Contacts of the helix formed by residues 137 - 171 (chain C) in PDB entry 4DAJ
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 137 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C GLY* 1.3 72.0 - - - -
138C LEU* 1.3 86.1 + - - +
140C CYS* 3.1 8.8 - - - +
141C ASP* 2.9 27.9 + - - +
207C GLN* 5.8 2.5 + - - +
208C TYR* 5.7 2.8 + - - -
213C ARG* 3.2 38.1 - - - +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU 4.9 0.8 + - - +
136C GLY 3.7 0.2 - - - -
137C ASN* 1.3 88.7 + - - +
139C ALA* 1.3 64.4 + - + +
141C ASP* 2.9 14.8 + - + +
142C LEU* 2.9 49.7 + - + +
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C LEU* 4.6 2.8 - - + +
133C TRP* 3.5 2.7 - - - -
135C LEU* 3.3 55.3 + - + +
137C ASN 3.4 0.4 - - - -
138C LEU* 1.3 83.3 - - + +
140C CYS* 1.3 56.7 + - - +
142C LEU* 4.1 5.2 - - - +
143C TRP* 2.9 32.6 + - - +
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Residues in contact with CYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C TRP* 3.3 27.7 - - + +
136C GLY 3.5 2.9 - - - +
137C ASN* 3.1 14.9 + - - +
139C ALA* 1.3 79.3 - - - +
141C ASP* 1.3 61.1 + - - +
143C TRP* 3.7 1.1 - - - +
144C LEU* 3.0 43.2 + - - +
213C ARG* 4.9 10.5 - - - -
215C VAL* 5.3 1.3 - - - -
220C CYS* 2.0 50.3 - - + -
221C PHE 4.3 4.3 - - - -
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Residues in contact with ASP 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ASN* 2.9 25.2 + - - +
138C LEU* 2.9 13.3 + - + +
140C CYS* 1.3 77.6 - - - +
142C LEU* 1.3 60.8 + - + +
144C LEU* 3.4 3.4 + - - +
145C SER* 2.9 32.8 + - - -
203C ILE* 4.1 11.9 - - + +
204C LEU* 3.6 26.0 - - + +
207C GLN* 3.6 23.1 + - - -
213C ARG* 3.4 15.3 + - - -
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 2.9 43.5 + - + +
139C ALA* 4.1 4.9 - - - +
141C ASP* 1.3 71.7 - - + +
143C TRP* 1.3 61.3 + - - +
145C SER* 3.5 7.6 - - - +
146C ILE* 2.9 48.0 + - + +
204C LEU* 5.0 12.6 - - + -
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Residues in contact with TRP 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 4.2 6.1 - - + -
120C SER* 3.3 26.6 + - - +
123C LEU* 3.1 46.8 - - + +
124C PHE* 3.3 49.4 - + + -
127C TYR* 5.3 6.3 - + + -
133C TRP* 4.3 12.8 - + + -
139C ALA 2.9 21.0 + - - +
140C CYS 3.7 1.3 - - - +
142C LEU* 1.3 76.1 - - - +
144C LEU* 1.3 89.4 + - + +
146C ILE* 3.7 5.7 - - - +
147C ASP* 2.9 36.4 + - - +
220C CYS* 4.1 23.8 - - + -
529C TYR* 5.2 6.5 - + - -
533C TYR* 4.6 5.8 - - - -
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C CYS* 3.0 21.2 + - - +
141C ASP* 3.9 4.0 - - - +
143C TRP* 1.3 101.0 - - + +
145C SER* 1.3 66.4 + - - +
147C ASP* 3.2 4.9 + - + +
148C TYR* 2.9 45.9 + - + -
203C ILE* 3.9 18.8 - - + -
220C CYS* 3.7 12.6 - - - -
221C PHE* 3.3 41.7 - - - +
222C ILE* 3.8 9.0 - - + +
529C TYR* 4.9 4.3 - - - +
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASP 2.9 21.6 + - - -
142C LEU* 3.1 14.2 + - - +
144C LEU* 1.3 70.8 - - - +
146C ILE* 1.3 70.0 + - - +
148C TYR* 4.1 0.2 - - - +
149C VAL* 2.9 32.3 + - - +
200C ALA* 4.4 14.8 - - - -
203C ILE* 3.5 20.3 - - - +
204C LEU* 4.0 22.5 - - - +
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Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ILE* 3.8 31.8 - - + +
116C ILE* 6.3 0.2 - - - -
119C ILE* 4.0 32.5 - - + -
120C SER* 4.6 7.2 - - - +
142C LEU* 2.9 36.8 + - + +
143C TRP* 3.7 4.0 - - - +
145C SER* 1.3 78.3 + - - +
147C ASP* 1.3 67.6 + - - +
149C VAL* 3.9 3.2 - - - +
