Contacts of the helix formed by residues 83 - 129 (chain A) in PDB entry 6JJY
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 ASP 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.6 14.2 - - + -
80A GLN* 4.2 0.2 - - - -
81A ILE 3.5 2.6 + - - -
82A GLU* 1.3 70.4 - - - +
84A PRO* 1.3 65.9 - - - +
85A ARG* 2.5 55.1 + - - -
86A VAL* 3.2 27.4 + - + +
87A GLN* 2.9 26.2 + - - +
90A ARG* 5.6 0.2 + - - -
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Residues in contact with PRO 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.3 30.0 - - + -
55A LEU* 4.2 5.6 - - + -
59A TRP* 3.6 36.3 - - + -
71A PHE* 3.6 24.0 - - + -
80A GLN* 3.6 11.7 - - - +
82A GLU 3.2 6.9 - - - +
83A ASP* 1.3 88.7 - - - +
85A ARG* 1.3 59.9 + - - +
87A GLN* 3.8 10.0 - - + +
88A TRP* 2.9 28.1 + - - +
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.6 26.7 - - + -
50A CYS* 5.8 1.6 - - + -
52A SER 4.9 3.8 - - - +
53A ASP* 2.6 50.1 + - - +
54A GLU 3.7 11.2 - - - +
55A LEU* 3.8 23.2 - - + +
61A GLU* 4.6 10.5 + - - -
71A PHE* 3.9 12.7 - - - -
83A ASP* 2.5 36.0 + - - +
84A PRO* 1.3 78.1 - - - +
86A VAL* 1.3 63.3 + - + +
88A TRP* 3.4 6.6 + - - +
89A ARG* 3.1 22.0 + - - +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 3.2 30.7 + - + +
85A ARG* 1.3 77.0 - - + +
87A GLN* 1.3 60.1 + - - +
89A ARG* 3.2 7.1 + - - +
90A ARG* 2.9 48.5 + - + +
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 5.5 0.5 - - - -
80A GLN* 3.5 34.9 + - - +
82A GLU* 3.2 25.6 + - + +
83A ASP 2.9 15.0 + - - +
84A PRO* 3.8 8.3 - - + +
86A VAL* 1.3 76.8 - - - +
88A TRP* 1.3 56.7 + - - +
90A ARG* 3.3 24.6 + - - +
91A GLU* 2.8 53.8 + - + +
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Residues in contact with TRP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 5.1 3.8 + - - -
47A PHE* 3.5 40.4 - + + +
48A ALA* 3.6 37.3 - - + +
84A PRO 2.9 20.4 + - - +
85A ARG* 3.6 7.4 - - - +
86A VAL 3.2 0.2 - - - -
87A GLN* 1.3 76.7 - - - +
89A ARG* 1.3 71.1 + - + +
91A GLU* 3.2 17.3 + - - +
92A GLN* 3.0 61.7 + - + +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG 3.1 11.2 + - - +
86A VAL* 3.2 8.9 + - - +
88A TRP* 1.3 88.7 - - + +
90A ARG* 1.3 62.3 + - - +
92A GLN* 3.3 6.9 + - - +
93A GLU* 3.2 21.3 + - - +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.5 36.2 + - - +
86A VAL* 2.9 35.7 + - + +
87A GLN* 3.4 30.4 - - - +
89A ARG* 1.3 76.9 - - - +
91A GLU* 1.3 65.3 + - + +
93A GLU* 3.3 6.1 + - - +
94A HIS* 3.0 57.3 + - + +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLN* 2.8 49.6 + - + +
88A TRP* 3.2 20.1 + - - +
90A ARG* 1.3 75.8 - - + +
92A GLN* 1.3 69.5 + - - +
94A HIS* 3.8 6.8 - - - +
95A MET* 3.1 25.1 + - - +
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Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 3.0 67.9 + - + +
89A ARG* 3.7 7.9 - - - +
90A ARG 3.2 0.2 - - - -
91A GLU* 1.3 84.6 + - - +
93A GLU* 1.3 61.0 + - - +
95A MET* 3.4 27.5 + - - +
96A LEU* 3.3 29.2 + - + +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG 3.2 12.5 + - - +
90A ARG* 3.3 8.3 + - - +
92A GLN* 1.3 78.3 - - - +
94A HIS* 1.3 66.7 + - + +
96A LEU* 3.2 9.9 + - - +
