Contacts of the helix formed by residues 50 - 65 (chain A) in PDB entry 5OQN
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 TYR 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ASP* 4.8 4.6 + - - -
9A ILE* 3.7 52.2 - - + +
10A ASN* 4.5 13.2 - - + -
13A ILE* 3.7 17.0 - - + -
45A ALA* 2.8 19.3 + - + +
48A GLN* 3.2 23.1 - - + -
49A GLY* 1.3 73.9 - - - +
51A GLU* 1.3 63.3 + - - +
52A ASP 3.3 2.7 - - - +
53A ALA* 3.1 25.7 + - + +
54A PHE 3.4 8.0 + - - -
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Residues in contact with GLU 51 (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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42A GLN* 6.2 0.4 - - - +
45A ALA 3.6 2.5 + - - -
46A VAL* 3.9 30.1 - - + +
49A GLY 3.0 8.2 + - - +
50A TYR* 1.3 75.3 - - - +
52A ASP* 1.3 71.7 + - - +
54A PHE* 3.1 12.3 + - - +
55A ASN* 3.1 34.1 + - - +
110A ILE* 4.1 19.8 - - + +
113A ARG* 2.2 49.0 + - - +
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Residues in contact with ASP 52 (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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49A GLY 4.7 4.5 + - - +
50A TYR* 3.3 0.6 - - - +
51A GLU* 1.3 85.3 + - - +
53A ALA* 1.3 57.8 + - - +
55A ASN* 3.4 11.4 + - - +
56A PHE* 2.9 30.5 + - - +
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Residues in contact with ALA 53 (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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10A ASN* 4.7 18.2 - - - +
13A ILE* 3.9 12.6 - - + -
50A TYR* 3.1 34.7 + - + +
52A ASP* 1.3 79.0 - - - +
54A PHE* 1.3 61.0 + - - +
56A PHE* 3.4 5.3 + - - +
57A TRP* 3.0 33.9 + - + -
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Residues in contact with PHE 54 (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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13A ILE* 4.3 10.2 - - + +
17A VAL* 3.7 32.1 - - + -
38A LEU* 4.4 10.5 - - + -
41A ILE* 4.3 18.2 - - + -
42A GLN* 3.6 45.5 - - + -
45A ALA* 4.3 12.1 - - + -
46A VAL* 6.3 0.4 - - + -
50A TYR 3.4 6.9 + - - +
51A GLU* 3.1 9.9 + - - +
53A ALA* 1.3 78.2 - - - +
55A ASN* 1.3 76.7 + - - +
56A PHE 3.2 0.3 + - - -
57A TRP* 4.1 0.7 - - - +
58A PHE* 3.1 37.6 + + + +
85A PHE* 4.0 25.1 - + - -
114A PHE* 4.2 9.2 - + - -
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Residues in contact with ASN 55 (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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42A GLN* 4.7 2.1 + - - -
51A GLU* 3.1 33.6 + - - +
52A ASP* 3.9 11.5 + - - +
54A PHE* 1.3 83.0 - - - +
56A PHE* 1.3 60.8 + - - +
58A PHE* 4.6 0.2 - - - -
59A ASP* 2.6 32.9 + - - +
110A ILE* 6.2 0.2 - - - +
113A ARG* 4.2 5.5 + - - +
114A PHE* 3.5 47.5 - - + +
117A GLN* 3.6 24.0 + - + +
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Residues in contact with PHE 56 (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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52A ASP 2.9 18.8 + - - +
53A ALA* 3.7 7.0 - - - +
54A PHE 3.1 0.2 - - - -
55A ASN* 1.3 74.4 - - - +
57A TRP* 1.3 100.0 + + + +
59A ASP* 3.2 13.4 + - - +
60A LYS* 3.3 39.2 + - + +
117A GLN* 4.7 4.3 - - - +
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Residues in contact with TRP 57 (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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10A ASN* 2.4 42.8 + - - +
11A THR* 5.8 2.2 - - + -
13A ILE* 4.2 16.2 - - + -
14A PHE* 3.3 50.5 - + + -
17A VAL* 5.4 4.5 - - + -
53A ALA* 3.0 27.2 + - + +
54A PHE* 4.2 2.0 - - - +
56A PHE* 1.3 102.1 - + - +
58A PHE* 1.3 66.6 + - - +
60A LYS* 2.7 35.1 + - + +
61A LEU* 3.0 21.5 + - + +
468B ASP* 5.3 4.5 - - - -
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Residues in contact with PHE 58 (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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17A VAL* 4.3 11.1 - - + +
21A PHE* 3.3 40.4 - + - -
38A LEU* 4.5 13.7 - - + -
