Contacts of the helix formed by residues 876 - 895 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836E GLN* 3.9 13.9 - - - +
840E LEU* 6.2 0.9 - - + -
872E ARG 4.1 5.8 - - - +
873E ASP 3.3 19.2 + - - +
874E LEU 3.0 2.0 + - - -
875E ILE* 1.3 80.0 - - + +
877E SER* 1.3 63.8 + - - +
878E GLU 3.2 4.0 + - - -
879E MET* 3.5 25.8 + - + +
880E GLN* 3.2 28.9 + - - +
41F ASN* 4.2 0.7 - - - +
58F TRP* 3.7 31.6 - - + -
72F LEU* 3.6 34.8 - - + +
73F SER* 4.1 9.0 - - - +
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Residues in contact with SER 877 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749E HIS* 3.5 11.7 - - - -
752E THR* 3.4 24.5 - - - +
753E LEU* 4.9 4.3 - - - +
756E LEU* 5.4 0.7 - - - +
873E ASP 4.9 2.7 - - - -
874E LEU* 2.7 21.3 + - - -
875E ILE 3.2 0.4 - - - -
876E ILE* 1.3 77.6 - - - +
878E GLU* 1.3 61.5 + - - +
880E GLN* 3.5 15.4 - - - +
881E ARG* 2.7 32.7 + - - +
41F ASN* 6.5 0.2 - - - -
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Residues in contact with GLU 878 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749E HIS* 2.7 30.5 + - - -
753E LEU* 4.0 9.6 - - + +
785E LEU* 3.4 32.9 - - + +
789E HIS* 2.8 24.8 + - - -
825E LEU* 5.1 1.2 - - - +
829E ALA* 4.9 9.5 - - + +
832E PHE* 4.0 27.1 - - + -
833E CYS* 4.7 5.8 - - - -
875E ILE 4.1 1.6 + - - -
876E ILE 3.2 1.6 - - - -
877E SER* 1.3 78.0 + - - +
879E MET* 1.3 68.4 + - - +
880E GLN 3.0 0.2 + - - -
881E ARG* 3.1 0.5 + - - +
882E LEU* 3.0 35.3 + - + +
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Residues in contact with MET 879 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833E CYS* 4.0 22.6 - - + -
836E GLN* 5.8 1.1 - - - +
875E ILE 5.4 0.2 + - - -
876E ILE* 3.5 33.5 + - + +
877E SER 3.4 0.4 - - - -
878E GLU* 1.3 79.7 - - - +
880E GLN* 1.3 71.6 + - - +
882E LEU* 3.5 9.3 + - - +
883E THR* 3.1 33.5 + - - +
917E LEU* 5.2 0.2 - - - +
920E VAL* 5.8 2.0 - - + -
63F GLN* 3.5 32.1 - - - +
69F LEU* 3.5 49.6 - - + +
72F LEU* 4.5 7.9 - - + -
73F SER* 4.2 2.0 - - - +
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Residues in contact with GLN 880 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876E ILE* 3.2 20.6 + - - +
877E SER* 3.1 15.5 + - - +
878E GLU 3.0 1.0 - - - -
879E MET* 1.3 81.7 - - + +
881E ARG* 1.3 64.4 + - - +
883E THR* 2.6 22.8 + - - +
884E LYS* 3.1 21.9 - - + +
39F PHE 6.2 0.2 - - - -
40F GLU* 5.9 0.3 - - - -
41F ASN* 3.2 33.7 + - - +
58F TRP* 4.0 18.6 - - - -
59F ASP* 3.8 18.6 + - - +
63F GLN* 3.8 21.4 - - - +
73F SER* 4.3 3.8 + - - -
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Residues in contact with ARG 881 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742E LEU* 3.3 10.7 + - - +
745E THR* 2.5 39.1 + - - +
746E GLU* 2.7 45.8 + - - +
749E HIS* 3.2 50.1 - - + +
789E HIS* 4.4 1.8 - - + -
877E SER 2.7 11.1 + - - +
878E GLU* 3.7 1.8 - - - +
880E GLN* 1.3 72.6 - - - +
882E LEU* 1.3 63.4 + - - +
884E LYS* 3.1 19.1 + - - +
885E TYR* 3.4 34.2 + - + +
888E LEU* 4.2 13.7 - - - +
38F VAL* 4.5 10.3 - - - +
40F GLU* 5.3 1.2 + - - -
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Residues in contact with LEU 882 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789E HIS* 4.8 2.5 - - + -
