Contacts of the helix formed by residues 855 - 877 (chain A) in PDB entry 3H44
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 PRO 855 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853A GLU 3.9 0.4 - - - +
854A LYS* 1.4 91.9 - - + +
856A PRO* 1.3 76.7 - - + +
857A HIS* 3.2 33.0 - - + +
858A TYR* 2.8 26.9 + - + +
859A LEU* 3.3 8.2 + - - +
959A LEU* 5.9 1.3 - - + -
963A MET* 3.8 17.7 - - + -
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Residues in contact with PRO 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A SER* 3.6 24.0 - - - +
790A GLY 4.5 4.5 - - - +
791A ILE* 3.4 13.1 - - + +
854A LYS 3.8 0.2 - - - -
855A PRO* 1.3 84.2 - - + +
857A HIS* 1.3 63.0 + - - +
859A LEU* 3.1 15.8 + - + +
860A GLU* 2.9 21.1 + - - +
957A HIS* 3.4 41.1 - - + +
958A VAL 4.7 3.4 - - - +
959A LEU* 3.7 22.2 - - + -
963A MET* 4.0 7.2 - - - -
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Residues in contact with HIS 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A PRO* 3.1 29.1 + - + +
856A PRO* 1.3 78.2 - - + +
858A TYR* 1.3 83.1 + + + +
860A GLU* 3.1 25.0 - - - +
861A SER* 3.4 8.0 + - - -
957A HIS* 4.1 9.7 + - + +
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Residues in contact with TYR 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A GLU* 4.6 0.9 + - - -
829A LEU* 3.8 15.6 - - + +
854A LYS* 3.9 31.7 + - + -
855A PRO* 2.8 26.9 + - + +
857A HIS* 1.3 88.3 + + + +
859A LEU* 1.3 68.0 + - + +
861A SER* 2.8 26.6 + - - -
862A ARG* 3.2 46.6 + - + +
980A LEU* 4.0 16.6 - - - +
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Residues in contact with LEU 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A SER* 4.2 5.6 - - - +
790A GLY 5.4 0.2 - - - -
791A ILE* 3.7 30.5 - - + +
829A LEU* 4.3 13.0 - - + -
850A ILE* 4.2 22.6 - - + +
852A SER* 3.6 35.2 - - - +
854A LYS* 3.8 24.0 - - + +
855A PRO 3.3 1.3 + - - +
856A PRO* 3.1 21.0 + - + +
858A TYR* 1.3 80.9 - - + +
860A GLU* 1.3 67.1 + - - +
862A ARG* 3.1 6.1 + - - +
863A VAL* 3.0 28.5 + - - +
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Residues in contact with GLU 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A TRP* 3.8 15.6 - - + -
791A ILE* 3.7 3.8 - - + +
793A ILE* 3.6 16.2 - - - +
856A PRO 2.9 17.3 + - - +
857A HIS* 3.1 12.3 - - - +
859A LEU* 1.3 76.7 - - - +
861A SER* 1.3 63.4 + - - +
863A VAL* 3.3 3.5 + - - +
864A GLU* 3.0 26.8 + - - +
953A LYS* 3.0 29.1 + - - -
955A SER* 2.6 26.4 + - - -
957A HIS* 2.9 30.2 - - + +
986A LEU* 4.7 10.1 - - + -
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Residues in contact with SER 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A HIS 3.4 5.7 + - - -
858A TYR* 2.8 28.9 + - - -
860A GLU* 1.3 80.9 - - - +
862A ARG* 1.3 61.4 + - - +
864A GLU* 3.2 7.2 + - - +
865A ALA* 2.7 30.3 + - - +
983A ALA* 3.4 23.0 - - - +
984A PRO 5.6 0.9 - - - -
986A LEU* 4.6 11.1 - - - +
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Residues in contact with ARG 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A LEU* 3.7 6.7 - - + +
827A GLU* 2.4 54.6 + - - +
829A LEU* 4.3 15.3 - - + -
858A TYR* 3.2 50.5 + - + +
859A LEU 3.1 6.5 + - - +
861A SER* 1.3 78.8 + - - +
863A VAL* 1.3 60.3 + - - +
865A ALA* 3.1 27.8 - - - +
866A PHE* 3.0 27.7 + - - +
980A LEU* 3.9 17.0 - - - +
981A SER* 2.7 36.7 + - - +
983A ALA* 4.2 6.7 - - - +
