Contacts of the helix formed by residues 866 - 886 (chain C) in PDB entry 3CMM
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 ILE 866 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 4.2 19.1 - - + +
25C VAL* 4.4 12.1 - - + -
26C LEU* 4.1 24.2 - - + -
58C ALA* 5.5 2.0 - - + -
372C GLN* 3.6 20.4 - - - +
375C LEU* 3.9 19.7 - - + -
480C ASN* 5.1 2.2 - - - -
481C ARG* 4.3 4.5 - - - +
570C GLY 3.6 26.1 + - - +
571C THR* 5.0 0.7 - - + -
865C ALA* 1.3 77.2 - - - +
867C ALA* 1.3 64.0 + - + +
868C THR* 2.8 31.5 + - + +
869C THR* 3.6 2.0 - - - +
870C THR* 3.1 21.3 + - - -
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Residues in contact with ALA 867 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 5.3 0.8 + - - +
53C LYS* 5.6 0.7 - - - -
54C ASN* 3.5 22.6 - - + +
57C LEU* 3.9 28.3 - - + -
448C GLU* 5.3 4.2 - - - +
480C ASN 4.3 3.9 + - - +
481C ARG* 3.8 23.3 - - + +
866C ILE* 1.3 75.8 - - + +
868C THR* 1.3 56.9 + - - +
870C THR* 3.6 5.3 - - - -
871C SER* 3.0 32.7 + - - -
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Residues in contact with THR 868 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASN* 4.7 6.4 - - - +
368C GLY* 3.4 21.1 + - - -
371C ALA* 3.9 6.8 - - - +
372C GLN* 3.0 64.4 + - + +
375C LEU* 4.7 4.0 - - - +
571C THR* 5.2 0.7 - - + -
866C ILE* 2.8 19.0 + - + +
867C ALA* 1.3 81.3 - - - +
869C THR* 1.3 84.8 + - - +
871C SER 3.3 0.2 + - - -
872C LEU* 3.3 15.4 + - - +
901C LEU* 3.7 2.2 - - + -
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Residues in contact with THR 869 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C THR* 4.2 8.5 - - + -
570C GLY 2.8 21.6 + - - +
571C THR* 3.3 21.7 + - - +
572C LYS 3.3 28.5 - - - +
573C GLY* 4.1 8.5 - - - +
866C ILE* 3.6 3.4 + - - +
868C THR* 1.3 87.2 - - - +
870C THR* 1.3 63.7 + - - +
872C LEU* 3.3 2.4 + - - +
873C VAL* 3.0 25.1 + - + +
899C VAL* 4.3 9.2 - - + -
901C LEU* 3.9 10.0 - - + +
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Residues in contact with THR 870 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ALA* 3.5 45.9 - - + +
445C ILE* 3.9 9.9 - - + +
448C GLU* 3.7 10.5 - - + -
481C ARG* 5.0 5.0 - - - +
568C THR* 4.1 21.3 + - - +
865C ALA* 5.5 1.4 - - - +
866C ILE 3.1 16.5 + - - -
867C ALA* 3.6 12.3 - - - -
868C THR 3.2 0.6 - - - -
869C THR* 1.3 78.8 - - - +
871C SER* 1.3 63.6 + - - +
873C VAL* 4.1 1.7 - - - +
874C THR* 3.1 27.4 + - - -
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Residues in contact with SER 871 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 3.4 15.4 + - - -
53C LYS* 4.1 2.2 - - - -
54C ASN* 3.3 19.6 + - - -
364C ALA* 3.6 14.2 + - - +
368C GLY* 3.5 12.3 + - - -
448C GLU* 3.3 31.6 - - - +
451C LYS* 5.0 0.7 - - - -
867C ALA 3.0 15.2 + - - -
868C THR 3.6 0.7 + - - -
870C THR* 1.3 75.5 - - - +
872C LEU* 1.3 59.1 + - - +
874C THR* 3.5 2.5 + - - -
875C GLY 2.9 22.7 + - - -
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Residues in contact with LEU 872 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ALA 3.8 9.9 - - - -
365C PHE* 3.2 54.0 - - + +
368C GLY* 4.3 2.2 - - - -
369C LEU* 3.6 24.7 - - + +
868C THR 3.3 10.4 + - - +
869C THR* 3.5 9.4 - - - +
871C SER* 1.3 77.1 + - - +
873C VAL* 1.3 68.7 + - + +
875C GLY* 3.0 12.6 + - - -
876C LEU* 3.0 24.4 + - + +
899C VAL* 4.1 20.0 - - + -
901C LEU* 4.2 19.5 - - + -
906C PHE* 4.2 2.2 - - + -
