Contacts of the helix formed by residues 59 - 83 (chain A) in PDB entry 3OV6
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 SER 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 1.3 74.5 - - - +
60A ASN* 1.3 68.1 + - - +
61A GLU* 3.3 14.0 + - - +
62A GLU* 3.0 35.3 + - - +
63A LEU* 3.2 22.9 + - - +
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 2.8 34.5 + - - +
58A PHE 5.0 0.5 - - - +
59A SER* 1.3 77.0 - - - +
61A GLU* 1.3 70.0 + - - +
63A LEU* 3.3 8.5 + - - +
64A SER* 2.9 33.9 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.2 11.8 - - - +
60A ASN* 1.3 92.7 + - - +
62A GLU* 1.3 60.3 + - + +
64A SER* 3.6 7.7 + - - -
65A ASP* 3.4 26.8 + - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN 4.8 0.9 - - - +
58A PHE* 3.8 23.3 - - + -
59A SER* 3.0 37.3 + - - +
61A GLU* 1.3 76.0 - - + +
63A LEU* 1.3 63.4 + - - +
65A ASP* 3.3 10.4 + - - +
66A LEU* 2.9 30.8 + - + +
169A ARG* 3.1 34.1 + - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 4.1 5.6 - - + +
49A PHE* 4.1 22.7 - - + -
55A LYS* 3.7 38.4 - - + +
58A PHE* 3.7 28.3 - - + +
59A SER 3.2 18.2 + - - +
60A ASN* 3.3 5.1 + - - +
62A GLU* 1.3 73.8 - - - +
64A SER* 1.3 65.5 + - - +
66A LEU* 3.5 8.5 + - + +
67A GLU* 3.1 28.8 + - - +
170A PHE* 4.2 11.0 - - + -
1105A MK0 4.0 26.2 - - + -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASN* 2.9 20.0 + - - +
61A GLU* 3.6 10.0 + - - -
62A GLU 3.2 0.2 - - - -
63A LEU* 1.3 76.7 - - - +
65A ASP* 1.3 60.4 + - - +
67A GLU* 3.2 13.0 + - - +
68A LEU* 3.0 29.3 + - - +
71A ARG* 5.2 1.2 + - - -
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Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU 3.4 14.5 + - - +
62A GLU* 3.3 12.6 + - - +
64A SER* 1.3 78.8 - - - +
66A LEU* 1.3 65.9 + - + +
68A LEU* 3.5 15.6 + - - +
69A LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 4.9 4.5 - - + -
58A PHE* 4.2 24.2 - - + -
62A GLU* 2.9 30.8 + - + +
63A LEU* 3.7 15.5 - - + +
65A ASP* 1.3 82.5 - - + +
67A GLU* 1.3 51.7 + - - +
69A LEU* 3.1 20.5 + - + +
70A PHE* 2.8 55.4 + - + -
162A LEU* 4.6 15.7 - - + -
166A THR* 4.8 8.7 - - + -
1105A MK0 4.7 17.7 - - + -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.9 4.2 - - - -
45A GLY 3.8 6.9 - - - +
46A THR* 3.4 25.2 - - - +
47A ILE* 3.3 45.8 + - + +
49A PHE* 4.8 6.1 - - - -
63A LEU 3.1 21.5 + - - +
64A SER* 3.2 13.5 + - - +
66A LEU* 1.3 75.4 - - - +
68A LEU* 1.3 57.4 + - - +
70A PHE* 3.3 9.9 + - - +
71A ARG* 2.9 43.3 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 3.0 8.4 + - - +
65A ASP* 3.6 19.5 - - - +
67A GLU* 1.3 75.1 - - - +
69A LEU* 1.3 68.2 + - - +
71A ARG* 3.1 30.2 + - + +
72A PHE* 3.1 63.6 + - + -
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Residues in contact with LEU 69 (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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65A ASP 2.8 22.3 + - - +
66A LEU* 3.3 15.7 - - + +
68A LEU* 1.3 74.0 - - - +
70A PHE* 1.3 65.5 + - + +
72A PHE* 3.3 10.4 + - + +
73A TYR* 3.0 22.7 + - - +
158A THR* 4.1 10.1 - - + -
162A LEU* 3.5 38.6 - - + -
1105A MK0 3.4 41.8 - - + +
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Residues in contact with PHE 70 (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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40A TRP* 3.8 29.4 - + + -
47A ILE* 4.7 2.7 - - + -
66A LEU* 2.8 37.2 + - + +
67A GLU* 3.6 4.7 - - - +
69A LEU* 1.3 79.5 - - + +
71A ARG* 1.3 57.8 + - - +
73A TYR* 3.1 9.5 + + + +
74A LEU* 2.8 38.4 + - + +
162A LEU* 5.1 1.3 - - + -
1105A MK0 3.7 118.7 - - + -
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 4.3 4.0 - - + -
44A SER 3.4 18.1 + - - -
45A GLY* 3.7 32.4 + - - +
46A THR* 5.1 3.2 - - - +
64A SER 5.2 1.2 + - - -
67A GLU* 2.9 24.4 + - - +
68A LEU* 3.1 37.6 + - + +
70A PHE* 1.3 75.5 - - - +
72A PHE* 1.3 66.3 + - + +
74A LEU* 3.6 9.5 - - + +
75A PHE* 3.0 22.4 + - - +
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Residues in contact with PHE 72 (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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68A LEU* 3.1 48.9 + - + -
69A LEU* 3.5 10.3 - - + +
71A ARG* 1.3 76.8 - - + +
73A TYR* 1.3 58.4 + - - +
75A PHE* 3.1 12.9 - + + +
76A GLY 2.8 24.1 + - - -
1105A MK0 3.4 41.5 - - - +
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Residues in contact with TYR 73 (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 GLN* 2.9 36.2 + - - -
69A LEU 3.0 2.2 + - - +
70A PHE* 3.1 13.9 + + + +
72A PHE* 1.3 80.2 - - - +
