Contacts of the helix formed by residues 784 - 805 (chain A) in PDB entry 4XUF
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 THR 784 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783A LEU* 1.3 80.3 - - - +
785A PHE* 1.3 65.8 + - - +
786A GLU* 3.5 19.4 + - - +
787A ASP* 2.8 32.6 + - - +
788A LEU* 3.2 17.1 - - - +
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Residues in contact with PHE 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784A THR* 1.3 72.1 - - - +
786A GLU* 1.3 66.9 + - - +
788A LEU* 3.2 21.9 + - + +
789A LEU* 3.2 38.5 + - + +
882A PHE* 3.6 24.5 - + - -
913A TYR* 3.2 28.7 - - + -
914A ALA* 4.4 2.7 - - - -
915A THR* 3.8 30.3 - - + -
918A ILE* 4.6 0.4 - - + -
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Residues in contact with GLU 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A THR* 3.2 11.4 + - - +
785A PHE* 1.3 83.3 - - - +
787A ASP* 1.3 68.8 + - - +
789A LEU* 3.2 10.6 + - + +
790A CYS* 2.6 51.2 + - + +
823A LYS* 4.0 20.0 + - - -
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Residues in contact with ASP 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A LEU* 3.4 24.7 + - + +
784A THR* 2.8 35.3 + - - +
786A GLU* 1.3 97.0 - - - +
788A LEU* 1.3 56.5 + - - +
790A CYS* 3.9 6.0 - - - +
791A PHE* 2.9 48.5 + - + -
823A LYS* 3.9 20.5 - - - +
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Residues in contact with LEU 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A LEU* 4.5 13.9 - - + -
783A LEU* 4.6 15.3 - - + -
784A THR 3.2 26.9 - - - +
785A PHE* 3.2 16.9 + - + +
787A ASP* 1.3 78.5 - - - +
789A LEU* 1.3 61.8 + - - +
791A PHE* 3.5 16.3 + - + +
792A ALA* 3.2 22.7 + - - +
881A ILE* 3.4 38.5 - - + +
882A PHE* 3.6 27.4 - - + -
884A LEU* 4.8 8.1 - - + -
913A TYR* 5.8 6.5 - - + +
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Residues in contact with LEU 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785A PHE* 3.2 37.0 + - + +
786A GLU* 3.2 12.7 + - + +
788A LEU* 1.3 75.1 - - - +
790A CYS* 1.3 61.6 + - - +
792A ALA* 3.3 2.2 + - - +
793A TYR* 2.8 31.8 + - - +
882A PHE* 3.8 8.5 - - + -
918A ILE* 3.7 34.8 - - + -
943A LEU* 4.1 23.3 - - + +
946A GLN* 4.3 31.2 - - + +
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Residues in contact with CYS 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786A GLU* 2.6 37.4 + - + +
787A ASP* 3.6 9.6 - - - +
789A LEU* 1.3 74.5 - - - +
791A PHE* 1.3 63.3 + - + +
793A TYR* 3.8 7.6 - - - +
794A GLN* 3.0 63.2 + - - +
823A LYS* 4.0 20.6 - - + -
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Residues in contact with PHE 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A LEU* 4.0 27.6 - - + -
702A TYR* 4.3 28.0 - + - -
703A LEU* 5.0 3.6 - - + -
783A LEU* 4.5 12.1 - - + -
787A ASP* 2.9 39.1 + - + +
788A LEU* 3.7 18.2 - - + +
789A LEU 3.2 0.2 - - - -
790A CYS* 1.3 77.9 - - + +
792A ALA* 1.3 58.0 + - - +
794A GLN* 3.2 3.8 + - - -
795A VAL* 3.0 34.6 + - + +
819A VAL* 5.0 14.1 - - + -
823A LYS* 3.6 32.8 - - + -
