Contacts of the helix formed by residues 90 - 112 (chain B) in PDB entry 1BJJ
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 ASN 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 5.6 1.7 - - - +
61B CYS* 5.0 2.6 - - - -
89B THR* 1.3 72.3 - - - +
91B CYS* 1.3 65.1 + - - +
93B GLU* 3.3 7.6 + - - +
94B GLN* 2.8 55.8 + - - +
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Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASN* 4.3 12.8 - - - -
61B CYS* 2.0 58.1 - - + -
71B ASP* 4.3 8.5 - - - +
89B THR* 3.1 6.8 + - - +
90B ASN* 1.3 83.2 - - - +
92B GLU* 1.3 56.3 + - - +
94B GLN* 3.0 2.9 + - - -
95B ILE* 2.7 44.2 + - + +
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ASP* 3.4 12.7 - - - +
72B ILE 3.3 17.0 - - - +
73B TYR* 3.7 18.5 - - + +
74B SER 5.0 1.0 + - - +
88B GLY* 3.4 4.2 - - - -
89B THR* 3.1 36.0 + - - +
91B CYS* 1.3 78.1 - - - +
93B GLU* 1.3 58.3 + - + +
95B ILE* 3.7 6.1 - - - +
96B CYS* 2.8 32.3 + - - +
70F SER 3.6 0.5 - - - +
71F ASP* 3.1 4.9 - - - +
72F ILE* 2.7 38.1 + - - +
134F CA 2.3 27.9 - - - -
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Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B CYS* 4.6 3.6 - - + +
85B GLY 3.6 20.0 - - - +
86B LYS* 2.7 38.6 + - - +
88B GLY* 3.1 17.6 + - - +
89B THR 2.8 24.5 + - - +
90B ASN* 3.7 6.7 - - - +
92B GLU* 1.3 72.1 - - + +
94B GLN* 1.3 64.0 + - - +
96B CYS* 3.6 6.3 + - - +
97B GLU* 3.1 33.1 + - - +
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.9 31.2 - - + +
90B ASN* 2.8 48.2 + - - +
91B CYS* 3.6 2.7 - - - +
93B GLU* 1.3 80.3 + - - +
95B ILE* 1.3 66.0 + - - +
97B GLU* 3.2 13.3 + - - +
98B CYS* 3.0 26.5 + - - -
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Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN 5.0 2.0 - - - +
52B TYR* 3.9 11.0 - - + +
55B LEU* 4.2 11.0 - - + -
61B CYS* 4.0 12.1 - - + -
67B ASN 3.9 8.5 - - - +
68B THR* 3.4 53.8 - - + +
71B ASP* 3.9 15.7 - - + +
73B TYR* 3.7 20.4 - - + -
91B CYS* 2.7 32.2 + - + +
92B GLU* 3.7 4.5 - - - +
94B GLN* 1.3 71.4 - - - +
96B CYS* 1.3 62.3 + - - +
98B CYS* 3.2 6.2 + - - +
99B ASP* 3.1 21.7 + - - +
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Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B MET* 4.1 4.6 - - - +
73B TYR* 3.6 41.0 - - + -
74B SER 4.1 1.8 - - - +
75B TYR* 3.9 8.1 - - - -
84B CYS* 2.0 52.3 - - + -
85B GLY 5.9 0.2 - - - +
92B GLU 2.8 19.3 + - - +
93B GLU* 3.8 4.5 - - - +
95B ILE* 1.3 78.6 - - - +
97B GLU* 1.3 55.8 + - - +
99B ASP* 3.3 2.3 + - - +
100B ARG* 2.9 27.0 + - - +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B CYS* 5.0 1.1 - - - -
84B CYS* 3.6 19.6 + - + +
93B GLU* 3.1 19.4 + - + +
94B GLN* 3.2 18.8 + - - +
96B CYS* 1.3 73.2 - - - +
98B CYS* 1.3 64.3 + - - +
100B ARG* 3.0 38.6 + - - -
101B VAL* 3.2 32.1 + - - +
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Residues in contact with CYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS* 3.4 13.7 + - - +
51B CYS* 2.0 64.6 - - + -
52B TYR* 3.5 19.1 - - + -
55B LEU* 3.9 11.9 - - - -
94B GLN* 3.0 19.4 + - - -
95B ILE 3.2 8.3 + - - +
97B GLU* 1.3 77.7 - - - +
99B ASP* 1.3 62.1 + - - +
101B VAL* 4.2 3.1 - - - +
102B ALA* 3.2 17.3 + - - +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN 4.5 2.9 + - - +
5B PHE* 3.5 32.9 + - + +
8B MET* 3.6 10.3 - - - -
48B HIS* 3.0 13.4 + - - -
52B TYR* 2.5 28.7 + - - -
73B TYR* 2.5 40.3 + - - +
95B ILE* 3.1 7.2 + - - +
96B CYS 3.6 4.5 - - - +
98B CYS* 1.3 75.4 - - - +
100B ARG* 1.3 66.2 + - - +
102B ALA 3.2 1.4 + - - -
103B ALA* 2.9 22.3 + - - +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET* 3.7 10.7 - - - -
82B ILE* 2.9 42.9 + - + +
83B THR* 4.7 2.5 - - - +
84B CYS* 4.3 8.5 - - - +
96B CYS 2.9 19.6 + - - +
97B GLU* 3.0 38.5 + - - +
99B ASP* 1.3 74.8 - - - +
101B VAL* 1.3 81.1 + - - +
