Contacts of the helix formed by residues 65 - 82 (chain O) 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 PHE 65 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9O ILE* 4.0 15.0 - - + -
12O PHE* 3.5 28.7 - + - -
13O LYS* 3.5 49.6 - - + -
16O PHE* 3.4 43.0 - + + -
64O ASP* 1.3 80.9 + - - +
66O PRO* 1.3 66.6 - - + +
68O PHE* 3.4 2.3 + - - +
69O LEU* 2.9 52.7 + - + +
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Residues in contact with PRO 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O ASP* 3.1 29.6 - - + +
65O PHE* 1.3 95.4 - - + +
67O GLU* 1.3 56.9 + - - +
69O LEU* 3.6 7.4 + - + +
70O THR* 2.8 33.7 + - - -
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Residues in contact with GLU 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O LEU* 5.4 0.9 - - - +
52O ILE* 5.3 1.0 - - - +
56O ASP* 5.8 3.6 - - + +
57O ALA* 3.2 17.5 - - + +
60O ASN* 5.4 5.6 - - - +
63O ILE* 3.2 35.2 - - + +
64O ASP* 3.2 19.3 + - + +
66O PRO* 1.3 76.4 - - - +
68O PHE* 1.3 80.4 + - - +
70O THR* 3.0 10.2 + - - -
71O MET* 2.9 64.4 + - + +
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Residues in contact with PHE 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O PHE* 3.3 39.9 - + - -
16O PHE* 4.5 8.3 - + + -
32O LEU* 3.5 30.1 - - + -
35O VAL* 3.5 27.4 - - + -
36O MET* 3.7 31.4 - - + -
39O LEU* 4.6 3.6 - - + -
63O ILE* 4.6 4.7 - - + -
64O ASP 3.0 12.6 + - - +
65O PHE* 3.8 7.6 - - - +
67O GLU* 1.3 84.9 + - - +
69O LEU* 1.3 59.6 + - - +
71O MET* 3.2 7.5 + - + +
72O MET* 2.9 50.0 + - + +
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Residues in contact with LEU 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ILE* 4.0 27.4 - - + -
12O PHE* 5.8 4.3 - - + -
65O PHE* 2.9 39.6 + - + +
66O PRO* 3.8 8.1 - - + +
68O PHE* 1.3 79.5 - - + +
70O THR* 1.3 59.6 + - - +
72O MET* 3.6 20.7 + - + +
73O ALA* 3.1 30.9 + - + +
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Residues in contact with THR 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66O PRO 2.8 18.9 + - - -
67O GLU* 3.0 12.5 + - - -
69O LEU* 1.3 76.3 - - - +
71O MET* 1.3 66.4 + - + +
73O ALA* 3.4 7.0 + - + +
74O ARG* 3.1 35.7 + - + +
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Residues in contact with MET 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O LEU* 5.6 5.6 - - + -
51O MET* 3.8 34.5 - - + +
54O GLU* 3.7 18.8 - - + -
56O ASP* 5.7 2.0 - - + -
57O ALA* 3.8 8.3 - - + +
67O GLU* 2.9 55.3 + - + +
68O PHE* 3.5 13.5 - - + +
70O THR* 1.3 71.7 - - + +
72O MET* 1.3 61.4 + - - +
74O ARG* 3.1 45.3 + - - +
75O LYS* 3.0 26.7 + - - +
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Residues in contact with MET 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ILE* 6.0 4.0 - - + -
12O PHE* 5.6 5.2 - - + -
39O LEU* 3.6 31.0 - - - -
41O GLN* 5.4 4.0 - - - +
51O MET* 4.7 4.2 - - - +
68O PHE* 2.9 32.5 + - + +
69O LEU* 3.7 24.0 - - + +
71O MET* 1.3 75.3 - - - +
73O ALA* 1.3 57.3 + - + +
75O LYS* 3.7 1.3 - - - -
76O MET* 2.9 42.0 + - + +
79O THR* 4.9 17.5 - - + -
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Residues in contact with ALA 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O LEU* 3.1 21.2 + - + +
70O THR* 3.4 9.1 + - + +
72O MET* 1.3 79.4 - - + +
74O ARG* 1.3 61.3 + - - +
75O LYS 3.6 0.2 + - - -
76O MET* 3.7 18.3 + - - +
