Contacts of the helix formed by residues 65 - 82 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q ILE* 4.0 15.5 - - + -
12Q PHE* 3.5 37.9 - + - -
13Q LYS* 3.5 37.9 - - + -
16Q PHE* 3.3 37.2 - - + -
64Q ASP* 1.3 80.2 + - - +
66Q PRO* 1.3 65.9 - - + +
68Q PHE* 3.4 3.1 + - - +
69Q LEU* 2.9 50.5 + - + +
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Residues in contact with PRO 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Q ASP* 3.1 29.8 - - + +
65Q PHE* 1.3 95.9 - - + +
67Q GLU* 1.3 56.3 + - - +
69Q LEU* 3.6 7.3 + - + +
70Q THR* 2.8 33.3 + - - -
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Residues in contact with GLU 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q LEU* 5.4 0.5 - - - +
52Q ILE* 5.4 0.9 - - - +
56Q ASP* 5.9 2.7 - - + +
57Q ALA* 3.2 18.2 - - + +
60Q ASN* 5.4 5.8 - - - +
63Q ILE* 3.2 35.3 - - + +
64Q ASP* 3.1 19.9 + - + +
66Q PRO* 1.3 77.6 - - - +
68Q PHE* 1.3 82.1 + - - +
70Q THR* 3.0 11.1 + - - -
71Q MET* 2.9 63.5 + - + +
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Residues in contact with PHE 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q PHE* 3.3 39.7 - + - -
16Q PHE* 4.7 8.3 - + + -
32Q LEU* 3.5 33.7 - - + -
35Q VAL* 3.5 22.2 - - + -
36Q MET* 3.8 29.4 - - + -
39Q LEU* 4.6 3.4 - - + -
51Q MET* 6.0 0.4 - - + -
63Q ILE* 4.7 4.5 - - + -
64Q ASP 3.0 13.0 + - - +
65Q PHE* 3.4 7.6 + - - +
67Q GLU* 1.3 86.7 + - - +
69Q LEU* 1.3 58.7 + - - +
71Q MET* 3.2 7.5 + - + +
72Q MET* 2.9 50.5 + - + +
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Residues in contact with LEU 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q ILE* 4.1 26.5 - - + -
12Q PHE* 5.8 4.0 - - + -
65Q PHE* 2.9 38.4 + - + +
66Q PRO* 3.8 7.9 - - + +
68Q PHE* 1.3 79.7 - - + +
70Q THR* 1.3 58.5 + - - +
72Q MET* 3.6 22.3 + - + +
73Q ALA* 3.0 31.3 + - + +
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Residues in contact with THR 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Q PRO 2.8 18.8 + - - -
67Q GLU* 3.0 12.1 + - - -
69Q LEU* 1.3 76.0 - - - +
71Q MET* 1.3 64.3 + - + +
73Q ALA* 3.3 7.8 + - + +
74Q ARG* 3.1 35.7 + - + +
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Residues in contact with MET 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q LEU* 5.6 5.6 - - + -
51Q MET* 3.7 35.6 - - + +
54Q GLU* 3.7 19.7 - - + -
56Q ASP* 5.6 2.0 - - + -
57Q ALA* 3.8 7.9 - - + +
67Q GLU* 2.9 55.2 + - + +
68Q PHE* 3.2 13.4 + - + +
70Q THR* 1.3 72.1 - - + +
72Q MET* 1.3 61.8 + - - +
74Q ARG* 3.1 45.3 + - - +
75Q LYS* 3.0 27.5 + - - +
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Residues in contact with MET 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q ILE* 6.0 4.0 - - + -
12Q PHE* 5.7 4.5 - - + -
39Q LEU* 3.6 30.7 - - - -
41Q GLN* 5.4 4.7 - - - +
51Q MET* 4.6 4.2 - - - +
68Q PHE* 2.9 35.2 + - + +
69Q LEU* 3.7 24.5 - - + +
71Q MET* 1.3 72.8 - - - +
73Q ALA* 1.3 56.3 + - - +
75Q LYS* 5.3 1.1 - - - -
76Q MET* 2.9 41.9 + - + +
79Q THR* 4.9 17.7 + - + -
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Residues in contact with ALA 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q LEU* 3.0 21.9 + - + +
70Q THR* 3.3 9.2 + - + +
72Q MET* 1.3 80.2 - - + +
74Q ARG* 1.3 60.4 + - - +
76Q MET* 3.7 18.9 - - - +
