Contacts of the helix formed by residues 784 - 810 (chain A) in PDB entry 4YOZ
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 ARG 784 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ILE* 5.9 6.1 - - - +
531A PHE* 5.0 0.2 - - - -
532A TYR* 3.3 45.6 + - - +
535A LYS* 5.7 2.0 - - - +
577A ALA* 3.6 31.6 - - + +
580A VAL* 5.2 2.0 - - + -
783A LYS* 1.3 119.6 - - + +
785A THR* 1.3 54.4 + - - +
786A GLY 3.3 2.0 - - - -
787A SER* 3.5 15.7 + - - -
788A LEU* 2.5 40.1 + - - +
1004A SO4 3.2 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A SER* 4.4 7.1 + - - -
781A ARG* 4.3 15.7 - - + -
782A PRO* 2.6 43.6 + - + +
783A LYS 3.1 2.6 + - - -
784A ARG* 1.3 77.0 - - - +
786A GLY* 1.3 59.4 + - - +
788A LEU* 3.5 7.8 - - - +
789A ALA* 2.9 30.3 + - + +
1004A SO4 3.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A ARG 3.3 0.6 - - - -
785A THR* 1.3 79.8 - - - +
787A SER* 1.3 57.2 + - - +
789A ALA* 3.3 7.1 + - - +
790A LEU* 3.0 30.0 + - - +
1004A SO4 3.3 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 4.0 18.3 - - - -
532A TYR* 5.4 0.9 - - - -
534A TYR* 4.4 1.7 + - - -
535A LYS* 3.9 23.3 - - - +
784A ARG* 3.1 26.8 + - - -
786A GLY* 1.3 73.7 - - - +
788A LEU* 1.3 64.5 + - - +
790A LEU* 4.1 3.8 - - - +
791A PHE* 3.0 26.9 + - - +
1004A SO4 3.2 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 4.4 2.5 - - + -
574A LEU* 3.9 23.3 - - + -
577A ALA* 3.7 25.1 - - + +
578A LEU* 3.8 30.1 - - + -
581A SER* 3.4 32.3 - - - +
584A LYS 4.5 4.9 - - - +
586A PRO* 4.6 9.2 - - + -
784A ARG 2.5 21.4 + - - +
785A THR* 3.5 6.1 - - - +
787A SER* 1.3 71.9 - - - +
789A ALA* 1.3 64.1 + - - +
791A PHE* 3.9 0.8 - - - +
792A TYR* 3.0 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A PRO* 4.9 2.4 - - + +
591A VAL* 3.5 26.8 - - + +
785A THR* 2.9 19.7 + - + +
786A GLY* 3.7 7.6 - - - +
787A SER 3.3 0.2 - - - -
788A LEU* 1.3 76.5 - - - +
790A LEU* 1.3 58.1 + - - +
793A ARG* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A TYR* 3.4 13.2 - - + +
535A LYS* 3.5 34.8 - - + -
538A GLU* 5.2 4.9 - - - +
786A GLY 3.0 17.8 + - - +
787A SER* 4.1 3.1 - - - +
789A ALA* 1.3 73.2 - - - +
791A PHE* 1.3 66.4 + - - +
793A ARG* 3.2 36.3 + - - +
794A LYS* 3.0 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 3.5 27.8 - + + -
534A TYR* 3.1 24.6 + + - +
562A ILE* 5.2 0.9 - - + -
563A LEU* 3.7 27.4 - - + -
567A ALA* 3.6 32.3 - - + -
568A TRP* 3.6 37.9 - + - -
574A LEU* 4.0 13.9 - - + -
787A SER 3.0 19.0 + - - +
788A LEU 3.9 2.0 - - - +
790A LEU* 1.3 75.0 - - - +
792A TYR* 1.3 72.4 + + - +
794A LYS* 3.1 6.6 + - - +
795A VAL* 2.9 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A TRP* 3.6 33.9 - + - -
574A LEU* 4.2 3.5 - - + +
578A LEU* 3.6 20.5 - - + +
585A VAL* 3.5 31.4 - - + +
586A PRO* 3.6 30.7 - - + -
591A VAL* 4.6 1.8 - - + -
788A LEU* 3.0 44.4 + - + +
789A ALA 4.2 1.3 - - - +
791A PHE* 1.3 86.5 - + - +
793A ARG* 1.3 61.0 + - - +
795A VAL* 3.6 10.9 - - + +
796A TYR* 2.8 59.2 + + + -
828A LEU* 4.6 13.3 + - + -
