Contacts of the helix formed by residues 876 - 895 (chain A) in PDB entry 3T06
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 876 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836A GLN* 4.0 16.6 - - - +
840A LEU* 5.9 2.2 - - + -
872A ARG 4.5 5.6 - - - +
873A ASP 3.1 17.0 + - - +
875A ILE* 1.3 79.8 - - + +
877A SER* 1.3 59.3 + - - +
878A GLU 3.2 3.5 + - - -
879A MET* 3.4 20.1 + - + +
880A GLN* 3.1 34.3 + - + +
41B ASN* 4.7 0.4 - - - +
58B TRP* 3.9 22.7 - - + -
72B LEU* 3.2 45.3 - - + +
73B SER* 4.1 13.2 - - - +
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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
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749A HIS* 3.0 25.5 + - - -
752A THR* 3.3 24.7 - - - +
753A LEU* 4.8 4.2 - - - +
756A LEU* 5.5 0.3 - - - +
873A ASP 4.9 1.1 - - - -
874A LEU* 2.7 22.7 + - - -
876A ILE* 1.3 77.2 - - - +
878A GLU* 1.3 64.2 + - - +
880A GLN* 3.8 17.2 - - - +
881A ARG* 3.1 13.7 + - - +
41B ASN* 6.5 0.9 - - - -
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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
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749A HIS* 2.7 33.1 + - + -
753A LEU* 4.2 4.1 - - + +
785A LEU* 3.4 41.3 - - + +
789A HIS* 2.9 25.0 + - - -
825A LEU* 4.9 2.4 - - - +
829A ALA* 4.6 4.7 - - + +
832A PHE* 4.3 16.4 - - + -
833A CYS* 4.5 9.4 - - - -
875A ILE 4.0 3.0 + - - +
876A ILE 3.2 1.2 - - - -
877A SER* 1.3 77.2 + - - +
879A MET* 1.3 68.4 + - - +
881A ARG* 3.0 5.0 + - - +
882A LEU* 3.0 43.6 + - + +
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Residues in contact with MET 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A CYS* 4.0 22.3 - - - -
836A GLN* 5.1 0.7 - - - +
876A ILE* 3.4 27.6 + - + +
878A GLU* 1.3 80.7 - - - +
880A GLN* 1.3 74.8 + - - +
882A LEU* 3.5 9.4 + - - +
883A THR* 3.3 29.3 + - + +
917A LEU* 5.2 0.2 - - - +
920A VAL* 6.2 0.4 - - + -
63B GLN* 3.2 44.6 - - + +
69B LEU* 3.5 48.7 - - + +
72B LEU* 4.6 9.9 - - + -
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Residues in contact with GLN 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A ILE* 3.1 27.3 + - + +
877A SER* 3.8 18.2 - - - +
878A GLU 3.1 0.8 - - - -
879A MET* 1.3 88.5 - - - +
881A ARG* 1.3 63.6 + - - +
883A THR* 2.6 25.2 + - - -
884A LYS* 3.2 18.5 + - - +
41B ASN* 2.9 41.0 + - - +
58B TRP* 4.0 15.0 - - - -
59B ASP 4.2 13.3 + - - -
63B GLN* 4.1 8.9 - - - +
73B SER* 4.5 4.2 + - - -
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Residues in contact with ARG 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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742A LEU* 3.4 8.3 + - - +
745A THR* 2.8 44.3 + - - -
746A GLU* 2.7 43.6 + - - +
749A HIS* 3.4 31.1 - - + +
789A HIS* 4.4 2.0 - - + -
877A SER 3.1 18.7 + - - +
878A GLU* 3.0 4.1 + - - +
880A GLN* 1.3 74.7 - - - +
882A LEU* 1.3 66.0 + - - +
884A LYS* 2.9 18.7 + - - +
885A TYR* 3.5 33.8 + - + +
888A LEU* 3.8 18.5 - - - +
38B VAL* 4.2 10.3 - - - +
40B GLU* 5.4 2.1 + - - -
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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
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789A HIS* 5.2 0.9 - - + -
817A PHE* 5.0 0.7 - - + -
825A LEU* 4.1 23.3 - - + -
829A ALA* 3.7 25.6 - - + -
833A CYS* 5.7 0.9 - - - -
878A GLU* 3.0 44.7 + - + +
879A MET* 3.6 11.0 - - - +