825A VAL* 3.6 15.7 - - + +
881A ILE* 4.7 8.1 - - + -
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Residues in contact with ALA 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788A LEU 3.2 14.0 + - - +
789A LEU* 3.8 2.2 - - - +
791A PHE* 1.3 78.5 - - - +
793A TYR* 1.3 57.8 + - - +
795A VAL* 3.4 3.7 + - - +
796A ALA* 2.9 18.9 + - - +
874A TYR* 2.5 30.3 + - - +
878A LEU* 3.6 22.0 - - + -
881A ILE* 4.3 12.9 - - + +
882A PHE* 4.6 2.7 - - + -
943A LEU* 3.6 15.0 - - + -
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Residues in contact with TYR 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789A LEU 2.8 18.8 + - - +
790A CYS* 3.8 8.3 - - - +
792A ALA* 1.3 76.9 - - - +
794A GLN* 1.3 68.2 - - + +
796A ALA* 3.4 5.0 + - - +
797A LYS* 2.8 63.2 + - + +
939A LEU 6.0 0.2 - - - -
940A THR* 3.2 40.4 - - + +
943A LEU* 3.7 15.4 - - + +
944A GLY* 3.9 22.7 - - - -
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Residues in contact with GLN 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A ASN* 3.2 39.0 - - - +
790A CYS* 3.0 41.5 + - - +
791A PHE* 4.3 0.5 - - - -
793A TYR* 1.3 84.3 - - + +
795A VAL* 1.3 60.0 + - - +
797A LYS* 4.1 5.4 - - - -
798A GLY 2.8 23.6 + - - -
823A LYS* 3.2 15.7 + - - +
824A VAL* 3.8 16.0 - - - +
825A VAL* 3.0 34.9 + - + +
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Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A LEU* 5.8 1.1 - - + -
791A PHE* 3.0 23.5 + - + +
792A ALA* 3.7 6.7 - - - +
794A GLN* 1.3 75.9 - - - +
796A ALA* 1.3 58.1 + - - +
798A GLY 3.2 0.7 + - - -
799A MET* 2.8 33.4 + - + +
812A LEU* 4.6 3.4 - - + -
817A VAL* 4.3 19.5 - - + -
825A VAL* 3.7 17.7 - - + -
827A ILE* 3.5 18.5 - - + +
874A TYR* 3.6 19.5 - - + -
877A LEU* 3.7 23.1 - - + -
881A ILE* 5.2 5.6 - - + -
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Residues in contact with ALA 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A ALA 2.9 10.3 + - - +
793A TYR* 3.7 5.2 - - - +
795A VAL* 1.3 77.3 - - - +
797A LYS* 1.3 58.1 + - - +
799A MET* 3.5 6.6 + - - +
800A GLU* 3.1 26.3 + - - +
874A TYR* 3.3 31.2 - - + +
936A PHE* 4.2 7.1 - - + +
939A LEU* 4.1 25.4 - - + +
940A THR* 3.6 10.7 + - - +
943A LEU* 5.5 0.7 - - + -
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Residues in contact with LYS 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A HIS* 3.7 24.0 + - + +
672A GLU* 4.8 7.3 - - - +
673A ASN* 2.5 28.0 + - - +
793A TYR* 2.8 53.2 + - + +
794A GLN* 3.7 6.3 - - - +
795A VAL 3.2 0.2 - - - -
796A ALA* 1.3 77.3 - - - +
798A GLY* 1.3 61.8 + - - +
800A GLU* 3.4 23.5 + - - +
801A PHE* 3.5 5.0 + - - +
940A THR* 3.7 21.5 + - + +
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Residues in contact with GLY 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A HIS* 3.7 18.8 - - - -
673A ASN* 3.8 8.2 + - - -
674A ILE* 3.9 2.0 - - - +
794A GLN 2.8 17.3 + - - -
795A VAL 3.2 2.0 + - - -
797A LYS* 1.3 76.2 - - - +
799A MET* 1.3 63.1 + - - +
801A PHE* 3.2 17.8 + - - +
802A LEU* 3.4 13.9 + - - +
827A ILE* 3.8 11.4 - - - -