825E LEU* 4.4 22.0 - - + -
829E ALA* 3.7 26.7 - - + -
833E CYS* 6.2 0.9 - - - -
878E GLU* 3.0 33.1 + - + +
879E MET* 3.6 9.2 - - - +
881E ARG* 1.3 78.5 - - - +
883E THR* 1.3 61.0 + - - +
885E TYR* 3.3 41.9 + - + +
886E PRO* 3.7 5.2 - - - +
916E ILE* 4.3 12.6 - - + -
917E LEU* 3.7 22.9 - - + +
920E VAL* 4.2 15.9 - - + -
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Residues in contact with THR 883 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879E MET* 3.1 28.2 + - - +
880E GLN* 2.6 23.7 + - - -
882E LEU* 1.3 77.9 - - - +
884E LYS* 1.3 67.5 + - - +
885E TYR 3.3 0.6 + - - -
886E PRO* 3.7 10.4 - - - +
887E LEU* 4.1 3.6 + - - +
917E LEU* 3.8 24.2 - - + +
61F ALA 3.9 3.3 + - - -
62F GLY* 3.7 31.9 - - - +
63F GLN* 4.1 16.6 + - + +
66F TYR* 5.4 0.4 - - + -
69F LEU* 4.5 9.4 - - + -
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Residues in contact with LYS 884 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880E GLN* 3.1 29.8 - - + +
881E ARG* 3.1 19.2 + - - +
883E THR* 1.3 78.8 - - - +
885E TYR* 1.3 64.9 + - - +
886E PRO 3.4 0.7 - - - -
887E LEU* 3.1 15.0 + - + +
888E LEU* 3.0 30.8 + - + +
37F THR 5.4 1.5 + - - -
38F VAL* 3.6 41.9 - - + +
39F PHE 4.2 14.6 + - - +
59F ASP* 4.0 26.5 + - - +
61F ALA* 3.3 32.0 + - - +
63F GLN* 5.8 0.6 - - - +
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Residues in contact with TYR 885 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742E LEU* 4.1 15.3 - - + -
746E GLU* 2.7 31.2 + - - -
789E HIS* 3.6 13.2 - + - -
792E TRP* 3.4 23.0 - + - -
817E PHE* 3.6 27.8 - + + -
825E LEU* 5.6 0.7 - - + -
881E ARG* 3.4 33.4 + - + -
882E LEU* 3.6 39.7 - - + +
883E THR 3.3 0.4 - - - -
884E LYS* 1.3 79.3 - - - +
886E PRO* 1.3 72.2 - - + +
888E LEU* 3.5 3.8 + - + +
889E LEU* 3.0 30.6 + - + +
913E CYS* 3.8 15.7 - - - -
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Residues in contact with PRO 886 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882E LEU 3.7 9.6 - - - +
883E THR 3.7 8.7 - - - +
885E TYR* 1.3 94.6 - - + +
887E LEU* 1.3 59.1 + - + +
889E LEU* 3.2 5.9 + - + +
890E GLU* 2.8 39.6 + - - +
910E ARG* 4.2 11.2 - - + +
913E CYS* 4.0 19.9 - - + +
914E ARG* 4.3 26.7 - - + +
917E LEU* 4.3 17.5 - - + -
66F TYR* 5.2 0.9 - - - +
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Residues in contact with LEU 887 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883E THR 4.1 7.6 - - - +
884E LYS* 3.1 18.6 + - + +
886E PRO* 1.3 85.3 - - + +
888E LEU* 1.3 57.0 + - - +
890E GLU* 3.6 14.3 + - - +
891E SER* 3.1 27.0 + - - -
37F THR* 3.7 28.4 - - + +
61F ALA* 4.0 14.8 - - + +
62F GLY* 3.8 35.7 - - - +
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Residues in contact with LEU 888 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738E VAL* 3.9 7.8 - - + +
741E GLU* 4.1 11.4 - - + +
742E LEU* 4.2 41.3 - - + +
745E THR* 4.9 1.8 - - - +
881E ARG* 4.2 11.7 - - - +
884E LYS* 3.0 31.8 + - + +
885E TYR* 4.0 5.6 - - + +
887E LEU* 1.3 72.5 - - - +
889E LEU* 1.3 60.6 + - + +
891E SER* 3.2 5.0 + - - -
892E ILE* 2.9 36.8 + - + +
37F THR* 3.5 32.5 - - + +
38F VAL* 3.7 22.9 - - + -