881A ARG* 1.3 76.6 - - - +
883A THR* 1.3 60.3 + - - +
885A TYR* 3.3 44.0 + - + +
886A PRO* 3.6 5.5 - - - +
913A CYS* 5.6 0.7 - - - +
916A ILE* 4.9 10.3 - - + -
917A LEU* 3.8 23.4 - - + +
920A VAL* 5.4 5.8 - - + -
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Residues in contact with THR 883 (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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879A MET* 3.3 29.2 + - + +
880A GLN* 2.6 25.0 + - - -
882A LEU* 1.3 76.8 - - - +
884A LYS* 1.3 63.8 + - - +
885A TYR 3.3 1.0 + - - -
886A PRO* 3.6 9.0 - - - +
887A LEU* 3.8 15.1 + - - +
917A LEU* 3.9 22.8 - - + +
61B ALA 3.9 7.6 + - - -
62B GLY* 3.8 27.5 - - - +
63B GLN* 4.1 8.2 + - + +
66B TYR* 4.6 1.1 - - + -
69B LEU* 4.1 9.2 - - + -
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Residues in contact with LYS 884 (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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880A GLN* 3.2 19.7 + - - +
881A ARG* 2.9 20.4 + - - +
883A THR* 1.3 78.9 - - - +
885A TYR* 1.3 61.0 + - - +
886A PRO 3.5 0.7 - - - -
887A LEU* 3.4 15.0 + - + +
888A LEU* 2.9 35.9 + - + +
37B THR 4.8 3.6 + - - +
38B VAL* 3.5 33.0 - - + +
39B PHE 3.7 26.6 + - - +
59B ASP* 3.9 22.5 + - - +
61B ALA* 3.1 33.2 + - - +
63B GLN* 5.7 2.5 - - - +
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Residues in contact with TYR 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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742A LEU* 4.1 16.6 - - + +
746A GLU* 2.7 37.0 + - - -
789A HIS* 3.2 16.3 - + - -
792A TRP* 3.5 24.6 - + - -
817A PHE* 3.6 22.2 - + + -
825A LEU* 5.7 0.7 - - + -
881A ARG* 3.5 34.0 + - + -
882A LEU* 3.3 35.0 + - + +
883A THR 3.3 0.4 - - - -
884A LYS* 1.3 76.7 - - - +
886A PRO* 1.3 70.1 - - + +
888A LEU* 3.6 4.5 + - + +
889A LEU* 3.0 34.0 + - + +
913A CYS* 3.9 15.7 - - - -
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Residues in contact with PRO 886 (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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882A LEU 3.6 7.6 - - - +
883A THR 3.6 13.7 - - - +
885A TYR* 1.3 93.7 - - + +
887A LEU* 1.3 64.4 + - + +
889A LEU* 3.8 5.7 - - + +
890A GLU* 2.8 33.8 + - - +
910A ARG* 4.5 10.3 - - + +
913A CYS* 3.7 22.9 - - + -
914A ARG* 4.4 26.0 - - + +
917A LEU* 3.8 17.0 - - + -
66B TYR* 5.2 0.4 - - - +
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Residues in contact with LEU 887 (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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883A THR 3.8 19.5 - - - +
884A LYS* 3.4 17.4 + - + +
885A TYR 3.3 0.4 - - - -
886A PRO* 1.3 78.9 - - + +
888A LEU* 1.3 67.1 + - - +
890A GLU* 3.6 7.4 - - + +
891A SER* 3.1 23.2 + - - -
914A ARG* 6.3 0.9 - - - +
37B THR* 3.6 26.4 - - + +
61B ALA* 3.8 28.5 - - + +
62B GLY* 3.8 12.6 - - - +
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Residues in contact with LEU 888 (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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738A VAL* 3.8 7.5 - - + +
741A GLU* 4.4 10.5 - - + +
742A LEU* 3.9 38.4 - - + +
745A THR* 4.5 3.1 - - - +
881A ARG* 3.8 26.5 - - - +
884A LYS 2.9 24.1 + - - +
885A TYR* 3.9 6.1 - - + +
887A LEU* 1.3 77.1 - - - +
889A LEU* 1.3 62.5 + - + +
891A SER* 3.3 5.3 + - - -
892A ILE* 3.1 28.0 + - + +
37B THR* 3.5 31.0 - - + +
38B VAL* 3.8 16.6 - - + -
