Contacts of the helix formed by residues 65 - 82 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.0 15.3 - - + -
12C PHE* 3.5 33.0 - + - -
13C LYS* 3.5 51.1 - - + -
16C PHE* 3.4 38.1 - - + -
64C ASP* 1.3 80.7 + - - +
66C PRO* 1.3 66.6 - - + +
68C PHE* 3.4 2.7 + - - +
69C LEU* 2.9 52.5 + - + +
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Residues in contact with PRO 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ASP* 3.1 29.6 - - + +
65C PHE* 1.3 94.3 - - + +
67C GLU* 1.3 57.4 + - - +
69C LEU* 3.6 7.9 + - + +
70C THR* 2.8 33.5 + - - -
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 5.4 0.7 - - - +
52C ILE* 5.3 1.2 - - - +
56C ASP* 5.8 3.4 - - - +
57C ALA* 3.2 17.5 - - + +
60C ASN* 5.5 4.9 - - - +
63C ILE* 3.2 35.9 - - + +
64C ASP* 3.2 19.2 + - + +
66C PRO* 1.3 75.6 - - - +
68C PHE* 1.3 81.4 + - - +
70C THR* 3.0 11.4 + - - -
71C MET* 2.9 64.8 + - + +
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.3 40.2 - + - -
16C PHE* 4.5 7.9 - + + -
32C LEU* 3.5 33.4 - - + -
35C VAL* 3.5 23.6 - - + -
36C MET* 3.7 30.7 - - + -
39C LEU* 4.6 3.1 - - + -
63C ILE* 4.6 5.2 - - + -
64C ASP 3.0 12.9 + - - +
65C PHE* 3.8 7.6 - - - +
67C GLU* 1.3 86.3 + - - +
69C LEU* 1.3 59.4 + - - +
71C MET* 3.2 6.7 + - + +
72C MET* 2.9 48.3 + - + +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.0 27.4 - - + -
12C PHE* 5.8 4.0 - - + -
65C PHE* 2.9 39.8 + - + +
66C PRO* 3.8 8.1 - - + +
68C PHE* 1.3 79.4 - - + +
70C THR* 1.3 59.1 + - - +
72C MET* 3.7 20.9 - - + +
73C ALA* 3.1 31.0 + - + +
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PRO 2.8 18.9 + - - -
67C GLU* 3.0 11.6 + - - -
69C LEU* 1.3 75.6 - - - +
71C MET* 1.3 64.9 + - + +
73C ALA* 3.4 7.3 + - + +
74C ARG* 3.1 34.4 + - + +
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Residues in contact with MET 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 5.6 5.8 - - + -
51C MET* 3.8 34.6 - - + +
54C GLU* 3.7 18.6 - - + -
56C ASP* 5.7 2.2 - - + -
57C ALA* 3.8 8.3 - - + -
67C GLU* 2.9 55.8 + - + +
68C PHE* 3.5 13.5 - - + +
70C THR* 1.3 71.9 - - + +
72C MET* 1.3 62.1 + - - +
74C ARG* 3.1 44.5 + - - +
75C LYS* 3.0 27.0 + - - +
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Residues in contact with MET 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 6.0 4.0 - - + -
12C PHE* 5.6 5.2 - - + -
39C LEU* 3.6 31.2 - - + -
41C GLN* 5.4 4.0 - - - +
51C MET* 4.7 3.5 - - - +
68C PHE* 2.9 31.8 + - + +
69C LEU* 3.7 24.2 - - + +
71C MET* 1.3 75.4 - - - +
73C ALA* 1.3 57.3 + - + +
75C LYS* 4.7 1.3 - - - +
76C MET* 2.9 42.5 + - + +
79C THR* 5.0 17.3 - - + -
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Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 3.1 21.4 + - + +
70C THR* 3.4 9.4 + - + +
72C MET* 1.3 79.7 - - + +
74C ARG* 1.3 61.0 + - - +
76C MET* 3.7 18.6 + - - +