832A PRO* 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A GLU* 4.6 12.1 + - - -
591A VAL* 3.7 33.7 - - + +
592A ILE* 4.8 11.8 - - + +
789A ALA 3.0 20.3 + - - +
790A LEU* 3.2 32.2 + - - +
792A TYR* 1.3 77.6 - - - +
794A LYS* 1.3 75.8 + - - +
796A TYR* 4.0 2.3 - - - +
797A HIS* 2.9 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A TYR* 3.7 23.0 + - + -
535A LYS* 5.8 1.4 - - - +
538A GLU* 3.9 26.2 + - - +
559A GLU* 3.3 36.7 + - - -
563A LEU* 3.7 22.9 - - + +
790A LEU* 3.0 28.1 + - + +
791A PHE 3.1 6.7 + - - +
793A ARG* 1.3 95.9 - - - +
795A VAL* 1.3 61.2 + - - +
797A HIS* 3.4 10.3 + - + +
798A LEU* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A LEU* 4.2 15.7 - - + +
568A TRP* 4.0 7.6 - - + -
791A PHE* 2.9 52.9 + - + +
792A TYR* 3.6 12.1 - - + +
794A LYS* 1.3 74.3 - - - +
796A TYR* 1.3 60.2 + - - +
798A LEU* 3.3 5.4 + - - +
799A ALA* 2.9 29.8 + - - +
824A PHE* 5.2 0.9 - - + -
828A LEU* 3.9 26.7 - - + -
840A LEU* 4.0 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A VAL* 4.5 0.2 - - - +
586A PRO 2.9 29.1 + - - -
587A THR 3.6 1.6 - - - -
588A CYS* 3.3 45.4 + - + -
591A VAL* 3.7 11.0 - - + -
592A ILE* 4.8 3.6 - - + -
792A TYR* 2.8 37.1 + + + +
793A ARG* 4.0 4.0 - - - +
795A VAL* 1.3 73.2 - - + +
797A HIS* 1.3 61.6 + - - +
799A ALA* 4.7 0.7 - - - -
800A SER* 3.1 21.3 + - - -
821A TRP* 3.2 30.5 - + - -
824A PHE* 4.8 1.8 - + - -
825A GLU* 3.8 15.7 - - + +
828A LEU* 3.6 31.5 - - + +
829A VAL* 3.3 22.0 - - - +
967A PRO* 4.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ILE* 5.9 2.2 - - + +
793A ARG* 2.9 28.7 + - + +
794A LYS* 3.7 11.9 - - + +
796A TYR* 1.3 77.9 - - - +
798A LEU* 1.3 63.1 - - - +
800A SER* 2.7 22.7 + - - -
801A VAL* 3.3 28.2 - - + +
967A PRO* 5.3 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLU* 3.8 36.6 - - + +
563A LEU* 4.0 29.8 - - + -
564A GLU 4.6 0.9 - - - +
794A LYS 2.9 18.8 + - - +
795A VAL 3.3 4.0 + - - +
797A HIS* 1.3 80.7 - - + +
799A ALA* 1.3 63.5 + - - +
801A VAL* 3.3 10.1 + - + +
802A ARG* 3.1 62.5 + - + +
840A LEU* 4.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A VAL 2.9 17.1 + - - +
796A TYR 4.1 0.2 - - - +
798A LEU* 1.3 78.0 - - - +
800A SER* 1.3 57.0 + - - +
802A ARG* 3.4 6.5 + - - +
803A LEU* 2.8 30.1 + - - +
821A TRP* 3.9 7.4 - - + -
824A PHE* 3.5 37.2 - - + -
840A LEU* 4.3 10.1 - - + +
844A LEU* 3.7 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A TYR 3.1 14.6 + - - -
797A HIS* 2.7 27.4 + - - -
799A ALA* 1.3 75.8 - - - +
801A VAL* 1.3 60.5 + - - +
804A ARG* 2.9 33.2 + - - +
821A TRP* 3.6 9.1 - - - -
966A PHE* 3.5 26.4 - - - -
967A PRO* 3.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A HIS* 3.3 35.9 - - + +
798A LEU* 3.3 11.8 + - + +
800A SER* 1.3 79.6 + - - +
802A ARG* 1.3 65.1 + - + +
804A ARG* 3.5 9.1 + - - +
805A ASP* 3.2 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLU* 3.3 25.3 + - - +
564A GLU* 2.8 40.4 + - - +
798A LEU* 3.1 40.6 + - + +
799A ALA* 3.8 9.0 - - - +
801A VAL* 1.3 78.5 - - + +
803A LEU* 1.3 64.3 + - - +
805A ASP* 3.3 1.8 + - - -
806A LEU* 3.1 21.4 + - + +