97A LYS* 2.9 30.0 + - + +
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Residues in contact with HIS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 3.0 54.9 + - + +
91A GLU* 3.8 7.1 - - - +
92A GLN 3.4 0.2 - - - -
93A GLU* 1.3 85.0 - - + +
95A MET* 1.3 58.2 + - - +
97A LYS* 3.3 8.4 + - + +
98A ASP* 2.8 41.3 + - - +
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Residues in contact with MET 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU 3.1 18.8 + - - +
92A GLN* 3.7 23.6 - - - +
93A GLU 3.2 0.2 - - - -
94A HIS* 1.3 74.7 - - - +
96A LEU* 1.3 66.4 + - + +
98A ASP* 3.2 11.2 + - + +
99A TYR* 2.9 60.5 + - + +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN* 3.3 14.5 + - + +
93A GLU* 3.2 10.1 + - - +
95A MET* 1.3 84.6 - - + +
97A LYS* 1.3 57.7 + - - +
99A TYR* 3.5 15.7 + - + +
100A LEU* 3.0 28.1 + - - +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 2.9 18.0 + - + +
94A HIS* 3.4 12.6 - - + +
96A LEU* 1.3 74.9 - - - +
98A ASP* 1.3 63.5 + - - +
100A LEU* 3.0 23.0 + - + +
101A VAL* 2.9 45.0 + - + +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A HIS* 2.8 35.2 + - - +
95A MET* 3.5 12.0 - - + +
97A LYS* 1.3 76.9 - - - +
99A TYR* 1.3 57.5 + - + +
101A VAL* 3.1 8.6 + - - +
102A VAL* 2.9 37.5 + - + +
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET* 2.9 55.3 + - + +
96A LEU* 3.8 16.2 - - + +
98A ASP* 1.3 77.3 - - + +
100A LEU* 1.3 62.6 + - - +
102A VAL* 3.5 16.4 - - + +
103A ALA* 3.1 23.6 + - - +
201A SO4 4.5 26.4 + - - -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU 3.0 14.7 + - - +
97A LYS* 3.0 26.4 + - + +
99A TYR* 1.3 76.9 - - - +
101A VAL* 1.3 63.7 + - + +
103A ALA* 3.3 8.8 + - + +
104A GLN* 3.1 49.4 + - + +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 2.9 39.2 + - + +
98A ASP* 3.6 10.3 - - - +
100A LEU* 1.3 75.0 - - + +
102A VAL* 1.3 67.8 + - + +
104A GLN* 3.1 21.0 + - - +
105A GLU* 3.0 44.5 + - + +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP* 2.9 23.0 + - + +
99A TYR* 3.5 25.4 - - + +
101A VAL* 1.3 78.7 - - + +
103A ALA* 1.3 62.2 + - + +
105A GLU* 3.7 16.3 - - + +
106A ALA* 2.8 31.2 + - - +
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Residues in contact with ALA 103 (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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99A TYR 3.1 18.8 + - - +
100A LEU* 3.5 11.2 - - + +
102A VAL* 1.3 80.4 - - + +
104A GLN* 1.3 57.9 + - + +
106A ALA* 3.9 5.8 - - - +
107A LEU* 3.0 29.1 + - - +
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.1 41.9 + - + +
101A VAL* 3.1 24.4 + - - +
103A ALA* 1.3 77.4 - - + +
105A GLU* 1.3 59.6 + - + +
107A LEU* 3.4 7.7 + - - +
108A SER* 2.9 29.0 + - - -
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.0 33.6 + - + +
102A VAL* 3.8 15.8 - - - +
104A GLN* 1.3 76.6 - - + +
106A ALA* 1.3 63.7 + - - +
108A SER* 3.4 6.7 + - - -
109A ALA* 3.0 25.1 + - - +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL 2.8 22.7 + - - +
103A ALA* 3.9 6.3 - - - +
105A GLU* 1.3 69.5 - - - +
107A LEU* 1.3 68.0 + - - +
109A ALA* 3.4 5.3 + - - +
110A GLN* 3.0 29.6 + - + +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 3.0 19.2 + - - +