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Residues in contact with ARG 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C MET* 5.9 4.7 - - - -
53C ASN 5.5 2.0 + - - -
54C GLU* 2.5 32.2 + - - +
70C THR* 3.1 26.1 + - + +
71C MET* 3.1 43.5 - - - +
73C ALA* 1.3 76.0 - - - +
75C LYS* 1.3 70.4 + - + +
76C MET 3.5 0.6 + - - -
77C LYS* 5.0 9.5 - - - +
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU* 2.6 41.2 + - - +
50C ASP* 5.7 3.4 - - - +
51C MET* 3.7 46.2 - - + -
71C MET 3.0 16.1 + - - +
72C MET 3.7 1.1 - - - +
74C ARG* 1.3 86.6 - - + +
76C MET* 1.4 63.2 + - - +
77C LYS* 3.4 3.8 - - - +
78C ASP* 2.7 41.9 + - - +
79C THR* 3.0 23.9 + - - +
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Residues in contact with MET 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C MET* 2.9 25.7 + - + +
73C ALA* 3.7 15.9 - - - +
74C ARG 3.5 2.8 + - - -
75C LYS* 1.4 73.2 - - - +
77C LYS* 1.3 63.1 + - + +
79C THR* 3.1 7.1 + - + -
80C ASP* 2.8 58.4 + - - +
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Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ARG 5.0 11.0 - - - +
75C LYS 3.2 0.8 + - - -
76C MET* 1.3 82.3 - - + +
78C ASP* 1.3 88.9 + - - +
80C ASP* 3.7 9.0 + - - +
81C SER* 3.1 25.8 + - - -
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Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU* 3.3 9.4 - - - +
75C LYS* 2.7 50.1 + - - +
77C LYS* 1.3 107.3 + - - +
79C THR* 1.3 62.7 + - - +
81C SER* 3.2 20.6 - - - -
82C GLU* 3.6 10.4 + - - +
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C MET* 5.7 9.8 - - + +
41C GLN* 3.4 50.8 - - + +
43C PRO* 6.2 3.4 - - + -
47C GLU* 4.7 9.4 + - - -
51C MET* 4.7 9.2 - - - +
72C MET* 5.0 16.2 + - + -
75C LYS* 3.0 24.7 + - - +
76C MET* 3.3 11.9 - - + -
78C ASP* 1.3 76.3 - - - +
80C ASP* 1.4 61.3 + - - +
82C GLU* 3.3 16.4 + - - +
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLN* 4.3 12.2 + - - -
76C MET* 2.8 55.4 + - - +
77C LYS* 3.8 7.6 + - - +
79C THR* 1.4 68.4 - - - +
81C SER* 1.4 64.2 + - - +
82C GLU 3.2 1.8 - - - -
83C GLU* 3.1 31.4 + - + +
84C GLU* 4.1 3.3 + - - +
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A TYR* 4.0 3.1 + - - -
77C LYS 3.1 15.8 + - - -
78C ASP* 3.2 18.2 - - - -
79C THR 3.4 0.4 - - - -
80C ASP* 1.4 73.9 - - - +
82C GLU* 1.3 58.7 + - - +
83C GLU 3.2 4.7 + - - -
84C GLU* 3.4 22.5 + - - +
85C ILE* 5.3 1.0 - - - +
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799A ARG* 2.6 48.8 + - - -
800A TYR* 2.7 36.4 + - - -
41C GLN* 4.0 0.4 - - + -
42C ASN* 2.8 56.2 + - - +
43C PRO* 4.2 9.6 - - + -
44C THR* 3.8 8.3 - - - +
47C GLU* 4.6 7.6 - - - +
78C ASP 3.6 9.2 + - - +
79C THR* 3.3 14.6 + - - +
80C ASP 3.2 1.4 - - - -
81C SER* 1.3 77.0 - - - +
83C GLU* 1.3 51.1 + - - +
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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