Contacts of the helix formed by residues 886 - 906 (chain A) in PDB entry 2DFS
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 886 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A VAL* 2.7 32.0 + - + +
882A HIS* 2.8 19.8 + - - -
883A TYR 4.2 0.6 - - - -
885A ARG* 1.3 80.3 - - + +
887A LEU* 1.4 61.9 + - - +
888A LYS 3.4 2.5 - - - -
889A ALA* 2.8 23.8 + - - +
890A ILE* 3.0 18.0 + - - +
89G PHE* 4.8 3.1 - - + -
90G ARG 5.4 1.3 - - - +
91G VAL* 4.0 27.8 - - + -
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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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882A HIS 3.1 17.7 + - - +
883A TYR* 4.0 10.9 - - + +
886A THR* 1.4 79.5 + - - +
888A LYS* 1.3 57.7 + - - +
890A ILE* 3.1 23.7 + - + +
891A VAL* 2.9 34.7 + - + +
18F LEU* 3.7 51.6 - - + -
112G LEU* 4.5 8.7 - - + -
113G GLY* 4.5 17.7 - - - +
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Residues in contact with LYS 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A TYR* 3.3 28.0 + - + +
884A HIS* 5.4 3.6 - - - +
886A THR 3.4 0.6 - - - -
887A LEU* 1.3 78.3 - - + +
889A ALA* 1.3 58.0 + - - +
891A VAL* 3.3 18.3 - - + +
892A TYR* 2.8 71.5 + - + -
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Residues in contact with ALA 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ARG 4.0 14.0 - - - +
886A THR 2.8 16.0 + - - +
888A LYS* 1.3 70.7 - - - +
890A ILE* 1.4 63.0 + - - +
892A TYR* 3.8 7.8 + - - +
893A LEU* 3.4 21.5 + - - +
88G ALA* 5.6 0.8 - - - -
89G PHE* 3.6 29.4 + - + +
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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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886A THR* 3.0 16.4 + - - +
887A LEU* 3.1 22.0 + - + +
889A ALA* 1.4 73.5 - - - +
891A VAL* 1.4 63.1 + - - +
893A LEU* 3.3 6.2 + - - +
894A GLN* 3.1 39.8 + - - +
89G PHE* 3.6 32.1 - - + -
91G VAL* 5.2 3.4 - - + -
108G VAL* 3.9 26.5 - - + +
109G MET* 4.3 2.0 - - + -
112G LEU* 3.6 37.5 - - + -
113G GLY* 4.4 2.9 - - - +
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Residues in contact with VAL 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU* 2.9 23.6 + - + +
888A LYS* 3.3 31.0 - - + +
890A ILE* 1.4 71.2 - - - +
892A TYR* 1.4 72.7 + - + +
894A GLN* 3.1 10.8 + - - +
895A CYS* 3.0 33.0 + - - -
113G GLY* 3.5 28.9 - - - -
114G GLU* 4.0 15.6 - - + +
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Residues in contact with TYR 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A LYS* 2.8 59.0 + - + +
889A ALA* 4.2 7.0 - - - +
890A ILE 3.4 0.2 - - - -
891A VAL* 1.4 85.9 - - + +
893A LEU* 1.3 62.0 + - - +
895A CYS* 3.4 15.0 - - - +
896A CYS* 3.3 27.0 + - - -
82G GLU* 6.2 0.4 - - - -
85G ILE* 4.3 16.4 - - + -
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Residues in contact with LEU 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A ALA 3.4 12.0 + - - +
890A ILE 3.3 9.7 + - - +
892A TYR* 1.3 78.4 - - - +
894A GLN* 1.3 56.0 + - - +
896A CYS* 3.2 7.4 + - + +
897A TYR* 2.9 38.5 + - + +
85G ILE* 4.5 8.8 - - + +
87G GLU 4.4 5.8 - - - +
88G ALA* 3.3 40.2 - - + -
89G PHE* 3.8 20.9 - - + -
90G ARG* 4.8 6.5 - - - +
109G MET* 4.2 7.0 - - + -
145G MET* 3.5 35.2 - - + -
146G THR* 5.7 4.3 - - + -
