Contacts of the helix formed by residues 105 - 141 (chain A) in PDB entry 5DGY
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 PHE 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 3.9 26.5 - - - -
96A TYR* 3.7 29.2 - + + -
97A THR* 3.7 24.0 - - + -
103A PHE* 3.4 28.1 - + + -
104A VAL* 1.3 87.3 - - + +
106A GLY* 1.3 60.8 + - - +
108A THR* 3.7 14.0 + - - -
109A GLY* 3.8 14.7 + - - -
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Residues in contact with GLY 106 (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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24A PHE* 3.5 21.2 - - - -
103A PHE* 3.2 10.2 + - - -
104A VAL 3.3 5.4 - - - -
105A PHE* 1.3 76.4 - - - +
107A PRO* 1.3 72.3 - - - +
108A THR* 3.3 2.9 - - - -
109A GLY 3.2 1.9 + - - -
110A CYS* 3.0 24.6 + - - +
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Residues in contact with PRO 107 (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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8A ASN* 3.6 33.2 - - + +
24A PHE* 3.7 29.8 - - + -
106A GLY* 1.3 84.3 - - - +
108A THR* 1.3 59.2 + - + +
110A CYS* 3.4 2.5 + - + +
111A ASN* 3.0 40.2 + - - +
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Residues in contact with THR 108 (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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105A PHE 3.7 11.1 + - - -
106A GLY* 4.6 0.7 - - - -
107A PRO* 1.3 79.1 - - + +
109A GLY* 1.3 65.3 + - - +
111A ASN* 3.4 9.1 + - - +
112A LEU* 3.2 33.8 + - - +
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Residues in contact with GLY 109 (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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103A PHE* 3.6 8.2 - - - -
105A PHE* 3.8 20.2 + - - -
106A GLY 3.2 6.1 + - - -
108A THR* 1.3 82.3 + - - +
110A CYS* 1.3 57.5 + - - +
112A LEU* 3.9 7.3 - - - +
113A GLN* 2.9 31.5 + - - +
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Residues in contact with CYS 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.0 9.6 - - + -
103A PHE* 3.2 6.5 - - + -
106A GLY 3.0 15.5 + - - +
107A PRO* 3.6 6.7 - - + +
108A THR 3.3 0.2 - - - -
109A GLY* 1.3 76.2 - - - +
111A ASN* 1.3 60.4 + - - +
114A GLY* 3.0 24.3 + - - -
178A TYR* 3.9 6.8 - - - +
179A ILE* 3.7 9.4 - - - -
180A PRO* 3.7 23.6 - - - -
187A CYS* 2.0 54.2 - - - +
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Residues in contact with ASN 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PRO* 3.0 25.3 + - - +
108A THR* 3.6 8.4 - - - +
109A GLY 3.3 0.2 - - - -
110A CYS* 1.3 76.9 - - - +
112A LEU* 1.3 59.6 + - + +
115A PHE* 2.9 29.6 + - - +
172A LEU* 3.7 25.6 + - + +
178A TYR* 3.6 32.9 + - - +
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Residues in contact with LEU 112 (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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108A THR* 3.2 22.8 + - - +
109A GLY* 4.0 6.3 - - - +
110A CYS 3.4 0.2 - - - -
111A ASN* 1.3 77.9 - - + +
113A GLN* 1.3 64.4 + - - +
115A PHE* 3.6 10.9 - - + +
116A PHE* 3.1 51.8 + - + -
172A LEU* 5.8 5.8 - - + -