104A GLN* 3.7 7.4 - - - +
105A GLU 3.3 0.2 - - - -
106A ALA* 1.3 76.7 - - - +
108A SER* 1.3 62.8 + - - +
110A GLN* 3.2 8.9 + - + -
111A LYS* 3.0 25.1 + - + +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLN 2.9 18.3 + - - -
105A GLU* 3.7 8.1 - - - -
106A ALA 3.3 0.2 - - - -
107A LEU* 1.3 77.0 - - - +
109A ALA* 1.3 61.1 + - - +
111A LYS* 3.3 9.0 + - - +
112A GLU* 3.3 29.4 + - - +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU 3.0 17.4 + - - +
106A ALA* 3.9 5.2 - - - +
108A SER* 1.3 75.6 + - - +
110A GLN* 1.3 59.7 + - + +
112A GLU* 3.2 14.2 + - - +
113A ILE* 3.0 31.6 + - + +
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Residues in contact with GLN 110 (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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106A ALA* 3.0 22.2 + - + +
107A LEU* 3.2 10.1 + - + +
109A ALA* 1.3 74.6 - - - +
111A LYS* 1.3 66.5 + - - +
113A ILE* 3.7 24.8 - - - +
114A TYR* 2.9 24.7 + - - +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.0 17.4 + - + +
108A SER* 3.5 12.6 - - - +
109A ALA 3.2 0.4 - - - -
110A GLN* 1.3 76.0 - - - +
112A GLU* 1.3 63.4 + - + +
114A TYR* 3.3 8.5 + - - +
115A GLN* 3.0 32.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 3.3 18.0 + - - +
109A ALA* 3.2 14.0 + - - +
110A GLN 3.2 0.4 - - - -
111A LYS* 1.3 76.0 - - + +
113A ILE* 1.3 57.9 + - + +
115A GLN* 3.0 15.6 + - - +
116A VAL* 2.9 33.4 + - + +
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Residues in contact with ILE 113 (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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109A ALA* 3.0 17.8 + - + +
110A GLN* 3.4 28.7 + - - +
112A GLU* 1.3 75.1 - - + +
114A TYR* 1.3 58.4 + - - +
116A VAL* 3.0 12.2 + - + +
117A LYS* 2.8 52.1 + - + +
----------------------------------------------------------
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLN 2.9 16.7 + - - +
111A LYS* 3.4 11.0 - - - +
113A ILE* 1.3 73.1 - - - +
115A GLN* 1.3 62.9 + - + +
117A LYS* 3.3 10.9 + - + +
118A GLN* 3.0 56.0 + - + +
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.0 22.2 + - - +
112A GLU* 3.0 14.9 + - - +
114A TYR* 1.3 78.6 - - + +
116A VAL* 1.3 67.2 + - - +
118A GLN* 3.2 29.4 - - - +
119A GLN* 3.0 35.0 + - - +
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Residues in contact with VAL 116 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 2.9 20.0 + - + +
113A ILE* 3.4 15.0 - - + +
115A GLN* 1.3 77.0 - - - +
117A LYS* 1.3 61.5 + - + +
119A GLN* 3.0 20.4 + - + +
120A ARG* 2.9 55.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 2.8 37.3 + - + +
114A TYR* 3.5 13.9 - - + +
116A VAL* 1.3 86.6 - - + +
118A GLN* 1.3 56.9 + - - +
120A ARG* 3.3 22.5 + - + +
121A LEU* 3.0 25.8 + - - +
----------------------------------------------------------
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 3.0 46.0 + - + +
115A GLN* 3.2 41.6 - - - +
117A LYS* 1.3 76.6 - - - +
119A GLN* 1.3 62.0 + - + +
121A LEU* 3.4 12.7 + - + +
122A GLU* 3.2 30.0 + - + +
----------------------------------------------------------