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Residues in contact with GLN 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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890A ILE* 3.1 20.3 + - - +
891A VAL* 3.1 8.7 + - - +
893A LEU* 1.3 71.2 - - - +
895A CYS* 1.3 59.0 - - - +
897A TYR* 3.3 9.0 - - - +
898A ARG* 3.0 34.0 + - - +
108G VAL 3.8 4.2 + - - -
109G MET* 2.9 44.6 + - + +
112G LEU 2.8 23.4 + - - -
113G GLY* 3.3 8.3 - - - -
114G GLU* 2.7 35.3 + - + -
115G LYS 3.5 6.4 - - - +
116G LEU* 4.0 14.2 - - + +
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Residues in contact with CYS 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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891A VAL* 3.0 30.2 + - - -
892A TYR* 3.4 17.9 - - + +
894A GLN* 1.3 74.0 - - - +
896A CYS* 1.3 57.9 + - - +
898A ARG* 3.3 7.0 + - - +
899A ARG* 3.1 32.1 + - - +
42G ASN 3.8 12.8 - - - +
43G PRO 3.9 3.8 - - - +
44G THR* 3.5 33.9 - - + +
82G GLU* 5.1 2.5 - - - +
114G GLU* 3.5 21.7 + - - -
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Residues in contact with CYS 896 (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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892A TYR 3.3 14.8 + - - +
893A LEU* 3.2 13.8 + - + +
895A CYS* 1.3 76.5 - - - +
897A TYR* 1.3 59.0 + - - +
899A ARG* 3.2 1.6 + - - +
900A MET* 2.8 30.7 + - - +
42G ASN* 3.4 44.3 - - - +
82G GLU* 4.2 3.6 - - - -
85G ILE* 3.5 26.7 - - + -
145G MET* 5.5 8.2 - - + +
146G THR* 6.1 4.0 - - + -
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Residues in contact with TYR 897 (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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893A LEU* 2.9 27.4 + - + +
894A GLN* 3.3 12.3 - - - +
896A CYS* 1.3 68.6 - - - +
898A ARG* 1.4 58.8 + - - +
900A MET* 3.2 7.9 + - - +
901A MET* 2.9 47.7 + - + +
90G ARG* 6.2 0.2 - - - -
105G LEU* 3.9 5.9 - - + +
109G MET* 3.5 34.6 - - + +
116G LEU* 3.5 26.9 - - + -
120G GLU 5.4 0.2 - - - -
121G VAL* 5.7 3.2 - - + +
124G MET* 3.5 38.0 - - + +
141G PHE* 3.4 25.7 - + - -
145G MET* 3.6 33.8 - - + -
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Residues in contact with ARG 898 (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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894A GLN 3.0 16.0 + - - +
895A CYS* 3.6 6.5 - - - +
897A TYR* 1.4 78.2 - - - +
899A ARG* 1.3 58.1 + - - +
901A MET* 3.3 10.1 + - - +
902A ALA* 3.3 21.3 + - - +
37G ARG* 3.3 27.2 + - - +
43G PRO 5.5 0.2 - - - +
45G GLU* 3.8 25.0 - - - +
114G GLU* 2.9 46.1 + - - +
115G LYS 2.8 20.4 + - - -
116G LEU* 3.4 14.1 - - + +
117G THR* 4.4 1.8 - - - +
120G GLU* 2.8 42.7 + - - +
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Residues in contact with ARG 899 (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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895A CYS 3.1 8.2 + - - +
896A CYS 3.8 2.5 - - - +
897A TYR 3.1 0.4 - - - -
898A ARG* 1.3 76.3 - - - +
900A MET* 1.3 61.7 + - - +
903A LYS* 3.4 1.9 - - - +
33G GLY* 3.8 5.2 + - - -
36G MET* 3.0 37.6 - - - +
37G ARG* 2.9 66.4 - - - +
40G GLY 4.7 1.2 - - - +
41G GLN 3.0 24.5 - - - +
42G ASN* 3.3 20.0 - - + +
43G PRO* 2.6 43.9 + - - +
44G THR 2.7 23.2 + - - -
47G GLU* 3.1 15.0 + - - -
48G LEU* 3.7 14.3 - - - +
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Residues in contact with MET 900 (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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896A CYS 2.8 17.4 + - - +