54A PHE* 3.1 29.9 + + + +
55A ASN* 4.0 2.7 - - - +
57A TRP* 1.3 77.9 - - - +
59A ASP* 1.3 71.1 + - - +
61A LEU* 3.2 10.8 + - - +
62A VAL* 3.2 29.9 + - + +
81A LEU* 6.2 0.4 - - + -
82A VAL* 4.2 30.3 - - + -
85A PHE* 4.0 17.7 - + + -
86A ILE* 5.5 0.2 - - + -
114A PHE* 3.5 35.4 - + + -
118A PHE* 4.5 8.3 - + - -
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Residues in contact with ASP 59 (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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55A ASN* 2.6 22.3 - - - +
56A PHE* 3.2 7.6 + - - +
57A TRP 3.1 0.8 - - - -
58A PHE* 1.3 82.3 - - - +
60A LYS* 1.3 64.6 + - - +
61A LEU 3.1 0.3 + - - -
62A VAL* 3.2 9.7 + - - +
63A THR* 2.9 25.4 + - - -
114A PHE* 4.9 0.3 - - - -
117A GLN* 2.4 33.9 + - - +
118A PHE* 3.8 17.6 - - - +
121A HIS* 3.3 41.5 + - + +
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Residues in contact with LYS 60 (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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14A PHE* 6.2 1.1 - - + -
56A PHE* 3.3 44.7 + - + +
57A TRP* 2.7 29.6 + - + +
59A ASP* 1.3 73.2 - - + +
61A LEU* 1.3 60.4 + - + +
63A THR* 3.3 20.9 + - - -
64A LYS* 3.4 16.3 + - - +
121A HIS* 4.4 4.0 + - + -
468B ASP* 3.4 42.0 + - - +
471B GLU* 3.4 32.0 + - + +
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Residues in contact with LEU 61 (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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14A PHE* 4.5 11.2 - - + -
17A VAL* 3.7 22.7 - - + -
18A ALA* 4.1 18.2 - - + +
21A PHE* 4.2 15.7 - - + -
57A TRP* 3.0 34.7 + - + +
58A PHE* 3.6 11.0 - - - +
59A ASP 3.1 0.8 - - - -
60A LYS* 1.3 76.0 - - + +
62A VAL* 1.3 64.7 + - - +
63A THR 3.1 1.6 - - - -
64A LYS* 3.1 24.2 + - + +
65A ILE* 3.8 3.8 + - - +
463B PHE* 3.5 55.8 - - + +
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Residues in contact with VAL 62 (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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21A PHE* 4.3 11.4 - - + -
58A PHE* 3.2 20.6 + - + +
59A ASP 3.2 6.0 + - - +
61A LEU* 1.3 75.5 - - - +
63A THR* 1.3 60.1 + - - +
65A ILE* 3.1 28.4 - - + +
66A LEU* 3.6 9.9 - - + +
78A ILE* 5.6 0.4 - - + -
82A VAL* 4.1 24.0 - - + -
118A PHE* 4.0 24.5 - - + -
121A HIS* 6.1 0.9 - - + -
122A VAL* 4.9 3.4 - - + -
140A LEU* 3.3 35.2 - - + -
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASP 2.9 5.8 + - - -
60A LYS* 3.3 14.0 - - - -
61A LEU 3.1 0.4 - - - -
62A VAL* 1.3 77.2 - - - +
64A LYS* 1.3 63.9 + - + +
65A ILE 3.2 0.6 + - - -
66A LEU* 3.6 9.9 + - + +
67A PRO* 3.6 15.9 - - - +
121A HIS* 2.7 32.7 + - - -
470B PHE* 4.1 6.4 - - + -
471B GLU* 3.9 28.2 - - + +
474B VAL* 4.4 16.2 - - + +
475B PHE* 4.1 15.6 - - + -
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Residues in contact with LYS 64 (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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60A LYS* 3.5 15.3 - - - +
61A LEU* 3.1 17.4 + - + +
63A THR* 1.3 80.5 - - - +
65A ILE* 1.3 58.9 + - - +
67A PRO* 3.7 8.8 - - - +
68A LEU* 4.9 1.6 - - - +
461B ILE* 3.7 24.5 - - + +
462B ASP 3.7 17.8 + - - -
463B PHE* 4.1 25.0 + - + +
465B LYS 3.6 18.4 + - - -
467B ASP* 3.6 16.9 + - - -
468B ASP* 3.4 24.0 - - - -
470B PHE* 3.3 27.1 - - + -
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Residues in contact with ILE 65 (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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61A LEU 3.9 11.0 - - - +
62A VAL* 3.1 24.7 - - + +
64A LYS* 1.3 79.1 - - - +
66A LEU* 1.3 79.2 + - + +
67A PRO* 3.5 0.9 - - - -
68A LEU* 3.3 35.2 + - + +
74A ILE* 5.3 0.4 - - + -
75A GLY* 4.8 4.3 - - - +
78A ILE* 3.8 33.9 - - + -
79A VAL* 4.2 24.5 - - + -
136A ARG* 3.5 11.7 - - + -
140A LEU* 4.6 8.3 - - + -
461B ILE* 4.4 6.1 - - + -
463B PHE* 4.0 15.3 - - + -
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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