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Residues in contact with ARG 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O MET* 5.9 4.0 - - - -
53O ASN 5.5 1.8 + - - -
54O GLU* 2.5 32.3 + - - +
70O THR* 3.1 23.8 + - + +
71O MET* 3.1 43.6 - - - +
73O ALA* 1.3 77.5 - - - +
75O LYS* 1.3 71.9 + - + +
76O MET 3.8 0.2 + - - -
77O LYS* 5.0 10.0 - - - +
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Residues in contact with LYS 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O GLU* 2.6 46.2 + - - +
50O ASP* 5.7 4.0 - - - +
51O MET* 3.7 42.8 - - + -
71O MET 3.0 15.8 + - - +
72O MET 3.7 0.7 - - - -
74O ARG* 1.3 85.3 - - + +
76O MET* 1.4 63.6 + - - +
77O LYS* 3.4 3.4 - - - +
78O ASP* 2.7 41.8 + - - +
79O THR* 3.0 24.8 + - - +
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Residues in contact with MET 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O MET* 2.9 25.9 + - + +
73O ALA* 3.7 15.5 - - - +
74O ARG 3.5 2.0 + - - -
75O LYS* 1.4 73.8 - - - +
77O LYS* 1.3 62.7 + - + +
79O THR* 3.1 7.5 + - - -
80O ASP* 2.8 60.0 + - - +
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Residues in contact with LYS 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O ARG 5.0 11.4 - - - +
75O LYS* 3.2 1.3 + - - +
76O MET* 1.3 82.6 - - + +
78O ASP* 1.3 90.4 + - - +
80O ASP* 3.7 8.9 + - - +
81O SER* 3.2 26.0 + - - -
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Residues in contact with ASP 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O GLU* 3.2 11.1 - - - +
75O LYS* 2.7 50.1 + - - +
77O LYS* 1.3 108.7 + - - +
79O THR* 1.3 61.2 + - - +
81O SER* 3.2 20.6 - - - -
82O GLU* 3.6 10.6 + - - +
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Residues in contact with THR 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O MET* 5.7 9.3 - - + +
41O GLN* 3.3 51.0 - - + +
43O PRO* 6.2 3.6 - - + -
47O GLU* 4.7 8.0 + - - -
51O MET* 4.7 7.4 - - - +
72O MET* 4.9 17.6 + - + -
75O LYS* 3.0 26.4 + - - +
76O MET* 3.3 12.1 - - + -
78O ASP* 1.3 75.0 - - - +
80O ASP* 1.4 60.8 + - - +
82O GLU* 3.4 17.0 + - - +
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Residues in contact with ASP 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O GLN* 4.3 12.9 + - - -
76O MET* 2.8 56.1 + - - +
77O LYS* 3.8 7.5 + - - +
79O THR* 1.4 68.7 - - - +
81O SER* 1.4 63.8 + - - +
82O GLU 3.2 2.0 - - - -
83O GLU* 3.0 31.3 + - + +
84O GLU* 4.1 3.5 + - - +
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Residues in contact with SER 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800M TYR* 4.1 3.3 + - - -
77O LYS 3.2 14.3 + - - -
78O ASP* 3.2 18.4 - - - -
80O ASP* 1.4 74.9 - - - +
82O GLU* 1.3 56.6 + - - +
83O GLU 3.3 4.3 + - - -
84O GLU* 3.4 22.6 + - - +
85O ILE* 5.2 1.2 - - - +
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Residues in contact with GLU 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799M ARG* 2.6 47.5 + - - -
800M TYR* 2.7 37.7 + - - -
41O GLN* 5.3 0.2 - - + -
42O ASN* 2.8 51.0 + - - +
43O PRO* 4.2 9.4 - - + -
44O THR* 3.5 16.1 - - - +
47O GLU* 4.6 7.4 - - - +
78O ASP 3.6 10.3 + - - +
79O THR* 3.4 13.8 + - - +
80O ASP 3.2 1.6 - - - -
81O SER* 1.3 77.1 - - - +
83O GLU* 1.3 55.7 + - - +
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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
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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