Contacts of the helix formed by residues 57 - 78 (chain u) in PDB entry 5GJQ
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 57 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119o MET* 3.4 39.7 - - + -
120o MET 5.0 0.2 - - - -
121o VAL* 5.9 0.4 - - + -
6u VAL* 3.0 22.7 + - + +
7u THR* 5.2 0.7 - - - -
8u GLY 5.7 2.5 - - - -
39u ILE* 3.5 29.3 - - + +
40u SER* 2.5 36.8 + - - -
41u ARG* 3.7 13.2 - - + -
53u ALA 5.9 0.9 - - - -
55u GLY 3.3 5.2 + - - +
56u ASP* 1.3 71.8 - - - +
58u ALA* 1.3 60.6 - - - +
60u PHE* 3.2 28.1 + + + +
61u GLN* 2.9 53.6 + - + +
64u LYS* 4.9 4.2 + - - +
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Residues in contact with ALA 58 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88o TYR* 4.3 7.8 - - + -
91o ARG* 4.0 10.8 - - - +
117o GLY* 4.1 9.9 - - - +
118o GLY 3.9 7.9 - - - +
119o MET* 3.8 33.0 - - + +
56u ASP* 3.2 14.2 + - - +
57u TYR* 1.3 76.5 - - - +
59u ASP* 1.3 67.3 + - - +
61u GLN* 3.1 6.8 + - - +
62u TYR* 3.0 21.0 + - - +
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Residues in contact with ASP 59 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88o TYR* 3.2 17.9 + - - -
91o ARG* 2.7 21.9 + - - -
1u THR* 2.6 23.7 + - - +
56u ASP* 3.1 12.4 + - - +
57u TYR 3.3 0.2 - - - -
58u ALA* 1.3 81.0 - - - +
60u PHE* 1.3 54.1 + - - +
62u TYR* 3.2 8.6 + - - +
63u LEU* 2.9 31.9 + - - +
106u LEU* 3.6 19.0 - - + +
107u TRP 3.0 21.1 + - - +
108u ASN* 3.2 20.0 - - - +
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Residues in contact with PHE 60 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40u SER 3.8 10.1 - - - -
41u ARG* 3.8 21.8 - - + -
42u ILE 4.4 0.7 - - - -
43u MET* 4.5 15.3 - - + -
51u LEU* 4.6 23.6 - - + -
53u ALA* 3.3 28.0 - - + -
56u ASP 3.2 12.9 + - - +
57u TYR* 3.4 45.3 - + + +
58u ALA 3.1 0.6 - - - -
59u ASP* 1.3 77.7 - - - +
61u GLN* 1.3 58.8 + - - +
63u LEU* 3.3 5.4 + - + +
64u LYS* 3.0 51.0 + - + +
108u ASN* 3.6 13.6 + - - +
110u MET* 5.3 2.5 - - + -
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Residues in contact with GLN 61 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84o LYS* 4.4 12.8 - - + +
118o GLY 4.1 3.3 - - - +
119o MET* 3.4 8.8 - - - -
120o MET* 2.6 52.6 + - - +
57u TYR* 2.9 45.3 + - + +
58u ALA 3.1 8.0 + - - +
60u PHE* 1.3 75.9 - - + +
62u TYR* 1.3 66.3 + - - +
64u LYS* 3.2 13.7 - - + +
65u GLN* 3.0 23.6 + - - +
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Residues in contact with TYR 62 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84o LYS* 6.4 0.2 - - - +
85o GLU* 5.9 1.1 - - - -
88o TYR* 3.8 41.7 - + + +
58u ALA 3.0 12.4 + - - +
59u ASP 3.3 10.1 - - - +
61u GLN* 1.3 77.7 - - - +
63u LEU* 1.3 72.5 + - + +
65u GLN* 3.1 22.8 + - - +
66u VAL* 3.0 47.0 + - + +
99u ARG* 4.9 7.8 + - - -
106u LEU* 4.3 18.8 - - + -
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Residues in contact with LEU 63 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43u MET* 4.9 1.1 - - - -
51u LEU* 5.1 6.5 - - + -
59u ASP 2.9 13.9 + - - +
60u PHE* 3.7 6.5 - - + +
62u TYR* 1.3 80.7 - - + +
64u LYS* 1.3 60.5 + - - +
