Contacts of the helix formed by residues 105 - 141 (chain B) in PDB entry 4ZWJ
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER* 4.0 25.6 - - - -
96B TYR* 3.7 29.4 - + + -
97B THR* 3.7 23.8 - - + -
103B PHE* 3.4 27.9 - + + -
104B VAL* 1.3 87.3 - - + +
106B GLY* 1.3 61.2 + - - +
108B THR* 3.7 14.4 + - - -
109B GLY* 3.8 14.4 + - - -
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Residues in contact with GLY 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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24B PHE* 3.5 21.7 - - - -
103B PHE* 3.3 10.1 - - - -
104B VAL 3.3 5.4 + - - -
105B PHE* 1.3 76.7 - - - +
107B PRO* 1.3 71.8 - - - +
108B THR 3.3 2.2 - - - -
109B GLY 3.2 1.9 + - - -
110B CYS* 3.0 24.3 + - - +
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Residues in contact with PRO 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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8B ASN* 3.6 32.1 - - + +
24B PHE* 3.7 30.0 - - + -
106B GLY* 1.3 83.7 - - - +
108B THR* 1.3 60.9 + - + +
110B CYS* 3.3 2.7 + - + +
111B ASN* 3.0 40.1 + - - +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE 3.7 9.9 + - - -
106B GLY 4.6 0.2 - - - -
107B PRO* 1.3 78.1 - - + +
109B GLY* 1.3 66.7 + - - +
111B ASN* 3.4 10.5 + - - +
112B LEU* 3.1 31.6 + - - +
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Residues in contact with GLY 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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103B PHE* 3.6 7.8 - - - -
105B PHE* 3.8 20.6 + - - -
106B GLY 3.2 6.1 + - - -
108B THR* 1.3 81.0 + - - +
110B CYS* 1.3 59.9 + - - +
112B LEU* 3.5 8.0 + - - +
113B GLN* 3.0 31.4 + - - +
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Residues in contact with CYS 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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24B PHE* 4.0 9.4 - - + -
103B PHE* 3.2 6.7 - - + -
106B GLY 3.0 16.6 + - - +
107B PRO* 3.6 5.4 - - + +
108B THR 3.3 0.2 - - - -
109B GLY* 1.3 74.0 - - - +
111B ASN* 1.3 61.8 + - - +
114B GLY* 3.0 24.8 + - - -
178B TYR* 3.9 8.3 - - - +
179B ILE* 3.7 9.0 - - - -
180B PRO* 3.7 23.8 - - - -
187B CYS* 2.0 53.2 - - - +
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO* 3.0 23.2 + - - +
108B THR* 3.6 11.0 - - - +
109B GLY 3.3 0.2 - - - -
110B CYS* 1.3 77.1 - - - +
112B LEU* 1.3 59.8 + - + +
115B PHE* 2.9 29.8 + - - +
172B LEU* 3.6 32.3 + - + +
178B TYR* 3.7 26.7 + - - +
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Residues in contact with LEU 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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108B THR* 3.1 21.7 + - - +
109B GLY* 4.1 6.5 - - - +
110B CYS 3.4 0.2 - - - -
111B ASN* 1.3 76.8 - - + +
113B GLN* 1.3 66.1 + - - +
115B PHE* 3.4 10.3 + - + +
116B PHE* 3.1 51.0 + - + -
172B LEU* 6.0 4.9 - - + -
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Residues in contact with GLN 113 (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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89B GLY 3.4 24.1 - - - +
90B GLY* 3.1 11.5 + - - +
93B SER* 3.3 14.7 - - - +
94B THR* 2.7 42.4 + - - +
103B PHE* 3.3 21.0 - - + -
109B GLY 3.0 19.7 + - - +
110B CYS 4.2 1.1 - - - +
112B LEU* 1.3 76.0 - - - +