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Residues in contact with GLN 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLY 3.4 25.0 - - - +
90A GLY* 3.1 6.4 + - - +
93A SER* 3.3 14.1 - - - +
94A THR* 2.8 47.3 + - - +
103A PHE* 3.3 17.5 - - + -
109A GLY 2.9 19.0 + - - +
110A CYS 4.1 1.1 - - - +
112A LEU* 1.3 75.3 - - - +
114A GLY* 1.3 57.8 + - - +
116A PHE* 3.4 2.7 + - - +
117A ALA* 2.9 31.7 + - + +
185A CYS 4.6 1.6 + - - -
187A CYS* 3.1 33.8 + - - +
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Residues in contact with GLY 114 (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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110A CYS 3.0 18.1 + - - -
113A GLN* 1.3 76.9 - - - +
115A PHE* 1.3 55.0 + - - +
117A ALA* 3.9 1.9 - - - +
118A THR* 2.7 36.9 + - - -
178A TYR* 3.3 19.5 - - - -
187A CYS* 3.8 21.2 - - - +
188A GLY* 4.9 0.6 - - - -
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Residues in contact with PHE 115 (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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111A ASN 2.9 19.5 + - - +
112A LEU* 3.6 11.7 - - + +
113A GLN 3.2 0.2 - - - -
114A GLY* 1.3 77.3 - - - +
116A PHE* 1.3 84.8 + + - +
118A THR* 3.8 1.7 - - - -
119A LEU* 2.8 41.1 + - + +
165A LEU* 3.9 23.8 - - + -
168A ALA* 3.4 40.8 - - + +
169A ALA* 4.0 5.8 - - + -
172A LEU* 3.5 25.4 - - + -
178A TYR* 3.7 8.9 - - + -
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Residues in contact with PHE 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 4.2 27.3 - + + +
89A GLY* 4.0 30.1 - - - -
112A LEU* 3.1 37.2 + - + +
113A GLN* 4.0 2.9 - - - +
115A PHE* 1.3 100.1 - + - +
117A ALA* 1.3 60.3 + - - +
119A LEU* 3.8 13.4 - - + +
120A GLY* 2.8 27.2 + - - -
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Residues in contact with ALA 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A MET* 4.3 17.4 - - + +
90A GLY* 4.7 16.1 - - - +
113A GLN* 2.9 19.7 + - + +
114A GLY* 3.9 7.4 - - - +
116A PHE* 1.3 75.6 - - - +
118A THR* 1.3 62.0 + - - +
120A GLY* 4.1 0.3 - - - -
121A GLY* 3.1 19.1 + - - -
187A CYS 4.6 8.3 - - - +
296A LYS* 6.5 0.9 - - - -
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Residues in contact with THR 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLY 2.7 23.6 + - - -
115A PHE 3.8 0.7 - - - -
117A ALA* 1.3 75.6 - - - +
119A LEU* 1.3 59.3 + - - +
121A GLY* 3.2 1.3 + - - -
122A GLU* 2.8 53.7 + - + +
167A CYS* 4.8 1.8 - - - +
168A ALA* 4.2 14.1 - - + +
178A TYR* 3.3 26.9 - - - +
188A GLY* 5.5 1.6 - - - -
189A ILE* 3.9 26.4 + - + +
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Residues in contact with LEU 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 5.0 16.4 - - + -
115A PHE* 2.8 36.5 + - + +
116A PHE* 3.8 14.6 - - + +
118A THR* 1.3 77.2 - - - +
120A GLY* 1.3 57.6 + - - +
122A GLU* 4.6 2.9 - - - +
123A ILE* 2.9 58.2 + - + +
164A ALA* 3.9 15.9 - - + -
165A LEU* 3.7 32.8 - - + +
168A ALA* 4.3 8.7 - - + +
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Residues in contact with GLY 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 3.3 30.1 - - - +
