Contacts of the helix formed by residues 875 - 893 (chain A) in PDB entry 4AGD
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 875 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870A LEU* 4.5 0.6 - - - +
873A GLY 4.2 7.6 - - - +
874A ALA* 1.3 81.7 - - - +
876A HIS* 1.3 65.1 + - - +
877A SER* 2.9 22.6 + - - -
878A GLU* 2.6 35.5 + - - +
879A HIS* 3.1 11.6 + - - +
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Residues in contact with HIS 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A THR* 1.3 74.4 - - - +
877A SER* 1.3 56.4 + - - +
879A HIS* 3.6 24.1 - + + +
880A ARG* 2.8 70.7 + - - +
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Residues in contact with SER 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A THR* 2.9 16.9 + - - -
876A HIS* 1.3 79.7 - - - +
878A GLU* 1.3 68.5 + - - +
880A ARG* 3.4 11.1 + - - +
881A ALA* 3.0 20.0 + - - +
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Residues in contact with GLU 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A PHE* 3.3 54.1 - - + -
870A LEU* 3.5 21.2 - - + +
874A ALA* 3.9 4.0 - - + -
875A THR* 2.6 44.3 + - - +
877A SER* 1.3 76.5 - - - +
879A HIS* 1.3 59.1 + - - +
881A ALA* 2.6 31.9 + - - +
882A LEU* 2.8 12.5 + - - +
1049A LEU* 4.4 11.3 - - + +
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Residues in contact with HIS 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A LEU* 3.7 24.3 - - + +
875A THR 3.1 2.8 + - - +
876A HIS* 3.6 33.3 + + + +
878A GLU* 1.3 79.4 - - - +
880A ARG* 1.3 63.1 + - - +
882A LEU* 3.4 5.8 + - - +
883A MET* 2.9 36.1 + - + +
912A LEU* 3.7 40.0 + - + +
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Residues in contact with ARG 880 (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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876A HIS* 2.8 55.9 + - - +
877A SER* 3.6 10.6 + - - +
879A HIS* 1.3 78.6 + - - +
881A ALA* 1.3 63.6 + - - +
883A MET* 3.1 10.5 + - + +
884A SER* 2.7 28.2 + - - -
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Residues in contact with ALA 881 (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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802A LEU* 3.4 18.5 - - + +
877A SER 3.0 13.3 + - - +
878A GLU* 2.6 21.5 + - - +
880A ARG* 1.3 72.4 - - - +
882A LEU* 1.3 54.3 + - - +
884A SER* 3.0 27.8 + - - -
885A GLU 3.0 6.2 + - - -
1049A LEU* 4.4 20.2 - - + -
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Residues in contact with LEU 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A LYS* 4.4 13.5 - - + +
869A MET* 4.0 5.6 - - - +
870A LEU* 4.0 35.0 - - + +
878A GLU 2.8 12.4 + - - +
879A HIS* 3.6 9.6 - - - +
881A ALA* 1.3 67.8 - - - +
883A MET* 1.3 65.1 + - - +
884A SER 3.1 1.3 - - - -
885A GLU* 4.4 18.6 - - + +
886A LEU* 3.3 21.1 + - - +
912A LEU* 3.9 41.0 - - + +
914A VAL* 3.7 22.0 - - + +
1049A LEU* 5.1 7.1 - - + +
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Residues in contact with MET 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A TYR* 5.8 4.9 - - + -
879A HIS* 2.9 26.0 + - + +
880A ARG* 3.1 13.0 + - + +
882A LEU* 1.3 76.1 - - - +
884A SER* 1.3 59.7 + - - +
886A LEU* 3.7 8.6 + - + +
887A LYS* 2.8 55.8 + - + +
906A THR* 4.0 31.6 - - + +
912A LEU* 3.8 21.7 - - + +
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Residues in contact with SER 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A LEU* 4.6 9.6 - - - -
880A ARG* 2.7 19.6 + - - +
881A ALA* 3.0 15.7 + - - -
883A MET* 1.3 75.6 - - - +
885A GLU* 1.3 62.8 - - - +
887A LYS* 3.0 9.5 + - - +
888A ILE* 2.9 27.1 + - - +
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Residues in contact with GLU 885 (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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802A LEU* 3.9 23.4 - - + +
804A ILE 6.1 0.4 - - - +
868A LYS* 3.0 43.7 + - - +
881A ALA 3.0 7.3 + - - +
882A LEU* 3.4 19.9 + - + +
884A SER* 1.3 75.2 - - - +
886A LEU* 1.3 53.9 + - - +