114B GLY* 1.3 57.3 + - - +
116B PHE* 3.4 2.9 + - - +
117B ALA* 2.9 32.6 + - + +
185B CYS 4.7 1.0 + - - -
187B CYS* 3.2 29.3 + - - +
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Residues in contact with GLY 114 (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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110B CYS 3.0 18.1 + - - -
113B GLN* 1.3 76.8 - - - +
115B PHE* 1.3 55.1 + - - +
117B ALA* 4.0 1.9 - - - +
118B THR* 2.8 36.0 + - - -
178B TYR* 3.2 19.0 - - - -
187B CYS* 3.8 21.6 - - - +
188B GLY* 4.9 0.7 - - - -
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Residues in contact with PHE 115 (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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111B ASN 2.9 20.2 + - - +
112B LEU* 3.6 11.9 - - + +
113B GLN 3.2 0.2 - - - -
114B GLY* 1.3 78.2 - - - +
116B PHE* 1.3 83.4 + + - +
118B THR* 3.9 1.4 - - - -
119B LEU* 2.9 41.1 + - + +
165B LEU* 3.8 24.2 - - + -
168B ALA* 3.4 39.0 - - + +
169B ALA* 4.0 7.0 - - + -
172B LEU* 3.5 24.7 - - + -
178B TYR* 3.7 8.7 - - + -
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Residues in contact with PHE 116 (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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85B PHE* 4.3 26.1 - + + +
89B GLY* 4.1 30.7 - - - -
112B LEU* 3.1 39.3 + - + +
113B GLN 4.0 2.7 - - - +
115B PHE* 1.3 99.0 - + - +
117B ALA* 1.3 61.1 + - - +
119B LEU* 3.8 13.5 - - + +
120B GLY* 2.8 27.2 + - - -
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Residues in contact with ALA 117 (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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86B MET* 4.4 15.5 - - + +
90B GLY* 4.7 15.8 - - - +
113B GLN* 2.9 19.9 + - + +
114B GLY* 4.0 7.4 - - - +
116B PHE* 1.3 76.6 - - - +
118B THR* 1.3 62.2 + - - +
120B GLY* 4.1 0.3 - - - -
121B GLY* 3.2 18.7 + - - -
187B CYS 4.6 8.5 - - - +
296B LYS* 6.5 1.1 - - - -
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Residues in contact with THR 118 (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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114B GLY 2.8 23.1 + - - -
115B PHE 3.9 0.7 - - - -
117B ALA* 1.3 76.8 - - - +
119B LEU* 1.3 60.5 + - - +
121B GLY* 3.2 1.7 + - - -
122B GLU* 2.8 53.0 + - + +
167B CYS 4.7 2.2 - - - +
168B ALA* 4.1 13.5 - - + +
178B TYR* 3.2 27.7 - - - +
188B GLY* 5.5 1.7 - - - -
189B ILE* 3.9 26.2 + - + +
207B MET* 5.7 0.2 - - + -
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Residues in contact with LEU 119 (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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85B PHE* 5.1 15.7 - - + -
115B PHE* 2.9 36.5 + - + +
116B PHE* 3.8 13.5 - - + +
118B THR* 1.3 76.5 - - - +
120B GLY* 1.3 57.2 + - - +
122B GLU* 4.6 2.0 - - - -
123B ILE* 2.9 52.0 + - + +
161B TRP 5.0 0.2 - - - +
164B ALA* 3.9 24.0 - - + -
165B LEU* 3.7 31.9 - - + +
168B ALA* 4.2 9.8 - - + +
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Residues in contact with GLY 120 (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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82B ALA* 3.4 29.4 - - - +
85B PHE* 4.3 6.9 - - - +
86B MET* 3.7 13.8 - - - +
116B PHE 2.8 17.4 + - - -
