.8 19.4 + - - +
776i GLY* 3.1 8.3 + - - +
778i PHE* 1.3 77.1 - - - +
780i ALA* 1.3 61.3 + - - +
782i PHE* 3.2 6.6 + - - +
783i HIS* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 780 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776i GLY 2.8 13.2 + - - +
777i ALA* 3.5 10.8 - - - +
779i ALA* 1.3 77.7 - - - +
781i ASP* 1.3 57.9 + - - +
783i HIS* 2.7 29.2 - - + +
784i LYS* 3.2 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 781 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623i GLN* 5.9 6.7 - - + -
777i ALA 2.9 11.7 + - - +
778i PHE* 2.8 14.0 + - - +
780i ALA* 1.3 76.2 - - - +
782i PHE* 1.3 62.6 + - - +
784i LYS* 3.0 18.0 + - - +
785i ARG* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 782 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744i PRO 4.9 3.1 - - - +
745i VAL 4.3 17.3 - - - +
746i TYR* 5.5 2.9 - - - -
747i LEU 6.1 0.4 - - - +
778i PHE 2.8 11.3 + - - +
779i ALA* 3.4 11.7 - - - +
781i ASP* 1.3 77.5 - - - +
783i HIS* 1.3 52.3 + - - +
785i ARG* 3.2 8.7 + - - +
786i PHE* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 783 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779i ALA 3.1 9.1 + - - +
780i ALA* 2.7 22.7 - - - +
782i PHE* 1.3 76.8 - - - +
784i LYS* 1.4 59.0 + - - +
786i PHE* 3.4 19.1 + - - +
787i LEU 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 784 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780i ALA 3.2 4.4 + - - +
781i ASP* 3.0 12.3 + - - +
783i HIS* 1.4 80.6 - - - +
785i ARG* 1.3 59.8 + - - +
786i PHE 3.7 0.2 + - - -
787i LEU* 4.6 5.5 + - - +
788i SER 5.3 0.5 + - - -
858i MET 4.4 7.4 - - - +
859i PRO* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 785 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781i ASP 3.1 16.5 + - - +
782i PHE* 3.4 10.5 - - - +
784i LYS* 1.3 74.8 - - - +
786i PHE* 1.3 53.2 + - - +
787i LEU 3.3 1.6 - - - -
788i SER* 2.7 41.4 + - - -
789i LEU* 3.0 8.1 + - + +
858i MET 4.5 4.0 - - - -
859i PRO* 4.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 786 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782i PHE 2.8 12.6 + - - +
783i HIS* 3.4 17.7 - - - +
784i LYS 3.3 1.4 - - - -
785i ARG* 1.3 73.1 - - - +
787i LEU* 1.3 63.7 + - - +
789i LEU* 3.2 7.7 + - - +
790i LEU* 3.0 23.2 + - - +
799i SER* 5.2 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 787 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783i HIS 5.0 0.2 + - - -
784i LYS 4.6 5.4 + - - +
785i ARG 3.0 0.8 + - - -
786i PHE* 1.3 78.8 - - - +
788i SER* 1.3 63.6 + - - +
790i LEU* 3.2 5.5 + - - +
791i SER* 3.1 23.9 + - - -
857i LEU* 4.1 1.3 - - - +
858i MET* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 788 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784i LYS 5.3 0.4 + - - -
785i ARG* 2.7 21.9 + - - -
787i LEU* 1.3 73.8 - - - +
789i LEU* 1.3 59.5 + - - -
792i TYR* 3.0 8.3 + - - +
856i ASP* 3.5 7.4 - - - -
857i LEU* 2.7 42.1 + - - +
858i MET* 2.7 45.6 - - - +
859i PRO* 3.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 789 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747i LEU* 5.3 16.8 - - + +
785i ARG* 3.0 13.5 + - + +
786i PHE* 3.7 10.1 - - - +
788i SER* 1.3 75.6 - - - +
790i LEU* 1.3 68.0 + - - +
792i TYR* 3.0 3.6 + - - +
793i LYS* 2.8 25.2 + - - +
797i PHE 5.1 1.3 - - - +
799i SER* 5.5 8.1 - - - -
856i ASP* 3.8 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 790 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786i PHE 3.0 10.7 + - - +
787i LEU* 3.8 8.3 - - - +
789i LEU* 1.3 80.2 - - - +
791i SER* 1.3 62.6 + - - +
793i LYS 3.3 0.5 + - - -
796i GLU* 2.7 31.6 - - - +
797i PHE 3.8 22.2 - - - +
798i PRO* 4.3 12.6 - - + -
799i SER 5.2 1.1 - - - +
889j LEU* 4.5 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 791 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787i LEU 3.1 7.8 + - - -
790i LEU* 1.3 81.5 - - - +
792i TYR* 1.3 63.6 + - - +
793i LYS 3.3 0.5 + - - -
794i PHE* 3.4 10.6 + - - -
796i GLU* 4.6 2.4 - - - +
857i LEU* 3.6 22.9 - - - -
791j SER* 5.8 8.5 - - - -
889j LEU 4.7 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 792 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749i GLN* 6.5 0.7 - - + -
788i SER 3.0 17.2 + - - +
789i LEU* 3.0 5.5 + - - +
791i SER* 1.3 75.5 - - - +
793i LYS* 1.3 67.0 + - - +
794i PHE* 2.9 6.6 + - - +
856i ASP* 4.0 14.6 - - + -
857i LEU* 3.8 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 793 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749i GLN* 5.5 7.7 - - - +
789i LEU 2.8 11.6 + - - +
790i LEU 3.5 2.9 - - - +
791i SER 3.2 0.4 - - - -
792i TYR* 1.3 78.1 - - - +
794i PHE* 1.4 56.2 + - - +
795i ARG* 2.6 21.3 + - + +
796i GLU* 2.9 25.8 - - - +
797i PHE* 3.6 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 794 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791i SER 3.4 9.5 + - - -
792i TYR 2.9 8.9 + - - +
793i LYS* 1.4 78.2 - - - +
795i ARG* 1.3 62.6 + - - +
796i GLU* 2.8 10.8 + - - +
890j GLN 4.2 2.4 - - - +
891j ARG* 4.5 7.1 - - - +
----------------------------------------------------------
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