66u VAL* 4.1 2.6 - - + +
67u LEU* 2.8 36.8 + - - +
91u TRP* 4.9 12.6 - - + -
92u LEU* 4.0 22.2 - - + -
95u ALA* 5.0 7.2 - - + -
96u MET* 4.0 11.4 - - - -
106u LEU* 3.9 20.9 - - + -
108u ASN* 3.8 18.8 - - - +
110u MET* 3.6 36.8 - - + -
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Residues in contact with LYS 64 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40u SER* 4.5 10.5 + - - -
42u ILE 4.1 10.5 + - - -
43u MET* 3.3 54.7 - - + +
57u TYR* 4.9 3.2 + - - -
60u PHE* 3.0 37.6 + - + +
61u GLN* 3.2 19.1 - - + +
63u LEU* 1.3 77.3 - - - +
65u GLN* 1.3 64.3 + - - +
67u LEU 4.0 0.2 - - - -
68u GLY* 3.0 19.9 + - - -
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Residues in contact with GLN 65 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100n SER* 3.8 38.8 + - - +
84o LYS* 3.6 11.3 - - - +
85o GLU* 3.5 24.8 + - - +
61u GLN 3.0 13.8 + - - +
62u TYR* 3.1 24.2 + - - +
64u LYS* 1.3 76.0 - - - +
66u VAL* 1.3 76.0 + - - +
68u GLY* 3.2 2.3 + - - -
69u GLN* 3.0 23.4 + - + +
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Residues in contact with VAL 66 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62u TYR* 3.0 52.7 + - + +
63u LEU* 4.1 5.2 - - + +
65u GLN* 1.3 85.1 - - - +
67u LEU* 1.3 62.5 + - - +
69u GLN* 3.2 8.8 + - + +
70u MET* 2.9 23.9 + - + +
91u TRP* 3.6 30.7 - - + -
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Residues in contact with LEU 67 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43u MET* 4.0 5.8 - - + -
45u VAL* 3.8 27.1 - - + -
51u LEU* 3.8 28.7 - - + -
63u LEU 2.8 17.4 + - - +
64u LYS 4.0 2.7 - - - +
66u VAL* 1.3 79.9 - - - +
68u GLY* 1.3 63.0 + - - +
70u MET* 3.1 13.1 + - + +
71u VAL* 2.9 28.0 + - + +
88u ILE* 3.9 42.0 - - + -
91u TRP* 3.9 26.2 - - + -
92u LEU* 5.0 4.3 - - + -
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Residues in contact with GLY 68 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43u MET* 5.5 1.7 - - - -
45u VAL* 6.0 0.6 - - - +
64u LYS 3.0 17.1 + - - -
65u GLN* 3.2 4.4 + - - -
67u LEU* 1.3 76.0 - - - +
69u GLN* 1.3 57.5 + - - +
71u VAL* 3.3 6.1 + - - +
72u ILE* 2.9 38.8 + - - +
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Residues in contact with GLN 69 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96n SER* 2.9 39.6 + - - +
99n ARG* 3.0 33.4 + - - +
100n SER* 4.0 16.4 - - - +
65u GLN* 3.0 12.7 + - + +
66u VAL* 3.5 10.8 - - + +
68u GLY* 1.3 75.6 - - - +
70u MET* 1.3 58.4 + - + +
72u ILE* 4.1 8.2 - - + +
73u ASP* 2.9 66.4 + - - +
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Residues in contact with MET 70 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99m PHE* 3.0 43.5 - - + -
66u VAL* 2.9 20.5 + - + +
67u LEU* 3.1 18.1 + - + +
69u GLN* 1.3 76.5 - - + +
71u VAL* 1.3 57.9 + - + +
73u ASP* 3.4 7.1 + - - +
74u GLU* 3.0 29.1 + - - +
83u TYR* 4.0 19.9 - - + +
88u ILE* 5.2 1.6 - - + -
91u TRP* 3.3 43.1 - - + -
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Residues in contact with VAL 71 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45u VAL* 3.7 26.9 - - + -
46u ASN* 4.2 27.1 - - + +
