Contacts of the helix formed by residues 773 - 791 (chain B) in PDB entry 3LJ1
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 773 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B TYR* 1.3 73.4 - - - +
774B PRO* 1.3 76.8 - - - +
775B ILE* 3.5 18.6 - - - +
776B SER* 3.2 42.8 + - - -
777B LEU* 3.5 10.5 + - - +
821B ASN* 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 774 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B TYR* 3.3 17.2 - - + +
773B ASN* 1.3 91.8 - - - +
775B ILE* 1.3 62.4 + - + +
777B LEU* 3.3 11.4 + - + +
778B LEU* 3.1 27.9 + - - +
913B ILE* 4.1 15.0 - - + -
914B LEU* 3.8 16.4 - - + -
943B CYS* 4.4 20.0 - - + -
944B LEU* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 775 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B ASN* 3.3 15.6 - - - +
774B PRO* 1.3 78.1 - - - +
776B SER* 1.3 56.7 + - - +
778B LEU* 3.3 9.1 + - + +
779B ARG* 2.9 27.1 + - + +
914B LEU* 4.9 5.6 - - + -
944B LEU* 4.4 14.8 - - + -
949B LEU* 3.7 31.9 - - + -
979B LEU* 3.8 37.9 - - + +
980B PHE* 3.7 25.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 776 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B ASN* 3.2 33.5 + - - -
774B PRO 3.2 0.2 - - - -
775B ILE* 1.3 73.0 - - - +
777B LEU* 1.3 68.9 + - - +
779B ARG* 3.1 8.3 + - - +
780B GLN* 2.9 34.7 + - - +
820B GLU* 2.8 41.1 + - - +
822B LEU 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 777 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B LEU* 4.5 7.9 - - + -
755B LEU* 4.0 15.0 - - + -
772B TYR* 3.4 35.7 - - + +
773B ASN 3.5 11.2 + - - +
774B PRO* 3.3 10.9 + - + +
776B SER* 1.3 80.4 - - - +
778B LEU* 1.3 58.0 + - - +
780B GLN* 3.4 16.5 + - - +
781B ILE* 2.9 36.1 + - - +
822B LEU* 4.1 24.2 - - + +
824B ILE* 3.9 25.9 - - + +
913B ILE* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 778 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B PRO 3.1 20.8 + - - +
775B ILE* 3.4 11.9 - - + +
776B SER 3.2 0.4 - - - -
777B LEU* 1.3 74.9 - - - +
779B ARG* 1.3 63.5 + - - +
781B ILE* 3.2 3.4 + - - +
782B ALA* 3.0 19.4 + - - +
910B PHE* 3.5 53.0 - - + +
913B ILE* 3.4 37.5 - - + -
914B LEU* 4.0 30.1 - - + -
979B LEU* 4.3 15.9 - - + -
980B PHE* 3.8 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 779 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B ASN* 5.3 3.0 - - - +
775B ILE* 2.9 14.0 + - + +
776B SER* 3.4 8.4 + - - +
778B LEU* 1.3 76.1 - - - +
780B GLN* 1.3 77.2 + - - +
782B ALA* 3.2 4.1 + - - +
783B SER* 2.8 51.9 + - - -
817B THR* 4.8 11.6 + - - -
820B GLU* 3.6 28.5 + - - -
975B LEU* 3.5 16.1 - - + +
980B PHE* 3.4 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 780 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B ASN* 3.1 33.1 + - - +
776B SER* 2.9 37.4 + - - +
777B LEU* 3.6 15.3 - - - +
779B ARG* 1.3 92.7 - - - +
781B ILE* 1.3 65.9 + - - +
783B SER* 3.2 5.4 + - - -
784B GLY 3.0 19.1 + - - -
820B GLU* 4.3 8.4 + - - -
822B LEU 3.3 19.3 + - - +
823B ARG* 3.4 12.1 - - - -
824B ILE* 2.9 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 781 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B LEU* 4.4 0.7 - - + -
777B LEU 2.9 22.2 + - - +
778B LEU* 3.2 6.3 + - - +
780B GLN* 1.3 75.5 - - - +
782B ALA* 1.3 62.7 + - - +
784B GLY* 3.2 2.4 + - - -
785B VAL* 3.0 28.5 + - + +
798B LEU* 5.6 1.6 - - + -
803B ILE* 3.9 36.6 - - + -
824B ILE* 3.6 24.9 - - + -
826B ILE* 3.8 9.6 - - + +
906B MET* 3.6 27.1 - - + -
909B VAL* 4.0 5.8 - - + -
910B PHE* 4.3 3.1 - - + -
913B ILE* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 782 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B LEU 3.0 12.6 + - - +
779B ARG* 3.4 4.7 - - - +
781B ILE* 1.3 77.3 - - - +