74A LEU* 1.3 70.9 + - + +
76A GLY* 3.0 2.4 + - - -
77A LEU* 2.9 44.3 + - + +
98A VAL* 4.3 4.9 - - - +
114A PHE* 3.8 15.7 - + - -
1104A D12 3.3 46.0 - - + +
1105A MK0 3.2 68.6 + - + -
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Residues in contact with LEU 74 (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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16A PHE* 3.8 21.3 - - + -
40A TRP* 3.9 31.0 - - + +
70A PHE* 2.8 23.6 + - + +
71A ARG* 3.6 7.4 - - + +
73A TYR* 1.3 85.2 - - + +
75A PHE* 1.3 66.8 + - - +
76A GLY 3.0 1.2 + - - -
77A LEU* 3.2 3.5 + - - +
78A THR* 3.0 33.3 + - + +
1105A MK0 3.5 42.8 - - + -
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Residues in contact with PHE 75 (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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71A ARG 3.0 10.4 + - - +
72A PHE* 3.1 15.3 - + + +
74A LEU* 1.3 76.4 - - - +
76A GLY* 1.3 61.1 + - - +
78A THR* 2.8 21.9 + - - -
79A ARG* 3.1 69.2 + - + +
1105A MK0 5.0 10.5 - - - -
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Residues in contact with GLY 76 (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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72A PHE 2.8 12.8 + - - -
73A TYR 3.0 0.4 + - - -
74A LEU 3.0 0.6 - - - -
75A PHE* 1.3 75.4 - - - +
77A LEU* 1.3 65.7 + - - +
79A ARG* 3.9 2.7 - - - +
80A GLU* 3.0 28.1 + - - +
1104A D12 3.2 23.8 - - - -
1105A MK0 3.9 15.9 - - - -
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Residues in contact with LEU 77 (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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16A PHE* 4.9 20.9 - - + -
18A PHE* 5.9 0.4 - - - -
73A TYR* 2.9 39.2 + - + +
74A LEU* 3.2 9.4 + - - +
76A GLY* 1.3 72.1 - - - +
78A THR* 1.3 53.2 + - + +
80A GLU* 3.2 5.3 + - + +
81A ILE* 2.7 58.3 + - + +
96A VAL* 5.9 1.6 - - + -
98A VAL* 5.9 1.3 - - + -
1104A D12 3.1 70.7 - - + -
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Residues in contact with THR 78 (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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16A PHE* 5.3 11.4 - - + -
18A PHE* 5.0 15.9 - - + -
74A LEU* 3.0 17.5 + - + +
75A PHE* 2.8 28.5 + - - -
77A LEU* 1.3 73.3 - - + +
79A ARG* 1.3 58.4 + - - +
81A ILE* 3.6 3.7 - - - +
82A GLN* 2.8 50.8 + - - +
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Residues in contact with ARG 79 (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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75A PHE* 3.1 58.6 + - + +
76A GLY* 3.9 3.4 - - - +
78A THR* 1.3 81.8 + - - +
80A GLU* 1.3 67.6 + - - +
82A GLN* 3.9 12.9 - - - +
83A ASP* 3.2 30.5 + - - +
1105A MK0 5.8 2.7 + - - -
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Residues in contact with GLU 80 (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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76A GLY* 3.0 22.7 + - - +
77A LEU* 3.3 7.4 - - + +
79A ARG* 1.3 80.6 - - - +
81A ILE* 1.3 63.9 + - + +
83A ASP* 2.9 23.3 - - - +
84A HIS* 4.2 3.8 + - - +
147A LEU* 5.2 12.7 - - + +
148A LEU* 6.4 1.6 - - + -
152A TYR* 5.9 4.0 - - - -
1104A D12 5.7 8.1 - - + -
1105A MK0 5.8 0.3 + - - -
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Residues in contact with ILE 81 (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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18A PHE* 3.7 27.4 - - + -
77A LEU* 2.7 43.0 + - + +
78A THR 4.0 2.7 - - - +
80A GLU* 1.3 76.9 - - + +
82A GLN* 1.3 57.2 + - - +
83A ASP 2.7 17.0 - - - +
84A HIS* 3.9 10.8 - - + +
92A TYR* 5.5 1.7 + - - -
94A PHE* 3.6 34.6 - - + -
96A VAL* 5.5 1.3 - - + -
144A VAL* 6.2 0.4 - - + -
1104A D12 3.4 35.4 - - + -
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Residues in contact with GLN 82 (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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18A PHE* 5.1 11.0 - - + -
21A GLN* 2.9 57.9 - - + +
22A SER* 5.2 2.6 - - - -
78A THR* 2.8 31.3 + - - +
79A ARG* 3.9 14.6 - - - +
81A ILE* 1.3 75.4 - - - +
83A ASP* 1.3 67.8 + - - +
84A HIS 4.0 0.9 - - - +
85A ALA* 3.3 5.0 - - - +
92A TYR* 5.0 1.7 + - - -
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.2 17.5 + - - +
80A GLU* 2.9 8.5 - - - +
81A ILE 2.7 19.4 - - - +
82A GLN* 1.3 77.9 + - - +
84A HIS* 1.3 74.4 + - - +
85A ALA* 4.2 4.9 - - - +
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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