897A TYR* 3.6 7.0 - - - +
899A ARG* 1.3 75.4 - - - +
901A MET* 1.3 62.2 + - - +
903A LYS* 3.4 25.8 - - + +
904A ARG* 2.9 45.7 + - - +
40G GLY 6.0 0.2 - - - -
42G ASN* 5.1 2.2 + - - +
124G MET* 4.7 6.3 - - + -
127G GLU* 4.7 3.6 - - - +
144G MET 4.2 6.1 - - - +
145G MET* 3.5 37.5 - - + +
147G ALA 4.2 15.7 - - - +
148G LYS* 5.5 7.6 - - + -
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Residues in contact with MET 901 (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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897A TYR* 2.9 44.2 + - + +
898A ARG* 3.3 15.0 + - - +
900A MET* 1.3 75.6 - - - +
902A ALA* 1.3 62.8 + - + +
904A ARG* 3.1 33.8 + - - +
905A GLU* 3.4 8.8 + - - +
116G LEU* 4.4 3.6 - - + -
120G GLU* 3.5 64.2 - - + +
123G GLU* 5.0 10.1 - - + +
124G MET* 4.2 9.0 - - + +
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Residues in contact with ALA 902 (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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898A ARG 3.3 4.8 + - - +
901A MET* 1.3 80.5 - - + +
903A LYS* 1.4 55.7 + - - +
905A GLU* 2.9 23.5 + - + +
906A LEU 3.1 12.0 + - - -
34G THR* 3.2 40.3 - - + +
37G ARG* 3.1 31.4 - - - +
38G SER* 3.1 5.2 - - - -
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Residues in contact with LYS 903 (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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899A ARG 3.4 14.6 + - - +
900A MET* 3.4 22.7 - - - +
902A ALA* 1.4 75.4 - - - +
904A ARG* 1.3 59.3 + - + +
907A LYS* 4.0 18.3 - - - +
11G GLU* 3.8 19.1 + - - +
37G ARG* 3.1 23.4 - - - +
38G SER* 2.7 48.5 + - - +
39G LEU 2.8 15.4 + - - -
40G GLY* 3.9 12.1 - - - +
148G LYS* 5.3 10.8 - - + -
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Residues in contact with ARG 904 (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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900A MET* 2.9 44.1 + - - +
901A MET* 3.1 18.0 + - - +
903A LYS* 1.3 77.9 - - + +
905A GLU* 1.4 65.6 + - + +
907A LYS* 3.0 17.0 + - - +
908A LYS* 3.5 13.4 + - - +
123G GLU* 2.6 44.1 + - - -
124G MET* 3.7 13.9 - - - +
126G ARG* 4.5 7.4 - - - +
127G GLU* 2.6 47.0 + - - +
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Residues in contact with GLU 905 (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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901A MET 3.4 11.6 + - - +
902A ALA* 2.9 20.1 + - + +
904A ARG* 1.4 78.3 - - + +
906A LEU* 1.4 55.1 + - - +
908A LYS* 2.6 65.9 + - - +
909A LEU* 3.1 19.6 + - - +
19G PHE* 5.1 8.0 - - + -
34G THR* 4.9 11.2 - - + +
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Residues in contact with LEU 906 (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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902A ALA 3.1 7.8 + - - +
905A GLU* 1.4 73.2 - - - +
907A LYS* 1.3 61.1 + - - +
909A LEU 3.4 11.1 - - - +
12G PHE* 4.1 6.5 - - + -
15G ALA* 3.1 61.7 - - + +
16G PHE* 3.6 6.3 - - - +
18G LEU* 5.4 0.5 - - - +
19G PHE* 3.8 22.4 - - + -
34G THR 4.5 1.8 - - - +
35G VAL* 3.4 28.9 - - + +
38G SER* 3.0 50.8 + - - +
39G LEU 3.8 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
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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