783B SER* 1.3 57.9 + - - +
784B GLY 3.1 0.5 + - - -
785B VAL* 3.2 2.1 + - - +
786B ALA* 2.8 32.2 + - - +
906B MET* 3.7 20.4 - - + -
910B PHE* 4.3 1.1 - - + -
971B ALA* 4.6 4.7 - - - +
974B VAL* 4.3 16.6 - - + -
975B LEU* 3.3 27.8 - - + -
980B PHE* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 783 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B HIS* 3.2 27.0 + - - -
727B ASN* 3.6 9.2 + - - -
779B ARG* 2.8 32.7 + - - -
780B GLN 3.2 9.6 + - - -
782B ALA* 1.3 71.6 - - - +
784B GLY* 1.3 61.0 + - - +
786B ALA* 3.6 2.9 - - - +
787B HIS* 3.3 16.1 + - - +
975B LEU* 3.6 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 784 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B HIS* 3.7 20.1 + - - -
727B ASN* 4.0 8.1 - - - -
728B VAL* 4.4 2.7 - - - +
780B GLN 3.0 13.0 + - - -
781B ILE 3.7 3.1 - - - -
782B ALA 3.1 0.2 - - - -
783B SER* 1.3 74.5 - - - +
785B VAL* 1.3 63.9 + - - +
787B HIS* 3.1 6.8 + - - +
788B LEU* 3.1 24.1 + - - +
826B ILE* 4.1 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 785 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B ILE* 3.0 18.2 + - + +
782B ALA 3.8 0.4 - - - +
784B GLY* 1.3 71.2 - - - +
786B ALA* 1.3 67.6 - - - +
788B LEU* 2.9 13.2 + - + +
789B HIS* 2.9 55.8 + - + +
795B HIS* 6.4 0.7 - - + -
798B LEU* 3.8 18.4 - - + -
826B ILE* 3.7 15.0 - - + +
902B ASP* 4.3 7.9 - - + +
906B MET* 3.3 35.9 - - + -
971B ALA* 4.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 786 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B ALA 2.8 17.9 + - - +
783B SER 3.6 5.8 - - - +
785B VAL* 1.3 75.7 - - - +
787B HIS* 1.3 57.1 + - - +
789B HIS* 3.4 3.2 + - - +
790B SER* 2.9 29.7 + - - -
971B ALA* 3.6 22.1 - - + +
972B MET* 4.0 22.1 - - + +
975B LEU* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 787 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B GLU 4.6 1.6 - - - -
722B SER* 3.4 27.8 + - - -
724B ASP* 5.3 4.4 - - + +
725B HIS* 3.7 40.1 + + + +
728B VAL* 4.6 2.8 - - - +
783B SER 3.3 10.5 + - - +
784B GLY 3.1 10.5 + - - +
785B VAL 3.1 0.2 - - - -
786B ALA* 1.3 78.9 - - - +
788B LEU* 1.3 63.3 + - - +
790B SER* 2.6 28.8 + - - -
791B LEU* 3.2 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 788 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B SER* 3.3 34.5 - - - +
728B VAL* 4.3 8.3 - - + -
784B GLY 3.1 13.9 + - - +
785B VAL* 2.9 16.6 + - + +
787B HIS* 1.3 77.9 - - - +
789B HIS* 1.3 64.4 + - + +
791B LEU* 3.1 10.4 + - - -
793B ILE* 2.8 45.9 + - + +
795B HIS* 4.5 22.4 - - + -
798B LEU* 5.9 0.2 - - + -
826B ILE* 4.6 11.4 - - + -
829B PHE* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 789 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B VAL* 2.9 38.5 + - + +
786B ALA* 3.8 6.1 - - - +
788B LEU* 1.3 78.8 - - + +
790B SER* 1.3 57.4 + - - +
792B LYS* 3.0 14.6 + - - +
793B ILE 3.5 17.9 - - - +
794B ILE* 4.8 0.2 - - - -
899B ARG* 3.1 74.8 + - + +
902B ASP* 2.8 26.6 + - + -
903B ILE* 4.1 11.1 - - + +
971B ALA* 4.0 14.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 790 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B ALA 2.9 14.5 + - - -
787B HIS* 2.6 28.2 + - - -
789B HIS* 1.3 75.4 - - - +
791B LEU* 1.3 66.4 + - - +
792B LYS* 3.2 6.4 + - - +
972B MET* 5.3 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 791 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B GLU* 3.6 30.4 - - + +
722B SER* 3.6 18.6 - - - +
787B HIS* 3.2 41.5 + - + +
788B LEU* 3.1 8.9 + - - +
790B SER* 1.3 81.9 + - - +
792B LYS* 1.3 71.4 + - - +
793B ILE* 3.3 17.1 + - + +
834B LYS* 3.6 14.7 - - - -
----------------------------------------------------------
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