67u LEU* 2.9 14.7 + - + +
68u GLY* 3.6 9.4 - - - +
70u MET* 1.3 73.8 - - + +
72u ILE* 1.3 62.2 + - + +
74u GLU* 3.2 7.8 + - - +
75u GLU* 2.9 54.1 + - + +
83u TYR* 4.9 10.1 - - + -
88u ILE* 5.4 1.1 - - + -
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Residues in contact with ILE 72 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70n ASP* 4.0 13.0 - - - +
71n ARG* 4.7 20.6 - - + +
99n ARG* 3.1 48.5 - - - +
68u GLY* 2.9 23.5 + - - +
69u GLN* 3.7 18.6 - - - +
71u VAL* 1.3 77.8 - - + +
73u ASP* 1.3 67.7 + - - +
75u GLU* 3.1 9.0 + - - +
76u LEU* 3.0 38.8 + - + +
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Residues in contact with ASP 73 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92n ARG* 5.0 8.2 + - - +
96n SER* 4.8 5.4 + - - -
69u GLN* 2.9 47.2 + - - +
70u MET* 3.6 6.5 - - - +
72u ILE* 1.3 80.9 - - - +
74u GLU* 1.3 63.2 + - - +
76u LEU* 3.5 22.3 + - - +
77u LEU* 3.8 11.8 - - - +
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Residues in contact with GLU 74 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101m ARG* 4.2 1.7 + - - -
107m ARG* 3.1 43.4 + - - +
46u ASN* 5.3 1.7 + - - -
70u MET 3.0 17.0 + - - +
71u VAL* 3.6 6.4 - - - +
72u ILE 3.1 0.2 - - - -
73u ASP* 1.3 77.8 - - - +
75u GLU* 1.3 64.8 + - + +
76u LEU 3.1 1.6 - - - -
77u LEU* 3.1 26.2 + - - +
78u GLY 3.8 2.3 + - - -
79u ASP* 4.6 1.9 - - - +
81u HIS 3.8 5.3 - - - +
82u SER* 3.3 13.5 + - - -
83u TYR* 2.9 61.1 + - + +
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Residues in contact with GLU 75 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68n ASN* 4.7 3.5 + - - -
71n ARG* 6.0 1.4 - - - +
46u ASN* 4.6 10.6 - - - +
71u VAL* 2.9 39.1 + - + +
72u ILE* 3.1 7.5 + - - +
74u GLU* 1.3 79.2 - - + +
76u LEU* 1.3 65.9 + - + +
77u LEU 3.2 0.2 - - - -
78u GLY* 3.7 12.4 + - - +
81u HIS 6.0 0.9 - - - -
82u SER* 6.5 0.9 - - - -
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Residues in contact with LEU 76 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68n ASN* 3.1 39.3 + - + +
69n VAL 2.8 27.1 - - - +
70n ASP* 3.3 37.7 - - - +
71n ARG* 3.5 7.4 - - + +
92n ARG* 3.3 36.3 + - + +
72u ILE* 3.0 30.1 + - + +
73u ASP* 3.5 16.8 - - - +
74u GLU 3.1 0.4 - - - -
75u GLU* 1.3 79.1 - - + +
77u LEU* 1.3 58.7 + - - +
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Residues in contact with LEU 77 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107m ARG* 4.1 28.7 - - + +
110m SER* 6.0 3.1 - - - +
64n LYS* 6.2 0.3 - - - -
68n ASN* 5.0 2.1 + - - -
92n ARG* 3.1 36.1 - - - +
73u ASP 3.8 10.3 - - - +
74u GLU* 3.1 14.3 + - - +
76u LEU* 1.3 79.5 - - - +
78u GLY* 1.3 65.8 + - - +
79u ASP* 3.2 28.8 + - + +
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Residues in contact with GLY 78 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64n LYS* 5.7 5.4 + - - -
68n ASN* 5.4 3.8 - - - -
74u GLU 3.8 4.0 + - - -
75u GLU* 3.7 11.6 + - - -
76u LEU 3.4 2.4 - - - -
77u LEU* 1.3 79.8 - - - +
79u ASP* 1.3 57.8 + - - +
80u GLY 3.2 8.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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