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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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742A LEU* 5.7 2.5 - - + -
813A MET* 3.9 32.1 - - + -
817A PHE* 5.0 6.5 - - + -
885A TYR* 3.0 22.9 + - + +
886A PRO 3.8 2.9 - - - +
887A LEU 3.2 0.2 - - - -
888A LEU* 1.3 73.9 - - + +
890A GLU* 1.3 56.4 + - - +
891A SER 2.9 2.4 + - - -
892A ILE* 2.9 17.5 + - + +
893A ILE* 2.7 42.6 + - + +
906A LEU* 4.3 10.3 - - + +
909A ALA* 3.7 15.0 - - + +
910A ARG* 3.4 42.6 - - + +
913A CYS* 4.3 10.8 - - - -
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Residues in contact with GLU 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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886A PRO 2.8 19.1 + - - +
887A LEU* 3.6 9.6 - - + +
889A LEU* 1.3 72.4 - - - +
891A SER* 1.3 61.3 + - - +
893A ILE* 3.5 12.1 + - - +
894A LYS* 3.2 22.5 + - - +
910A ARG* 3.1 29.8 + - - +
914A ARG* 2.5 35.0 + - - -
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Residues in contact with SER 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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738A VAL* 3.5 25.4 - - - +
887A LEU 3.1 12.9 + - - -
888A LEU 3.4 9.6 - - - -
889A LEU 2.9 2.0 + - - -
890A GLU* 1.3 73.2 - - - +
892A ILE* 1.3 64.8 + - - -
893A ILE 3.1 2.0 + - - -
894A LYS* 3.2 28.1 + - - +
895A HIS* 3.5 13.0 + - - -
34B TYR* 5.2 0.7 + - - -
37B THR* 3.8 17.6 + - - +
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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
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735A ARG* 4.7 5.9 - - + +
738A VAL* 3.7 20.6 - - + +
739A ILE* 3.8 38.4 - - + -
742A LEU* 4.7 11.7 - - + -
809A ILE* 4.5 17.7 - - + -
888A LEU* 3.2 15.9 - - + +
889A LEU* 2.9 24.5 + - + +
891A SER* 1.3 73.6 - - - +
893A ILE* 1.3 63.3 + - - +
895A HIS* 3.4 6.6 + - - +
896A THR* 3.2 25.0 + - - +
906A LEU* 3.8 20.9 - - + -
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Residues in contact with ILE 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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889A LEU* 2.7 26.6 + - + +
890A GLU* 3.7 11.9 - - - +
891A SER 3.1 0.2 - - - -
892A ILE* 1.3 74.5 - - - +
894A LYS* 1.3 59.5 + - - +
896A THR* 2.9 32.1 + - - +
903A HIS* 3.5 30.1 + - + +
906A LEU* 3.6 45.1 - - + +
907A CYS* 3.9 15.9 - - - +
910A ARG* 4.0 24.5 - - + +
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Residues in contact with LYS 894 (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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731A ARG* 3.8 17.6 + - - -
890A GLU 3.2 11.2 + - - +
891A SER* 3.2 15.2 + - - +
893A ILE* 1.3 80.1 - - - +
895A HIS* 1.3 95.0 + - + +
896A THR 3.4 1.1 - - - -
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Residues in contact with HIS 895 (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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731A ARG* 3.8 33.7 + - + +
734A ASP* 3.5 43.7 + - + +
735A ARG* 3.1 36.6 - - + +
738A VAL* 4.1 9.7 - - + +
891A SER* 3.5 14.4 + - - +
892A ILE 3.4 5.8 + - - +
893A ILE 3.0 0.8 - - - -
894A LYS* 1.3 125.5 + - + +
896A THR* 1.3 59.9 + - - +
897A GLU* 4.3 0.9 + - - +
34B TYR* 5.9 2.0 - + - -
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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