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Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 3.0 31.0 + - - +
116A VAL* 3.0 18.4 + - + +
118A GLN* 1.3 76.1 - - + +
120A ARG* 1.3 64.5 + - + +
122A GLU* 3.2 12.2 + - - +
123A LEU* 3.1 31.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 2.9 37.2 + - + +
117A LYS* 3.3 29.5 + - + +
119A GLN* 1.3 76.2 - - + +
121A LEU* 1.3 58.3 + - - +
123A LEU* 3.3 12.4 + - + +
124A ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 121 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS 3.0 14.4 + - - +
118A GLN* 3.6 14.8 - - + +
119A GLN 3.2 0.2 - - - -
120A ARG* 1.3 77.2 - - - +
122A GLU* 1.3 57.9 + - + +
124A ALA* 3.3 8.5 + - + +
125A GLN* 2.9 51.2 + - + +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.2 18.9 + - - +
119A GLN* 3.2 12.3 + - - +
121A LEU* 1.3 76.7 - - + +
123A LEU* 1.3 59.1 + - + +
125A GLN* 3.2 17.8 + - - +
126A GLN* 2.9 41.7 + - - +
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Residues in contact with LEU 123 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.1 20.6 + - + +
120A ARG* 3.8 13.0 - - + +
121A LEU 3.3 0.2 - - - -
122A GLU* 1.3 75.0 - - + +
124A ALA* 1.3 60.6 + - - +
126A GLN* 3.2 28.1 + - + +
127A GLU* 2.9 37.2 + - + +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG 2.9 16.4 + - - +
121A LEU* 3.7 11.4 - - + +
123A LEU* 1.3 74.8 - - - +
125A GLN* 1.3 62.2 + - - +
127A GLU* 3.9 10.1 - - - +
128A TYR* 3.1 24.6 + - - +
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Residues in contact with GLN 125 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 2.9 39.7 + - + +
122A GLU* 3.3 24.6 - - - +
123A LEU 3.1 0.2 - - - -
124A ALA* 1.3 74.5 - - - +
126A GLN* 1.3 59.2 + - - +
128A TYR* 3.2 5.0 + - - +
129A GLN* 2.9 54.4 + - - +
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Residues in contact with GLN 126 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 2.9 28.9 + - - +
123A LEU* 3.5 31.5 - - + +
125A GLN* 1.3 77.4 - - - +
127A GLU* 1.3 65.8 + - + +
128A TYR 3.1 0.7 + - - -
129A GLN* 3.2 11.5 + - - -
130A GLN* 3.2 25.5 + - + +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 2.9 27.6 + - + +
124A ALA* 3.9 8.4 - - - +
126A GLN* 1.3 73.9 - - + +
128A TYR* 1.3 62.2 + - - +
130A GLN* 3.4 29.8 - - - +
131A LEU* 4.9 3.8 - - - +
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Residues in contact with TYR 128 (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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124A ALA 3.1 19.3 + - - +
125A GLN* 3.6 5.2 - - - +
126A GLN 3.1 0.2 - - - -
127A GLU* 1.3 74.1 - - - +
129A GLN* 1.3 68.5 + - + +
130A GLN 3.0 9.5 + - - -
131A LEU* 3.6 38.2 + - + +
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Residues in contact with GLN 129 (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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125A GLN* 2.9 42.7 + - - +
126A GLN* 3.2 6.4 + - - +
128A TYR* 1.3 82.8 - - + +
130A GLN* 1.3 56.3 + - - +
131A LEU 3.3 12.2 + - - +
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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