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Residues in contact with VAL 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A ILE* 3.9 19.5 - - + -
795A TYR* 4.2 13.2 - - - +
823A LEU* 4.5 6.1 - - + -
848A PHE* 3.6 49.6 - - + -
850A ILE* 4.1 24.5 - - + -
859A LEU 3.0 14.8 + - - +
860A GLU 3.7 6.1 - - - +
862A ARG* 1.3 75.7 - - - +
864A GLU* 1.3 58.4 + - - +
866A PHE* 3.3 7.9 + - + +
867A LEU* 2.8 29.3 + - + +
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Residues in contact with GLU 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A ILE* 6.4 0.2 - - + -
795A TYR* 2.8 16.1 + - - +
860A GLU 3.0 17.8 + - - +
861A SER* 3.2 11.2 + - - +
863A VAL* 1.3 74.3 - - - +
865A ALA* 1.3 68.7 + - - +
867A LEU* 3.2 16.5 + - - +
868A ILE* 3.3 16.6 + - - +
946A VAL* 4.5 2.8 + - - +
951A ARG* 3.0 29.5 + - - -
953A LYS* 2.7 29.1 + - - +
984A PRO* 3.7 21.2 - - + +
986A LEU* 3.6 25.8 - - + +
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Residues in contact with ALA 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A GLU* 5.7 0.2 - - - +
861A SER 2.7 19.4 + - - +
862A ARG* 3.1 36.1 - - - +
864A GLU* 1.3 69.9 - - - +
866A PHE* 1.3 54.9 + - - +
868A ILE* 2.8 29.7 + - - +
869A THR* 3.3 12.4 + - - -
981A SER* 3.6 7.5 + - - +
982A GLN 3.4 22.6 - - - +
983A ALA* 3.8 3.4 - - - +
984A PRO* 3.7 1.6 - - - +
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Residues in contact with PHE 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A ILE* 3.9 16.6 - - + -
818A PRO* 3.4 22.7 - - + -
819A ALA* 3.3 31.4 - - + -
822A THR* 3.6 27.4 - - + -
823A LEU* 3.7 19.3 - - + -
848A PHE* 4.3 11.7 - + - -
862A ARG 3.0 16.9 + - - +
863A VAL* 3.4 7.6 - - - +
865A ALA* 1.3 79.0 - - - +
867A LEU* 1.3 67.1 + - + +
869A THR* 3.1 18.1 + - + -
870A MET* 3.0 55.9 + - + +
981A SER* 4.7 0.4 + - - -
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Residues in contact with LEU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A TYR* 3.7 39.5 - - + +
811A PHE* 4.7 22.4 - - + -
815A ILE* 4.9 0.7 - - + -
846A LEU* 5.0 2.0 - - + -
848A PHE* 4.0 24.7 - - + -
863A VAL 2.8 17.4 + - - +
864A GLU* 3.4 18.4 - - - +
865A ALA 2.9 0.4 + - - -
866A PHE* 1.3 82.8 - - + +
868A ILE* 1.4 60.7 + - - +
870A MET* 3.3 7.4 + - + +
871A GLU 3.3 16.5 + - - -
940A TYR* 3.4 29.2 + - + +
944A LEU* 4.9 8.1 - - + +
945A ALA* 6.2 0.2 - - - -
951A ARG* 4.5 5.6 - - - +
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Residues in contact with ILE 868 (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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864A GLU* 3.3 12.5 + - - +
865A ALA 2.8 13.5 + - - +
867A LEU* 1.4 67.3 - - - +
869A THR* 1.3 66.3 + - - +
870A MET 2.8 2.5 + - - -
871A GLU* 3.0 13.4 + - - +
872A LYS* 2.8 32.4 + - + +
940A TYR* 4.2 10.5 - - - +
946A VAL* 5.9 3.8 - - + -
982A GLN* 4.1 9.4 - - + +
984A PRO* 3.3 45.3 - - + -
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Residues in contact with THR 869 (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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818A PRO* 6.3 0.2 - - + -
822A THR* 5.1 6.9 - - + +
865A ALA 3.3 9.1 + - - -
866A PHE* 3.1 29.4 + - + +
868A ILE* 1.3 76.5 - - - +
870A MET* 1.3 66.3 + - - +
872A LYS* 3.9 7.9 - - - +
873A SER* 3.2 24.8 + - - +
981A SER* 3.9 16.3 + - - -
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Residues in contact with MET 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A PHE* 4.7 9.2 - - + -