119B LEU* 1.3 75.4 - - - +
121B GLY* 1.3 60.2 + - - +
123B ILE* 5.3 0.4 - - - -
124B ALA* 3.2 24.6 + - - +
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Residues in contact with GLY 121 (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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86B MET* 3.9 14.5 - - - -
117B ALA 3.2 16.2 + - - -
118B THR* 3.2 2.4 + - - -
120B GLY* 1.3 77.6 - - - +
122B GLU* 1.3 57.3 + - - +
124B ALA* 3.5 5.3 + - - +
125B LEU* 3.0 26.5 + - - +
265B TRP* 3.6 24.8 - - - -
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Residues in contact with GLU 122 (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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118B THR* 2.8 30.9 + - + +
121B GLY* 1.3 75.5 - - - +
123B ILE* 1.3 61.5 + - - +
125B LEU* 3.5 19.3 - - - +
126B TRP* 2.9 38.9 + - + -
164B ALA* 3.8 23.6 - - + +
167B CYS* 3.5 26.7 - - - -
207B MET* 3.8 20.8 - - - +
211B HIS* 3.4 22.8 - - - +
265B TRP* 5.4 7.1 - - + -
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Residues in contact with ILE 123 (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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78B ASN* 3.6 31.4 - - - +
81B VAL* 6.4 0.7 - - + -
82B ALA* 3.5 21.1 - - + -
85B PHE* 5.1 10.8 - - + -
119B LEU* 2.9 46.7 + - + +
122B GLU* 1.3 75.6 - - - +
124B ALA* 1.3 54.1 + - - +
127B SER* 2.7 38.6 + - - +
160B THR* 3.1 9.3 - - + +
161B TRP* 3.6 28.3 - - + +
164B ALA* 3.4 17.3 - - + -
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Residues in contact with ALA 124 (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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79B LEU* 3.6 23.9 - - + +
82B ALA* 3.6 6.0 - - + +
83B ASP* 4.0 13.9 - - - +
86B MET* 5.2 1.8 - - - -
120B GLY 3.2 21.7 + - - +
121B GLY* 3.6 6.5 - - - +
123B ILE* 1.3 77.9 - - - +
125B LEU* 1.3 63.2 + - - +
127B SER* 3.5 2.6 + - - -
128B LEU* 3.3 27.6 + - - +
265B TRP* 6.1 0.2 - - + -
302B ASN* 5.5 6.1 - - - +
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Residues in contact with LEU 125 (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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121B GLY 3.0 18.8 + - - +
122B GLU* 3.3 25.5 + - - +
124B ALA* 1.3 76.1 - - - +
126B TRP* 1.3 63.9 + - + +
128B LEU* 3.0 26.7 + - + +
129B VAL* 3.1 10.2 + - + +
211B HIS* 3.9 22.4 - - + +
212B PHE* 6.5 0.4 - - + -
215B PRO* 4.3 16.4 - - + -
219B ILE* 5.2 0.4 - - + -
261B PHE* 3.7 31.6 - - + -
265B TRP* 3.7 32.7 - - + +
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Residues in contact with TRP 126 (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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122B GLU* 2.9 33.5 + - - +
125B LEU* 1.3 75.5 - - + +
127B SER* 1.3 60.0 + - - +
129B VAL* 3.6 35.4 - - + +
130B VAL* 3.0 33.6 + - - +
159B PHE* 4.2 21.5 - + + -
160B THR* 3.7 22.0 - - + -
163B MET* 3.5 43.8 - - + +
164B ALA 4.3 0.9 - - - -
210B VAL* 5.2 4.9 - - + -
211B HIS* 3.5 41.5 + + - -
214B ILE* 4.1 17.5 - - + -
215B PRO* 4.0 26.0 - - + -
218B ILE* 5.1 1.6 - - + -
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Residues in contact with SER 127 (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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75B ILE* 3.4 29.1 - - - +