85A PHE* 4.3 6.4 - - - +
86A MET* 3.7 13.2 - - - +
116A PHE 2.8 20.2 + - - -
119A LEU* 1.3 72.9 - - - +
121A GLY* 1.3 61.8 + - - +
123A ILE* 4.9 0.7 - - - -
124A ALA* 3.2 23.9 + - - +
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Residues in contact with GLY 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A MET* 3.8 15.4 - - - -
117A ALA 3.1 15.4 + - - -
118A THR* 3.7 2.7 - - - -
120A GLY* 1.3 78.5 - - - +
122A GLU* 1.3 57.2 + - - +
124A ALA* 3.5 4.7 + - - +
125A LEU* 3.0 26.3 + - - +
265A TRP* 3.6 23.4 - - - -
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Residues in contact with GLU 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A THR* 2.8 34.4 + - + +
121A GLY* 1.3 72.1 - - - +
123A ILE* 1.3 59.4 + - - +
124A ALA 3.2 0.2 - - - -
125A LEU* 3.2 17.6 + - - +
126A TRP* 3.0 36.3 + - + -
164A ALA* 3.8 23.3 - - + +
167A CYS* 3.4 14.5 - - - -
207A MET* 3.4 23.9 - - - +
211A HIS* 3.1 35.6 - - - +
265A TRP* 5.5 6.9 - - + -
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Residues in contact with ILE 123 (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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78A ASN* 3.5 33.2 - - - +
81A VAL* 6.4 0.9 - - + -
82A ALA* 3.5 18.6 - - + +
85A PHE* 5.1 12.8 - - + -
119A LEU* 2.9 47.5 + - + +
122A GLU* 1.3 75.3 - - - +
124A ALA* 1.3 55.1 + - - +
127A SER* 2.7 38.6 + - - +
160A THR* 3.1 9.7 - - + +
161A TRP* 3.7 27.8 - - + +
164A ALA* 3.4 17.3 - - + -
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Residues in contact with ALA 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.6 23.5 - - + +
82A ALA* 3.6 5.5 - - + +
83A ASP* 4.0 14.1 - - - +
86A MET* 5.3 1.6 - - - -
120A GLY 3.2 21.0 + - - +
121A GLY* 3.6 7.2 - - - +
122A GLU 3.2 0.2 - - - -
123A ILE* 1.3 77.7 - - - +
125A LEU* 1.3 63.4 + - - +
127A SER* 3.5 2.8 + - - -
128A LEU* 3.3 27.7 + - - +
265A TRP* 6.1 0.4 - - + -
302A ASN* 5.5 5.6 - - - +
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Residues in contact with LEU 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLY 3.0 18.1 + - - +
122A GLU* 3.2 24.7 + - - +
124A ALA* 1.3 76.7 - - - +
126A TRP* 1.3 62.3 + - + +
128A LEU* 3.0 25.8 + - + +
129A VAL* 3.1 10.2 + - + +
211A HIS* 3.7 28.3 - - + +
215A PRO* 4.1 18.4 - - + -
219A ILE* 5.2 0.7 - - + -
261A PHE* 3.7 31.4 - - + -
265A TRP* 3.7 31.8 - - + +
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Residues in contact with TRP 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLU* 3.0 33.3 + - + +
125A LEU* 1.3 75.2 - - + +
127A SER* 1.3 58.9 + - - +
129A VAL* 3.6 34.9 - - + +
130A VAL* 3.0 33.3 + - - +
159A PHE* 4.1 22.2 - + + -
160A THR* 3.7 23.1 - - + -
163A MET* 3.5 46.1 - - + +
164A ALA 4.3 1.6 - - - -
210A VAL* 4.8 7.9 - - + -
211A HIS* 3.5 36.4 + + - -
214A ILE* 3.8 30.5 - - + -
215A PRO* 4.1 15.9 - - + -
218A ILE* 5.1 1.6 - - + -
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Residues in contact with SER 127 (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 ILE* 3.4 28.2 - - - +
78A ASN* 3.2 28.1 + - - +
79A LEU* 3.9 17.8 + - - -