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Residues in contact with VAL 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ILE* 4.9 3.4 - - + -
566C SER* 3.6 31.9 - - - +
567C GLY 4.2 7.6 - - - +
568C THR* 4.5 6.7 - - + -
573C GLY* 3.9 13.2 - - - -
574C ASN* 3.8 28.5 - - - +
575C THR* 3.6 3.2 - - + +
869C THR* 3.0 23.8 + - + +
870C THR 4.1 2.9 - - - +
872C LEU* 1.3 86.0 - - + +
874C THR* 1.3 58.5 + - - +
876C LEU* 3.2 10.5 + - + +
877C VAL* 2.9 26.7 + - - +
899C VAL* 4.6 3.6 - - + -
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Residues in contact with THR 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ILE* 3.9 20.9 + - - +
448C GLU* 3.5 14.2 - - + +
449C MET* 3.6 28.7 - - - +
452C ASN* 3.5 24.2 - - - +
870C THR 3.1 19.3 + - - -
871C SER 3.7 4.3 - - - -
873C VAL* 1.3 73.0 - - - +
875C GLY* 1.3 69.5 + - - +
877C VAL* 3.1 8.8 + - - +
878C ASN* 3.0 34.1 + - - +
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Residues in contact with GLY 875 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C GLY* 3.5 31.2 - - - -
364C ALA* 3.6 15.4 - - - +
365C PHE 4.1 2.0 - - - -
452C ASN* 5.0 0.2 - - - -
871C SER 2.9 11.9 + - - -
872C LEU 3.0 5.8 + - - -
874C THR* 1.3 77.2 - - - +
876C LEU* 1.3 62.3 + - - +
878C ASN* 3.0 13.1 + - - +
879C LEU* 3.2 10.3 + - - +
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Residues in contact with LEU 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C PHE* 3.5 26.7 - - + +
391C PHE* 4.1 14.8 - - + -
575C THR* 4.0 21.3 - - + +
872C LEU* 3.0 31.5 + - + +
873C VAL* 3.2 10.3 + - + +
875C GLY* 1.3 71.0 - - - +
877C VAL* 1.3 67.3 + - - +
879C LEU* 2.9 20.3 + - + +
880C GLU* 3.2 14.5 + - - +
897C GLY* 4.8 6.1 - - - -
898C PHE 5.5 0.2 - - - +
899C VAL* 4.9 8.7 - - + -
908C PHE* 3.9 35.4 - - + -
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Residues in contact with VAL 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ILE* 6.2 0.2 - - + -
449C MET* 3.4 29.6 - - + -
540C THR* 4.5 3.1 - - + -
564C LEU* 3.8 30.6 - - + +
565C GLU 4.2 5.2 - - - +
566C SER* 3.5 23.3 - - - +
575C THR* 3.4 25.1 - - + -
873C VAL 2.9 14.3 + - - +
874C THR* 3.1 9.8 + - - +
876C LEU* 1.3 74.1 - - - +
878C ASN* 1.3 57.7 + - - +
880C GLU* 3.0 11.0 + - - +
881C LEU* 2.9 23.9 + - - +
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Residues in contact with ASN 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C PRO* 6.0 0.2 - - + -
361C GLY* 4.4 13.0 - - - +
449C MET* 2.9 24.3 - - - +
452C ASN* 3.3 32.2 - - - +
453C TRP* 3.0 27.5 + - - -
456C LEU* 4.0 9.3 - - + +
874C THR* 3.0 18.8 + - - +
875C GLY 3.0 10.2 + - - +
877C VAL* 1.3 75.2 - - - +
879C LEU* 1.3 62.1 + - - +
881C LEU* 3.4 22.0 - - - +
882C TYR* 3.5 20.0 - - + -
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Residues in contact with LEU 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 4.2 10.1 - - + -
359C ILE* 4.3 0.4 - - + -
361C GLY* 3.9 27.1 - - - +
362C VAL* 4.0 16.8 - - + +
365C PHE* 5.3 0.7 - - + -
391C PHE* 3.8 24.5 - - + -
393C SER* 3.7 28.5 - - - +
396C SER* 3.0 19.0 + - - +
875C GLY 3.2 11.2 + - - +
876C LEU* 2.9 19.3 + - + +
878C ASN* 1.3 76.8 - - - +
880C GLU* 1.3 66.9 + - - +
881C LEU 3.4 0.2 - - - -
882C TYR* 3.7 28.6 - - + +
883C LYS* 3.6 6.6 - - - -
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Residues in contact with GLU 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C SER* 5.3 0.9 + - - -
564C LEU* 3.7 6.1 - - + -