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Residues in contact with LEU 889 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742E LEU* 5.9 2.7 - - + -
813E MET* 3.7 37.0 - - + -
817E PHE* 4.5 5.8 - - + -
885E TYR* 3.0 19.1 + - + +
886E PRO 3.6 3.6 - - - +
888E LEU* 1.3 71.0 - - + +
890E GLU* 1.3 61.4 + - - +
891E SER 3.0 2.4 + - - -
892E ILE* 3.1 12.5 + - + +
893E ILE* 2.8 37.4 + - + +
906E LEU* 4.7 9.6 - - + +
909E ALA* 3.6 11.0 - - + -
910E ARG* 3.4 41.1 - - + +
913E CYS* 3.8 21.5 - - + -
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Residues in contact with GLU 890 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886E PRO* 2.8 21.5 + - - +
887E LEU* 3.8 16.3 - - - +
889E LEU* 1.3 72.8 - - - +
891E SER* 1.3 56.5 + - - +
893E ILE* 3.7 11.5 - - + +
894E LYS* 3.1 28.2 + - - +
910E ARG* 3.2 22.4 + - - +
914E ARG* 2.8 31.0 + - - -
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Residues in contact with SER 891 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738E VAL* 3.6 26.7 - - - +
887E LEU 3.1 17.9 + - - -
888E LEU* 3.4 8.3 - - - -
889E LEU 3.0 0.6 - - - -
890E GLU* 1.3 78.9 - - - +
892E ILE* 1.3 61.4 + - - +
893E ILE 3.5 0.2 + - - -
894E LYS* 3.5 8.5 + - - +
895E HIS* 3.3 31.7 + - - -
34F TYR* 4.8 0.3 + - - -
37F THR* 3.8 15.1 + - - -
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Residues in contact with ILE 892 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735E ARG* 4.8 6.4 - - + +
738E VAL* 3.5 22.0 - - + +
739E ILE* 3.7 35.9 - - + -
742E LEU* 4.5 16.2 - - + -
809E ILE* 4.0 19.7 - - + -
888E LEU* 2.9 23.9 + - + +
889E LEU* 3.6 14.8 - - + +
891E SER* 1.3 74.8 - - - +
893E ILE* 1.3 63.5 + - - +
895E HIS* 3.3 13.2 + - - +
896E THR* 2.9 24.0 + - - +
906E LEU* 3.8 20.6 - - + -
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Residues in contact with ILE 893 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889E LEU* 2.8 26.1 + - + +
890E GLU* 3.7 7.2 - - + +
892E ILE* 1.3 73.8 - - - +
894E LYS* 1.3 60.9 + - - +
895E HIS 3.0 2.0 - - - -
896E THR* 2.7 37.9 + - - +
903E HIS* 3.7 27.0 + - + +
906E LEU* 3.6 41.7 - - + +
907E CYS* 3.9 20.6 - - - +
910E ARG* 4.1 25.4 - - + +
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Residues in contact with LYS 894 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731E ARG* 3.7 15.2 + - - -
890E GLU 3.1 16.7 + - - +
891E SER* 3.7 7.0 - - - +
892E ILE 3.4 0.4 - - - -
893E ILE* 1.3 82.7 - - - +
895E HIS* 1.3 85.3 + - + +
896E THR 3.6 2.1 + - - +
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Residues in contact with HIS 895 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731E ARG* 3.8 34.2 - - + +
732E GLU* 4.8 1.7 - - - +
734E ASP* 3.2 41.1 + - + +
735E ARG* 3.3 40.5 - - + +
738E VAL* 4.5 13.2 - - + +
891E SER* 3.3 20.9 + - - +
892E ILE 3.3 8.1 + - - +
893E ILE 3.0 1.0 - - - -
894E LYS* 1.3 107.0 + - + +
896E THR* 1.3 57.9 + - - +
897E GLU 4.4 0.2 + - - -
34F TYR* 6.3 0.7 - + - -
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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) + - + + + + + -
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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