814A ILE* 3.7 24.0 - - + +
815A ILE* 3.4 38.6 - - + -
818A PRO* 3.7 15.7 - - + -
866A PHE* 3.0 46.0 + - + +
867A LEU* 3.3 13.5 - - + +
868A ILE 2.8 5.1 + - - -
869A THR* 1.3 78.5 - - - +
871A GLU* 1.3 64.6 + - - +
873A SER* 3.0 18.9 + - - +
874A ILE* 2.8 30.3 + - + +
877A MET* 6.2 0.4 - - + -
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Residues in contact with GLU 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A PHE* 5.7 0.2 - - - -
867A LEU 3.3 2.2 + - - -
868A ILE* 3.0 15.7 + - - +
870A MET* 1.3 77.9 - - - +
872A LYS* 1.3 63.9 + - - +
873A SER 3.1 1.2 + - - -
874A ILE* 3.1 20.5 + - - +
875A GLU* 3.3 34.2 + - - +
937A ILE* 4.4 8.9 - - + +
940A TYR* 3.5 50.4 + - + -
941A LYS* 3.3 27.1 + - - -
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Residues in contact with LYS 872 (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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868A ILE* 2.8 30.5 + - + +
869A THR* 3.9 8.7 - - - +
871A GLU* 1.3 76.0 - - - +
873A SER* 1.3 55.2 + - - +
875A GLU* 4.0 16.2 - - - +
876A ASP* 3.3 47.4 + - - +
58B PRO* 4.0 26.9 + - - +
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Residues in contact with SER 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A THR* 3.2 15.8 + - - +
870A MET* 3.0 25.4 + - - +
872A LYS* 1.3 76.3 - - - +
874A ILE* 1.3 61.2 + - - +
875A GLU 3.1 1.3 - - - -
876A ASP* 3.8 11.3 - - - +
877A MET* 3.1 34.1 + - - +
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Residues in contact with ILE 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A PHE* 4.3 21.8 - - + -
814A ILE* 3.6 36.8 - - + -
870A MET* 2.8 34.5 + - + +
871A GLU* 3.1 8.0 + - - +
873A SER* 1.3 77.8 - - - +
875A GLU* 1.3 58.1 + - - +
877A MET* 3.4 18.8 - - + +
882A PHE* 5.1 3.6 - - + -
933A LYS* 3.0 35.1 + - + +
936A ILE* 4.7 13.7 - - + -
937A ILE* 3.7 25.4 - - + -
940A TYR* 6.5 0.4 - - + -
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Residues in contact with GLU 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A GLU* 3.3 44.2 + - - +
872A LYS* 4.0 18.3 - - - +
873A SER 3.1 0.2 - - - -
874A ILE* 1.3 76.4 - - - +
876A ASP* 1.3 64.6 + - - +
933A LYS* 2.5 27.4 + - - +
937A ILE* 3.8 20.7 - - + +
941A LYS* 4.9 2.6 + - - -
53B HIS* 4.0 42.2 + - + +
55B THR* 3.9 7.3 + - - +
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Residues in contact with ASP 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LYS* 3.3 45.9 + - - +
873A SER* 3.6 11.0 + - - +
875A GLU* 1.3 79.2 - - - +
877A MET* 1.3 56.0 - - - +
878A THR* 3.7 3.5 + - - +
53B HIS* 5.2 4.5 - - - -
55B THR* 3.2 22.6 - - - +
56B LYS* 4.0 17.5 + - - +
58B PRO* 3.8 23.1 - - + +
422B PHE* 6.0 0.7 - - - -
455B LEU* 5.5 2.9 - - - +
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Residues in contact with MET 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A ILE* 4.4 15.5 - - + +
870A MET* 6.2 0.4 - - + -
873A SER* 3.1 19.9 + - - +
874A ILE* 3.4 23.3 - - + +
875A GLU 3.1 1.6 + - - -
876A ASP* 1.3 76.4 - - - +
878A THR* 1.3 63.7 + - - +
881A ALA* 4.2 10.5 - - + -
882A PHE* 3.9 39.0 - - - -
885A HIS* 3.6 30.3 - - + +
933A LYS* 2.4 33.9 + - + +
55B THR* 4.6 0.9 - - - -
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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
------------------------------------------------------------
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