123A ILE* 2.7 26.0 + - - +
124A ALA 3.5 6.5 - - - -
125A LEU 3.2 0.2 - - - -
126A TRP* 1.3 78.9 - - - +
128A LEU* 1.3 58.1 + - - +
130A VAL 3.5 0.3 + - - -
131A LEU* 2.9 29.4 + - - +
160A THR* 3.6 0.6 - - - +
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Residues in contact with LEU 128 (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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79A LEU* 3.9 18.8 - - + -
124A ALA 3.3 15.7 + - - +
125A LEU* 3.0 11.9 + - + +
127A SER* 1.3 75.4 - - - +
129A VAL* 1.3 61.2 + - - +
131A LEU* 3.7 8.8 - - + +
132A ALA* 3.0 28.8 + - - +
219A ILE* 4.2 11.7 - - + +
223A TYR* 4.4 3.6 + - - -
261A PHE* 5.3 14.4 - - + -
265A TRP* 6.1 2.2 - - - +
302A ASN* 3.6 25.6 - - - +
306A TYR* 3.5 54.3 - - + +
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Residues in contact with VAL 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 3.1 13.2 + - + +
126A TRP* 3.6 39.0 - - + +
127A SER 3.3 0.4 - - - -
128A LEU* 1.3 74.9 - - - +
130A VAL* 1.3 61.3 + - + +
132A ALA* 3.2 4.7 + - - +
133A ILE* 3.0 48.2 + - + +
159A PHE* 5.6 1.6 - - + -
215A PRO* 3.7 32.5 - - + -
218A ILE* 4.0 19.9 - - + +
219A ILE* 3.7 13.0 - - + -
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Residues in contact with VAL 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 3.5 21.8 - - + -
126A TRP 3.0 21.6 + - - +
129A VAL* 1.3 74.9 - - + +
131A LEU* 1.3 57.8 + - - +
133A ILE* 3.2 13.2 + - + +
134A GLU* 2.8 54.2 + - + +
156A GLY* 3.7 19.7 - - - +
159A PHE* 4.2 19.5 - - + -
160A THR* 3.7 13.9 - - - +
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Residues in contact with LEU 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.7 4.9 - - + +
75A ILE* 3.7 25.4 - - + -
76A LEU* 3.6 24.0 - - + -
127A SER 2.9 19.2 + - - +
128A LEU* 3.7 11.7 - - + +
129A VAL 3.3 0.2 - - - -
130A VAL* 1.3 76.6 - - - +
132A ALA* 1.3 57.3 + - - +
134A GLU* 4.4 6.1 - - - +
135A ARG* 2.9 73.9 + - + +
223A TYR* 4.1 2.5 - - - +
306A TYR* 3.5 37.5 - - + -
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Residues in contact with ALA 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU 3.0 19.0 + - - +
129A VAL 3.2 4.7 + - - +
131A LEU* 1.3 74.0 - - - +
133A ILE* 1.3 66.4 + - - +
135A ARG* 4.0 1.0 - - - +
136A TYR* 3.1 18.0 + - - +
218A ILE 5.4 0.2 - - - -
219A ILE* 4.0 12.8 - - + -
222A CYS* 3.4 28.5 - - + +
223A TYR* 3.6 35.0 + - + -
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Residues in contact with ILE 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 3.0 38.3 + - + +
130A VAL* 3.2 14.6 + - + +
132A ALA* 1.3 73.2 - - - +
134A GLU* 1.3 68.2 + - + +
136A TYR* 3.2 3.5 + - + +
137A VAL* 3.0 36.9 + - + +
159A PHE* 6.1 3.4 - - + -
218A ILE* 3.6 25.1 - - + -
222A CYS* 3.6 10.1 - - - -
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Residues in contact with GLU 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PRO 5.0 0.3 - - - +
72A LEU* 3.7 24.3 - - + +
75A ILE* 3.4 27.8 - - - +
130A VAL* 2.8 45.1 + - + +
131A LEU* 3.8 4.8 - - - +
133A ILE* 1.3 75.8 - - + +
135A ARG* 1.3 57.6 + - + +
137A VAL* 3.3 8.0 - - + +