840A LEU* 4.9 2.8 - - - +
841A ASP* 2.8 38.9 + - - -
844A LEU* 4.0 11.9 - - + -
871A GLN* 3.2 29.5 + - - +
873A GLN* 3.3 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A ALA 2.8 18.5 + - - +
800A SER* 3.9 4.9 - - - +
802A ARG* 1.3 75.6 - - - +
804A ARG* 1.3 57.6 + - - +
806A LEU* 3.4 4.1 + - + -
807A CYS* 2.9 45.7 + - - -
817A ARG* 3.8 12.8 - - + +
820A ILE* 3.7 20.2 - - + -
821A TRP* 3.8 42.8 - - + +
844A LEU* 3.9 20.1 - - + +
848A PHE* 3.8 15.5 - - + -
966A PHE* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 804 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A SER* 2.9 17.0 + - - +
801A VAL* 3.7 8.3 - - - +
802A ARG 3.3 0.2 - - - -
803A LEU* 1.3 78.4 - - - +
805A ASP* 1.3 62.8 + - - +
807A CYS* 3.6 6.2 + - - +
808A LEU* 3.1 24.4 + - - +
817A ARG* 3.7 36.7 + - - +
966A PHE* 3.2 33.2 + - + -
967A PRO 4.0 12.6 + - - -
1003A SO4 4.3 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 805 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A VAL* 3.2 13.8 + - + +
802A ARG* 3.7 8.3 - - - +
803A LEU 3.3 0.2 - - - -
804A ARG* 1.3 74.3 - - - +
806A LEU* 1.3 59.8 + - - +
808A LEU* 3.1 11.7 + - - +
809A LYS* 2.9 55.6 + - - +
867A SER 4.9 0.5 - - - +
871A GLN* 3.1 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 806 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A ARG* 3.1 15.0 + - + +
803A LEU* 3.7 5.4 - - - +
805A ASP* 1.3 77.2 - - - +
807A CYS* 1.3 57.1 + - - +
809A LYS* 3.2 3.0 + - - +
810A LEU* 2.8 40.1 + - + +
844A LEU* 4.7 15.7 - - + -
845A LEU* 3.5 26.5 - - + -
848A PHE* 4.0 23.3 - - + -
864A ILE* 3.9 10.5 - - + +
867A SER* 3.9 12.3 - - - +
868A TYR* 3.7 36.8 - - + +
871A GLN* 3.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 807 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A LEU* 2.9 37.8 + - - +
804A ARG 3.8 4.3 - - - +
806A LEU* 1.3 76.0 - - - +
808A LEU* 1.3 57.8 + - - +
811A ASP* 2.8 21.7 + - - -
812A VAL* 2.8 35.9 + - + +
817A ARG* 3.5 45.1 - - + +
820A ILE* 4.7 1.6 - - - -
848A PHE* 3.8 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 808 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A ARG 3.1 14.8 + - - +
805A ASP* 3.3 15.0 - - - +
806A LEU 3.1 0.2 - - - -
807A CYS* 1.3 77.1 - - - +
809A LYS* 1.3 70.6 + - + +
811A ASP* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 809 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A ASP* 2.9 43.1 + - - +
806A LEU* 4.0 3.6 - - - +
808A LEU* 1.3 84.9 - - + +
810A LEU* 1.3 59.3 + - - +
811A ASP* 3.3 1.7 + - - +
867A SER* 4.1 31.1 + - - +
870A ASN* 3.3 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 810 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A LEU* 2.8 23.3 + - + +
809A LYS* 1.3 75.7 - - - +
811A ASP* 1.3 63.2 + - - +
812A VAL* 3.8 12.8 - - + -
848A PHE* 3.5 31.0 - - + -
859A ARG* 2.3 44.9 + - + +
863A GLU* 3.6 31.4 - - + +
864A ILE* 4.0 18.8 - - + -
867A SER* 3.3 26.9 - - - +
----------------------------------------------------------
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