78B ASN* 3.2 27.7 + - - +
79B LEU* 4.0 17.3 + - - -
123B ILE* 2.7 25.7 + - - +
124B ALA 3.5 6.5 - - - -
125B LEU 3.2 0.2 - - - -
126B TRP* 1.3 77.0 - - - +
128B LEU* 1.3 57.4 + - - +
130B VAL 3.5 0.3 + - - -
131B LEU* 2.9 30.1 + - - +
160B THR* 3.6 1.2 - - - +
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Residues in contact with LEU 128 (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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79B LEU* 3.9 19.3 - - + -
124B ALA 3.3 15.0 + - - +
125B LEU* 3.0 12.4 + - + +
127B SER* 1.3 75.1 - - - +
129B VAL* 1.3 60.2 + - - +
131B LEU* 3.7 9.2 - - + +
132B ALA* 3.0 27.9 + - - +
219B ILE* 4.3 12.2 - - + +
223B TYR* 4.3 3.8 + - - -
261B PHE* 5.4 13.5 - - + -
265B TRP* 6.1 2.0 - - - +
302B ASN* 3.6 26.2 - - - +
306B TYR* 3.5 52.0 - - + +
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Residues in contact with VAL 129 (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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125B LEU* 3.1 14.4 + - + +
126B TRP* 3.6 41.3 - - + +
127B SER 3.3 0.2 - - - -
128B LEU* 1.3 74.7 - - - +
130B VAL* 1.3 65.9 + - + +
132B ALA* 3.2 4.5 + - - +
133B ILE* 3.0 42.8 + - + +
159B PHE* 5.6 2.0 - - + -
215B PRO* 3.7 29.2 - - + -
218B ILE* 3.9 20.8 - - + +
219B ILE* 3.9 13.5 - - + -
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Residues in contact with VAL 130 (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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75B ILE* 3.5 21.1 - - + -
126B TRP 3.0 21.2 + - - +
129B VAL* 1.3 76.5 - - + +
131B LEU* 1.3 56.9 + - - +
133B ILE* 3.2 12.6 + - + +
134B GLU* 2.8 54.0 + - + +
156B GLY* 3.7 20.2 - - - +
159B PHE* 4.2 20.2 - - + -
160B THR* 3.7 14.1 - - - +
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Residues in contact with LEU 131 (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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72B LEU* 4.7 4.0 - - + +
75B ILE* 3.7 26.2 - - + +
76B LEU* 3.6 24.9 - - + -
127B SER 2.9 18.3 + - - +
128B LEU* 3.7 11.0 - - + +
130B VAL* 1.3 76.9 - - - +
132B ALA* 1.3 57.2 + - - +
134B GLU* 4.4 5.6 - - - +
135B ARG* 3.0 72.1 + - + +
223B TYR* 4.0 3.1 - - - +
306B TYR* 3.5 36.8 - - + -
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Residues in contact with ALA 132 (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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128B LEU 3.0 18.3 + - - +
129B VAL 3.5 5.2 - - - +
131B LEU* 1.3 74.8 - - - +
133B ILE* 1.3 64.5 + - - +
135B ARG* 4.0 1.2 - - - +
136B TYR* 3.1 25.3 + - - +
219B ILE* 4.2 12.1 - - + -
222B CYS* 3.4 21.1 - - + +
223B TYR* 3.5 35.4 + - + -
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Residues in contact with ILE 133 (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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129B VAL* 3.0 38.9 + - + +
130B VAL* 3.6 13.7 - - + +
132B ALA* 1.3 73.9 - - - +
134B GLU* 1.3 66.8 + - + +
136B TYR* 3.4 1.8 + - + +
137B VAL* 3.0 36.3 + - + +
159B PHE* 6.1 3.4 - - + -
218B ILE* 3.7 24.5 - - + -
222B CYS* 3.7 9.9 - - - -
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Residues in contact with GLU 134 (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 PRO 4.9 0.5 - - - +