138A VAL* 2.9 38.1 + - + +
148A PHE* 3.3 36.3 - - + -
152A HIS 5.3 0.2 - - - +
153A ALA* 4.8 4.7 - - - +
156A GLY* 4.9 2.4 - - - -
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Residues in contact with ARG 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 5.4 7.2 - - + -
76A LEU* 4.2 8.3 - - - +
131A LEU* 2.9 60.7 + - + +
132A ALA 4.1 3.1 - - - +
134A GLU* 1.3 76.7 - - + +
136A TYR* 1.3 61.3 + - - +
138A VAL* 4.8 2.0 - - - -
139A VAL* 3.2 35.7 + - + +
223A TYR* 3.9 15.8 + - + -
226A LEU* 3.5 16.6 - - + +
257A TYR* 3.1 38.4 + - - -
306A TYR* 4.3 4.0 + - - -
310A ASN* 3.9 20.4 - - - +
1077A GLY* 3.6 33.2 + - - -
1078A LEU* 5.3 7.1 - - + +
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Residues in contact with TYR 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ALA 3.1 18.8 + - - +
133A ILE* 3.6 2.9 - - + +
134A GLU 3.2 0.4 - - - -
135A ARG* 1.3 77.7 - - - +
137A VAL* 1.3 77.7 + - + +
140A CYS* 3.2 55.7 + - + +
221A PHE* 4.6 18.4 - + - -
222A CYS* 3.7 35.9 - - + +
225A GLN* 3.4 35.5 + - + +
226A LEU* 4.0 9.1 - - - +
229A THR* 4.9 1.3 - - - -
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Residues in contact with VAL 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 3.0 26.8 + - + +
134A GLU* 3.3 15.9 - - + +
136A TYR* 1.3 94.0 - - + +
138A VAL* 1.3 67.6 + - + +
140A CYS* 5.2 0.7 - - - -
141A LYS* 3.3 25.3 + - + +
144A SER* 2.7 26.0 + - - +
148A PHE* 6.4 1.3 - - + -
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Residues in contact with VAL 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.2 31.9 - - + -
134A GLU* 2.9 25.6 + - - +
135A ARG* 4.7 1.8 - - - +
137A VAL* 1.3 84.9 - - + +
139A VAL* 1.3 65.2 + - + +
141A LYS 2.9 16.8 - - - +
144A SER* 3.3 11.9 - - - +
145A ASN* 3.2 36.8 + - - +
148A PHE* 4.7 22.0 - - + -
1068A TYR* 4.6 2.8 - - + -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 3.2 28.6 + - + +
138A VAL* 1.3 84.3 - - + +
140A CYS* 1.3 68.9 + - - +
141A LYS 3.4 3.1 + - - -
142A PRO* 4.5 1.7 - - - +
226A LEU* 4.8 17.0 - - + -
230A VAL* 5.2 3.4 - - + -
1068A TYR* 4.3 17.2 + - + +
1074A ASP* 5.2 9.4 - - - +
1078A LEU* 5.7 6.7 - - + +
1079A THR* 4.4 22.2 - - + +
1251A TYR* 3.2 37.8 - - + +
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Residues in contact with CYS 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.2 50.0 + - + +
137A VAL* 4.8 0.7 - - - +
139A VAL* 1.3 82.3 - - - +
141A LYS* 1.3 64.5 + - + +
142A PRO* 3.7 5.2 - - - +
226A LEU* 4.4 11.9 - - - -
229A THR* 3.8 29.2 - - + -
230A VAL* 6.4 0.7 - - - -
1251A TYR* 3.3 32.0 + - + +
1252A SER* 4.8 4.9 + - - -
1254A ASP* 5.0 1.0 - - - +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.3 17.5 + - + +
138A VAL 2.9 11.3 - - - +
139A VAL 4.2 0.2 - - - -
140A CYS* 1.3 81.7 - - + +
142A PRO* 1.3 66.3 - - + +
143A MET 4.6 0.9 - - - +
144A SER* 2.6 33.6 + - - +
1252A SER* 5.2 3.1 - - - +
1254A ASP* 3.7 31.0 - - - +
1256A TYR* 4.4 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
------------------------------------------------------------
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