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Residues in contact with ARG 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Q MET* 5.9 3.4 - - - -
53Q ASN 5.5 1.8 + - - -
54Q GLU* 2.5 32.3 + - - +
70Q THR* 3.1 21.5 + - + +
71Q MET* 3.1 45.9 + - - +
73Q ALA* 1.3 76.4 - - - +
75Q LYS* 1.3 74.5 + - + +
76Q MET 3.7 0.5 + - - -
77Q LYS* 4.9 10.0 - - - +
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Residues in contact with LYS 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Q GLU* 2.7 41.9 + - - -
50Q ASP* 5.6 4.9 - - - +
51Q MET* 3.8 41.7 - - + -
71Q MET 3.0 14.8 + - - +
72Q MET 3.7 0.7 - - - -
74Q ARG* 1.3 87.8 - - + +
76Q MET* 1.4 63.6 + - - +
77Q LYS* 3.4 4.3 - - - +
78Q ASP* 2.7 52.7 + - - +
79Q THR* 3.1 16.2 + - - +
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Residues in contact with MET 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Q MET* 2.9 25.3 + - + +
73Q ALA* 3.7 15.7 - - - +
74Q ARG 3.4 2.4 + - - -
75Q LYS* 1.4 74.0 - - - +
77Q LYS* 1.4 63.2 + - + +
79Q THR* 3.1 7.5 + - + -
80Q ASP* 2.8 59.1 + - - +
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Residues in contact with LYS 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q ARG 4.9 11.9 - - - +
75Q LYS* 3.2 1.2 + - - +
76Q MET* 1.4 81.5 - - + +
78Q ASP* 1.4 96.7 + - - +
80Q ASP* 3.8 8.3 - - - +
81Q SER* 3.1 26.7 + - - -
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Residues in contact with ASP 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q GLU* 3.8 13.3 - - - +
75Q LYS* 2.7 50.6 + - - +
77Q LYS* 1.4 106.0 + - - +
79Q THR* 1.3 64.0 + - - +
81Q SER* 3.3 20.3 + - - -
82Q GLU* 3.5 13.0 + - - +
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Residues in contact with THR 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q MET* 5.7 7.1 - - + +
41Q GLN* 3.3 50.1 - - + +
43Q PRO* 5.8 6.7 - - + +
47Q GLU* 5.7 0.2 + - - -
51Q MET* 4.5 10.0 - - - +
72Q MET* 4.9 17.3 + - + -
75Q LYS* 3.1 23.0 + - - +
76Q MET* 3.4 11.9 - - - -
78Q ASP* 1.3 76.0 - - - +
80Q ASP* 1.3 61.3 + - - +
82Q GLU* 3.5 16.8 + - - +
83Q GLU 4.4 0.3 + - - -
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Residues in contact with ASP 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Q GLN* 4.2 15.0 + - - +
76Q MET* 2.8 55.2 + - - +
77Q LYS* 3.8 7.3 + - - +
79Q THR* 1.3 69.5 - - - +
81Q SER* 1.4 58.7 + - - +
82Q GLU 3.2 0.7 - - - -
83Q GLU* 2.9 33.2 + - + +
84Q GLU* 4.0 2.4 + - - +
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Residues in contact with SER 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77Q LYS 3.1 15.4 + - - -
78Q ASP* 3.3 15.7 - - - -
79Q THR 3.4 0.4 - - - -
80Q ASP* 1.4 74.7 - - - +
82Q GLU* 1.3 59.3 + - - +
83Q GLU 3.4 0.9 + - - -
84Q GLU* 3.6 20.9 - - - +
85Q ILE* 5.1 1.9 + - - +
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Residues in contact with GLU 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847M ALA* 4.6 7.3 - - - +
41Q GLN* 4.9 0.2 - - + -
42Q ASN* 2.7 55.6 + - - +
43Q PRO* 3.3 22.7 - - + +
44Q THR* 3.0 33.7 + - - +
47Q GLU* 4.8 7.8 - - + +
78Q ASP 3.5 11.2 + - - +
79Q THR* 3.5 13.8 + - - +
80Q ASP 3.1 0.6 + - - -
81Q SER* 1.3 77.4 - - - +
83Q GLU* 1.4 57.2 + - - +
84Q GLU 3.5 0.4 - - - -
85Q ILE* 3.8 19.6 - - - +
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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