888A ILE* 3.3 9.7 + - + +
889A LEU* 2.7 50.3 + - + +
914A VAL* 5.6 0.7 - - + -
1046A ASP* 3.2 23.1 - - + +
1048A GLY* 4.7 4.1 - - - -
1049A LEU* 4.6 11.3 + - - +
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Residues in contact with LEU 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A TYR* 4.4 11.0 - - + -
882A LEU 3.3 6.6 + - - +
883A MET* 3.7 21.1 - - - +
885A GLU* 1.3 78.1 - - - +
887A LYS* 1.3 57.8 + - + +
889A LEU* 3.2 7.4 + - - +
890A ILE* 2.8 50.5 + - + +
901A LEU* 3.4 33.4 - - + -
904A ALA* 3.8 19.7 - - + -
906A THR* 3.6 31.0 - - + -
912A LEU* 5.0 2.5 - - + -
914A VAL* 3.7 21.0 - - + +
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Residues in contact with LYS 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A LEU 5.8 1.5 + - - +
821A PRO* 5.9 1.4 - - - +
822A TYR* 4.3 29.5 - - - +
883A MET* 2.8 44.6 + - - +
884A SER* 3.0 14.0 + - - +
886A LEU* 1.3 86.3 - - + +
888A ILE* 1.3 57.5 + - - +
890A ILE* 3.4 10.8 + - + +
891A HIS* 2.9 24.7 + - - +
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Residues in contact with ILE 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A LEU* 6.0 1.3 - - + -
804A ILE* 3.0 46.0 - - + +
805A VAL* 3.8 8.7 - - + -
806A MET* 4.4 8.3 - - + +
884A SER* 2.9 20.5 + - - +
885A GLU* 3.4 16.8 - - + +
887A LYS* 1.3 72.9 - - + +
889A LEU* 1.3 67.0 + - + +
891A HIS* 3.0 8.6 + - + -
892A ILE* 2.8 35.3 + - + +
1024A CYS* 3.5 26.5 - - - -
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Residues in contact with LEU 889 (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 LYS* 5.0 4.3 - - + -
885A GLU* 2.7 36.0 + - + +
886A LEU* 3.3 5.8 - - - +
888A ILE* 1.3 78.6 - - - +
890A ILE* 1.3 62.3 + - - +
892A ILE* 3.2 29.1 - - + +
893A GLY* 3.3 5.0 + - - -
899A VAL* 4.0 17.7 - - + +
900A ASN 4.5 0.9 - - - -
901A LEU* 4.0 33.3 + - + +
914A VAL* 3.7 29.4 - - + -
916A VAL* 4.0 13.2 - - + -
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Residues in contact with ILE 890 (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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822A TYR* 3.8 26.7 - - + -
823A ASP* 5.2 1.6 - - + +
827A TRP* 3.6 42.9 - - + +
886A LEU* 2.8 36.0 + - + +
887A LYS* 3.6 10.3 - - + +
889A LEU* 1.3 70.2 - - - +
891A HIS* 1.3 70.8 + - - +
893A GLY* 3.5 8.4 + - - -
901A LEU* 3.6 19.1 - - + -
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Residues in contact with HIS 891 (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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806A MET* 3.3 32.1 - - + +
820A LEU* 6.0 4.2 - - - +
887A LYS 2.9 15.2 + - - +
888A ILE* 3.0 12.5 + - + +
890A ILE* 1.3 77.7 - - - +
892A ILE* 1.3 83.4 + - + +
893A GLY* 2.8 3.8 + - - -
1022A ARG* 2.9 63.5 + - - -
1023A LYS* 6.0 0.2 - - + -
1024A CYS* 4.4 1.1 - - - -
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Residues in contact with ILE 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A ILE* 5.5 1.6 - - + -
888A ILE* 2.8 29.7 + - + +
889A LEU* 3.2 26.9 - - + +
891A HIS* 1.3 75.0 - - + +
893A GLY* 1.3 88.6 + - - +
898A VAL* 4.6 11.2 - - + -
899A VAL 4.6 10.1 - - - +
900A ASN* 5.0 1.6 - - - +
901A LEU 5.9 0.2 - - - +
1018A PHE* 3.1 29.6 - - + -
1019A LEU* 4.3 14.8 - - + -
1022A ARG* 3.4 29.3 + - + +
1024A CYS* 3.5 31.2 - - - -
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Residues in contact with GLY 893 (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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827A TRP* 6.6 0.2 - - - -
889A LEU 3.3 5.5 + - - -
890A ILE* 3.9 7.2 - - - -
891A HIS 2.8 11.4 + - - -
892A ILE* 1.3 102.1 - - - +
894A HIS* 1.3 65.1 + - - -
895A HIS 3.4 2.6 + - - -
900A ASN* 3.7 2.5 + - - -
1018A PHE* 3.5 3.5 - - - -
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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
------------------------------------------------------------
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