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Residues in contact with MET 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795A VAL* 2.8 24.4 + - + +
796A ALA 3.8 0.4 - - - +
797A LYS 3.3 0.2 - - - -
798A GLY* 1.3 73.4 - - - +
800A GLU* 1.3 60.9 + - - +
802A LEU* 3.1 25.9 + - + +
803A GLU* 2.9 27.9 + - - +
807A CYS 5.6 0.2 - - - +
809A HIS* 4.5 9.0 - - + +
812A LEU* 4.0 24.9 - - + -
827A ILE* 3.9 13.5 - - + -
867A ILE* 4.2 9.0 - - + -
870A ASP* 3.9 24.2 - - + +
936A PHE* 3.7 51.4 - - + -
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Residues in contact with GLU 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796A ALA 3.1 14.1 + - - +
797A LYS* 3.4 21.0 - - - +
799A MET* 1.3 77.2 - - - +
801A PHE* 1.3 56.2 + - - +
803A GLU* 3.3 5.7 + - + +
804A PHE* 2.9 30.8 + - + +
936A PHE* 4.3 12.3 - - + +
937A PRO* 3.8 31.8 - - + +
940A THR* 4.0 20.1 + - - +
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Residues in contact with PHE 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668A LEU* 3.2 49.8 - - + -
669A GLY* 4.2 7.4 - - - -
670A SER 4.6 4.0 - - - -
671A HIS* 3.5 47.6 - + + +
674A ILE* 4.7 0.4 - - + -
797A LYS 3.5 2.9 + - - +
798A GLY 3.2 11.1 + - - +
799A MET 3.2 0.6 - - - -
800A GLU* 1.3 79.5 + - - +
802A LEU* 1.3 64.7 + - + +
804A PHE* 3.7 12.0 + + - +
805A LYS* 3.2 43.9 + - + +
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Residues in contact with LEU 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668A LEU* 4.4 17.0 - - + -
674A ILE* 3.8 24.2 - - + -
798A GLY 3.6 12.3 - - - +
799A MET* 3.1 33.2 + - + +
801A PHE* 1.3 87.0 - - + +
803A GLU* 1.3 54.6 + - - +
804A PHE 3.2 0.4 - - - -
805A LYS* 3.2 4.2 + - - -
806A SER 3.0 7.3 + - - -
807A CYS* 2.6 57.0 + - + +
808A VAL 5.7 0.2 - - - -
809A HIS* 4.4 14.4 - - + +
827A ILE* 5.2 0.7 - - + -
1001A P30 4.0 26.2 - - + -
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Residues in contact with GLU 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799A MET 2.9 12.8 + - - +
800A GLU* 3.3 5.4 + - - +
802A LEU* 1.3 74.0 - - - +
804A PHE* 1.3 61.3 + - - +
806A SER* 2.9 21.2 + - - +
807A CYS 4.2 2.2 + - - +
867A ILE* 3.6 43.8 - - + +
935A SER* 4.4 10.8 + - - -
936A PHE* 3.5 18.9 + - - +
937A PRO* 3.3 31.8 - - + +
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Residues in contact with PHE 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A GLU* 2.9 20.2 + - + +
801A PHE* 3.8 14.8 - + - +
803A GLU* 1.3 77.2 - - - +
805A LYS* 1.3 76.8 + - + +
806A SER* 3.1 4.6 + - - -
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Residues in contact with LYS 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A GLN 4.2 10.6 + - - +
668A LEU* 3.5 35.4 + - + +
669A GLY* 5.6 0.6 - - - -
801A PHE* 3.2 36.7 + - + +
802A LEU* 3.2 7.2 + - - +
803A GLU 3.2 0.6 - - - -
804A PHE* 1.3 89.8 - - + +
806A SER* 1.3 71.2 + - - +
807A CYS* 3.4 18.9 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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