575C THR* 5.4 6.3 - - - +
576C GLN 6.1 0.2 - - - -
577C VAL* 3.5 25.8 - - + +
876C LEU 3.2 11.8 + - - +
877C VAL* 3.0 9.9 + - - +
879C LEU* 1.3 77.3 - - - +
881C LEU* 1.3 56.4 + - - +
882C TYR 3.2 0.4 - - - -
883C LYS* 2.8 56.3 + - - +
884C LEU* 3.3 10.2 + - - +
894C TYR* 3.4 16.9 - - + +
895C LYS* 2.7 48.7 + - - +
908C PHE* 6.1 0.3 - - - -
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Residues in contact with LEU 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ILE* 5.3 2.7 - - + -
449C MET* 4.7 0.7 - - + -
453C TRP* 3.4 31.2 - - + +
456C LEU* 4.1 14.6 - - + -
458C LEU* 3.8 21.5 - - + -
538C PHE* 3.9 28.7 - - + -
564C LEU* 4.0 18.5 - - + +
877C VAL 2.9 12.5 + - - +
878C ASN* 3.4 19.3 - - - +
880C GLU* 1.3 75.4 - - - +
882C TYR* 1.3 69.1 + - + +
884C LEU* 3.1 16.8 + - - +
885C ILE* 3.1 30.1 + - + +
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Residues in contact with TYR 882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 4.8 0.2 - - + -
359C ILE* 3.4 30.3 - - + +
360C PRO* 4.1 2.3 - - - +
361C GLY 5.1 2.0 + - - -
396C SER* 3.7 29.5 - - - +
420C GLN* 4.5 2.4 + - - +
424C PHE* 3.5 35.8 - + + -
428C PHE* 3.5 28.6 - + + -
429C GLN* 5.6 0.6 + - - -
432C ILE* 3.8 24.2 - - + -
456C LEU* 3.3 31.5 - - + +
878C ASN* 3.5 21.5 + - + -
879C LEU* 3.7 16.1 + - + +
880C GLU 3.2 0.2 - - - -
881C LEU* 1.3 79.9 - - + +
883C LYS* 1.3 60.6 + - - +
885C ILE* 3.4 5.6 + - - -
886C ASP* 3.3 18.7 + - - +
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Residues in contact with LYS 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C SER* 4.6 4.6 + - - -
395C GLU* 3.3 27.2 - - - +
396C SER* 3.9 13.2 - - - +
879C LEU 3.6 14.8 - - - +
880C GLU* 2.8 54.4 + - - +
882C TYR* 1.3 69.8 - - - +
884C LEU* 1.3 62.1 + - - -
886C ASP* 3.3 6.4 + - - -
888C LYS* 3.2 49.4 + - + +
893C GLN 2.7 31.9 + - - +
894C TYR* 3.6 18.7 + - + -
895C LYS* 4.1 10.1 - - - +
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Residues in contact with LEU 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C PHE* 3.6 48.9 - - + -
562C PRO* 3.8 26.1 - - + +
563C LEU 5.1 1.3 - - - +
564C LEU* 3.8 28.0 - - + -
577C VAL* 5.0 2.0 - - + -
578C ILE 5.3 0.4 - - - +
579C ILE* 4.0 22.9 - - + -
880C GLU 3.3 8.7 + - - +
881C LEU* 3.1 11.0 + - - +
883C LYS* 1.3 75.7 - - - +
885C ILE* 1.3 59.3 + - - +
887C ASN* 2.9 26.4 + - - +
894C TYR* 4.3 11.0 - - + +
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Residues in contact with ILE 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C PHE* 3.6 26.5 - - + -
431C LYS* 3.4 48.8 + - + +
432C ILE* 4.3 20.9 - - + +
435C SER* 3.6 20.6 - - - +
458C LEU* 4.7 2.7 - - + -
538C PHE* 3.7 24.5 - - + -
881C LEU* 3.1 32.3 + - + +
882C TYR* 3.6 4.9 - - - +
883C LYS 3.3 0.2 - - - -
884C LEU* 1.3 76.4 - - - +
886C ASP* 1.3 57.9 + - - +
887C ASN* 3.3 5.4 + - - +
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Residues in contact with ASP 886 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C PRO* 3.6 18.2 - - + +
399C ASP* 2.8 41.1 + - - +
402C ASN* 4.8 5.4 - - - +
403C PHE* 3.9 16.2 - - - -
428C PHE* 4.0 3.6 - - + -
431C LYS* 5.5 0.2 - - - +
882C TYR 3.3 9.4 + - - +
883C LYS* 3.3 9.7 + - - +
884C LEU 3.2 0.8 - - - -
885C ILE* 1.3 77.0 - - - +
887C ASN* 1.3 72.6 + - - +
888C LYS* 2.9 23.9 + - - +
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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