103B ALA* 3.2 4.0 + - - +
104B GLU* 3.1 51.1 + - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 6.2 4.9 - - + -
97B GLU* 3.2 19.7 + - + +
98B CYS* 4.2 2.7 - - - +
100B ARG* 1.3 102.1 - - - +
102B ALA* 1.3 60.3 + - - +
104B GLU* 3.2 8.9 + - - +
105B CYS* 2.7 31.5 + - + +
108B ARG* 4.8 7.8 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 3.8 13.0 - - + -
44B CYS* 4.4 8.5 - - - +
48B HIS* 3.7 26.0 - - + +
98B CYS 3.2 18.3 + - - +
99B ASP 3.6 3.6 - - - +
101B VAL* 1.3 79.0 - - - +
103B ALA* 1.3 63.5 + - - +
105B CYS* 3.0 9.3 + - - +
106B PHE* 3.0 34.8 + - + -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.1 5.0 - - + -
8B MET* 3.8 33.0 - - + -
9B ILE* 4.1 3.4 - - - +
13B GLU* 3.3 28.3 - - + +
14B THR* 4.0 1.2 - - - +
82B ILE* 4.6 1.8 - - + -
99B ASP 2.9 17.4 + - - +
100B ARG 3.5 5.4 - - - +
102B ALA* 1.3 76.3 - - - +
104B GLU* 1.3 60.7 + - - +
106B PHE* 3.5 15.7 - - - +
107B ARG 3.4 10.9 + - - -
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 3.6 28.0 - - + +
81B TYR* 5.4 8.0 - - - -
82B ILE* 4.4 10.3 + - + +
100B ARG* 3.1 50.3 + - - +
101B VAL* 3.7 9.2 - - - +
103B ALA* 1.3 71.9 - - - +
105B CYS* 1.3 67.3 + - - +
106B PHE 3.1 1.8 - - - -
107B ARG* 3.0 21.4 + - - +
108B ARG* 3.0 35.6 + - - +
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Residues in contact with CYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLY 4.6 0.2 - - - -
43B ARG* 5.2 0.4 - - - -
44B CYS* 2.0 51.2 - - + -
47B VAL* 6.2 1.3 - - - -
101B VAL* 2.7 24.6 + - + +
102B ALA* 3.3 8.1 - - - +
104B GLU* 1.3 72.6 - - - +
106B PHE* 1.3 61.1 + - - +
108B ARG* 3.3 25.7 + - - +
109B ASN* 2.8 36.6 + - - -
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.2 8.7 - + - -
9B ILE* 4.1 30.5 - - + -
14B THR* 3.7 14.6 - - + -
22B TYR* 3.6 40.0 + + + +
41B THR* 3.8 12.0 + - + -
44B CYS* 3.4 27.6 - - + -
45B CYS* 3.4 31.0 - - - -
48B HIS* 6.3 0.2 - - + -
102B ALA* 3.0 27.2 + - + -
103B ALA* 3.5 14.4 - - - +
104B GLU 3.1 0.2 - - - -
105B CYS* 1.3 76.3 - - - +
107B ARG* 1.3 64.5 + - - +
109B ASN* 2.9 14.9 + - - -
110B LEU* 3.0 14.0 + - - +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 2.6 63.4 + - + +
14B THR* 4.1 3.9 - - - +
103B ALA 3.4 4.5 + - - +
104B GLU* 3.0 30.9 + - - +
106B PHE* 1.3 80.4 - - - +
108B ARG* 1.3 85.7 + - - +
109B ASN 3.4 0.5 + - - -
110B LEU* 3.4 28.6 + - + +
111B ASP* 4.9 1.2 - - - +
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 4.8 7.9 + - - +
104B GLU* 3.0 18.3 + - - +
105B CYS* 3.7 43.8 - - - +
106B PHE 3.2 0.4 - - - -
107B ARG* 1.3 95.8 - - - +
109B ASN* 1.3 66.3 + - - +
110B LEU 3.4 0.2 - - - -
111B ASP* 3.0 19.2 - - - +
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Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLY* 2.8 34.4 + - - -
41B THR* 3.4 24.8 + - - +
44B CYS* 3.9 6.1 - - - -
105B CYS* 2.8 29.0 + - - +
106B PHE 2.9 6.4 + - - +
108B ARG* 1.3 89.3 - - - +
110B LEU* 1.3 63.3 + - - +
111B ASP* 3.1 4.5 - - - -
112B THR* 3.0 22.8 + - - +
113B TYR 3.3 7.4 + - - -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU 5.1 0.2 - - - +
14B THR* 4.2 24.9 - - - +
16B LYS* 3.5 36.3 - - + +
22B TYR* 4.0 9.2 - - - +
106B PHE 3.0 10.3 + - - +
107B ARG* 3.4 29.4 + - + +
108B ARG 3.4 0.4 - - - -
109B ASN* 1.3 76.2 - - - +
111B ASP* 1.3 63.5 + - - +
113B TYR* 2.9 24.0 + - + +
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG 4.9 0.9 - - - +
108B ARG 3.0 23.7 - - - +
109B ASN* 4.4 0.8 - - - -
110B LEU* 1.3 80.4 + - - +
112B THR* 1.3 76.9 + - - +
113B TYR 3.3 2.3 + - - +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASP* 3.3 20.5 + - - +
40B GLY* 5.0 5.3 + - - -
109B ASN* 3.0 23.0 + - - +
111B ASP* 1.3 91.4 + - - +
113B TYR* 1.3 64.9 + - - +
114B ASN* 3.2 7.6 + - - +
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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