72B LEU* 3.6 26.0 - - + +
75B ILE* 3.3 29.3 - - - +
130B VAL* 2.8 44.5 + - + +
131B LEU* 3.7 5.6 - - + +
133B ILE* 1.3 77.0 - - + +
135B ARG* 1.3 58.7 + - + +
137B VAL* 4.9 2.2 - - - -
138B VAL* 2.8 39.9 + - + +
148B PHE* 3.2 38.6 - - + -
153B ALA* 4.9 3.1 - - - +
156B GLY* 5.1 1.7 - - - -
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Residues in contact with ARG 135 (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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72B LEU* 5.3 7.0 - - + -
76B LEU* 4.2 8.9 - - - +
131B LEU* 3.0 62.6 + - + +
132B ALA 4.1 2.2 - - - +
134B GLU* 1.3 76.9 - - + +
136B TYR* 1.3 61.1 + - - +
138B VAL* 4.8 2.2 - - - -
139B VAL* 3.1 36.5 + - + +
223B TYR* 3.9 16.3 + - + -
226B LEU* 3.6 16.1 - - + +
257B TYR* 3.2 39.3 + - - -
306B TYR* 4.7 4.6 + - - -
310B ASN* 4.0 21.6 - - - +
2077B GLY* 4.2 11.8 + - - -
2078B LEU* 4.4 18.5 - - + +
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Residues in contact with TYR 136 (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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132B ALA 3.1 19.0 + - - +
133B ILE* 3.7 2.9 - - + +
134B GLU 3.2 0.2 - - - -
135B ARG* 1.3 77.7 - - - +
137B VAL* 1.3 77.9 + - + +
140B CYS* 3.2 57.2 + - + +
221B PHE* 4.6 17.7 - + - -
222B CYS* 3.7 37.5 - - + +
225B GLN* 3.4 32.3 + - + +
226B LEU* 4.0 9.3 - - - +
229B THR* 4.9 1.6 - - - -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 3.0 28.6 + - + +
134B GLU* 4.0 2.7 - - - +
136B TYR* 1.3 93.2 - - + +
138B VAL* 1.3 62.4 + - + +
140B CYS* 5.3 0.7 - - - -
141B LYS* 3.1 37.4 + - + +
144B SER* 3.4 22.3 - - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 4.2 28.9 - - + -
134B GLU* 2.8 30.9 + - - +
135B ARG* 4.7 1.8 - - - +
137B VAL* 1.3 73.7 - - + +
139B VAL* 1.3 65.5 + - + +
141B LYS 2.9 19.8 - - - +
142B PRO* 4.2 4.2 - - - +
144B SER* 4.2 15.5 - - - +
145B ASN* 3.8 32.3 + - + +
148B PHE* 4.5 20.4 - - + -
2068B TYR* 4.6 7.0 - - + -
2074B ASP* 6.1 2.0 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 3.1 28.0 + - + +
136B TYR 4.5 0.2 - - - +
138B VAL* 1.3 82.2 - - + +
140B CYS* 1.3 73.5 + - - +
141B LYS 3.3 3.3 + - - -
142B PRO* 4.2 3.6 - - - +
226B LEU* 5.0 9.6 - - + -
230B VAL* 5.1 11.4 - - + -
2068B TYR* 4.4 26.3 + - + +
2074B ASP* 6.4 1.8 - - + -
2078B LEU* 6.1 2.9 - - + -
2079B THR* 4.2 31.0 - - + +
----------------------------------------------------------
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Residues in contact with CYS 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 3.2 50.7 + - + +
137B VAL* 5.3 0.4 - - - -
139B VAL* 1.3 85.0 - - - +
141B LYS* 1.3 59.7 + - + +
142B PRO* 3.5 8.5 - - - +
226B LEU* 4.6 8.7 - - - -
229B THR* 3.7 34.9 - - + +
230B VAL* 6.3 0.4 - - - -
----------------------------------------------------------
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 3.1 25.8 + - + +
138B VAL 2.9 16.7 - - - +
140B CYS* 1.3 77.5 - - + +
142B PRO* 1.3 66.7 - - + +
143B MET* 4.0 17.7 - - + +
144B SER* 3.3 40.0 + - - +
147B ARG* 5.4 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) + - + + + + + -
------------------------------------------------------------
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