150C ALA* 2.9 26.7 + - + +
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Residues in contact with ASP 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 4.1 12.5 - - - +
120C SER* 3.2 25.9 + - - +
143C TRP* 2.9 27.7 + - + +
144C LEU* 3.6 5.2 - - + +
146C ILE* 1.3 74.0 - - - +
148C TYR* 1.3 55.4 - - + +
150C ALA* 3.5 4.6 - - - +
151C SER* 2.8 34.5 + - - -
529C TYR* 4.0 7.1 + - - +
533C TYR* 2.7 26.4 + - - -
2000C 0HK 3.0 27.0 - - - -
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Residues in contact with TYR 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 2.9 35.3 + - + +
147C ASP* 1.3 74.5 - - + +
149C VAL* 1.3 65.7 + - - +
151C SER* 2.8 17.8 + - - -
152C ASN* 3.0 17.5 + - - +
199C TRP* 3.9 32.2 + + + -
203C ILE* 4.0 11.0 - - + -
222C ILE* 3.5 33.8 - - + +
225C LEU* 4.4 11.0 - - + +
506C TYR* 4.7 5.2 + - - -
529C TYR* 3.7 22.9 + - - -
2000C 0HK 3.1 56.9 - + + +
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C SER 2.9 28.3 + - - +
146C ILE* 4.0 3.1 - - - +
148C TYR* 1.3 71.6 - - - +
150C ALA* 1.3 57.6 + - - +
153C ALA* 2.9 31.4 + - - +
192C TRP* 4.5 15.7 - - + +
195C SER* 3.7 5.6 - - - -
196C PHE* 3.6 41.3 - - + +
199C TRP* 3.8 28.0 - - + -
200C ALA* 4.0 11.7 - - + +
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ALA* 4.0 11.7 - - + +
115C ILE* 4.0 30.1 - - + -
116C ILE* 5.0 8.7 - - + +
146C ILE* 2.9 19.5 + - + +
147C ASP* 3.5 5.6 - - - +
149C VAL* 1.3 75.3 - - - +
151C SER* 1.3 66.1 + - - +
153C ALA* 3.2 8.1 + - - +
154C SER* 2.9 22.2 + - - -
192C TRP* 4.9 7.9 - - + -
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Residues in contact with SER 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ILE* 5.3 10.0 - - - +
147C ASP* 2.8 21.9 + - - -
148C TYR 2.8 11.4 + - - -
150C ALA* 1.3 72.7 - - - +
152C ASN* 1.3 55.9 + - - +
154C SER* 2.8 24.6 + - - -
155C VAL* 3.0 15.2 + - - +
503C TRP* 4.1 13.0 - - - -
2000C 0HK 3.0 45.0 + - - +
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Residues in contact with ASN 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C TYR 3.0 10.5 + - - +
149C VAL 4.4 0.4 - - - +
151C SER* 1.3 74.1 + - - +
153C ALA* 1.3 66.9 + - - +
155C VAL* 2.9 33.4 - - - +
156C MET* 2.9 29.9 + - - +
195C SER* 3.8 9.5 + - - +
198C LEU* 5.0 7.2 - - - +
199C TRP* 3.4 27.9 + - + +
238C ALA* 4.1 14.0 - - - +
2000C 0HK 3.1 28.0 - - + +
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Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ALA* 5.4 1.3 - - + -
149C VAL 2.9 23.9 + - - +
150C ALA* 3.2 8.0 + - - +
152C ASN* 1.3 76.6 - - - +
154C SER* 1.3 57.4 + - - +
156C MET* 3.6 5.2 + - - +
157C ASN* 2.9 29.2 + - - +
191C ALA* 5.2 5.0 - - - +
192C TRP* 4.3 34.6 + - + +
195C SER* 3.2 20.3 + - - +
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Residues in contact with SER 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 3.7 15.5 - - - +
112C ALA* 4.2 15.4 - - - +
113C ASP* 4.2 12.0 + - - -
150C ALA 2.9 11.4 + - - -
151C SER* 2.8 17.0 + - - -
153C ALA* 1.3 74.9 - - - +
155C VAL* 1.3 63.3 + - - -
157C ASN* 3.0 11.0 + - - +
158C LEU* 3.0 26.8 + - - +
499C PHE* 5.9 1.4 - - - -
503C TRP* 5.7 4.2 - - - -
535C ASN* 5.3 3.3 + - - -
536C SER* 5.0 3.5 + - - -
539C ASN* 5.0 3.6 + - - -
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Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C SER 3.0 4.7 + - - +
152C ASN* 2.9 33.8 + - - +
154C SER* 1.3 74.1 - - - +
156C MET* 1.3 78.2 + - + +
158C LEU* 2.9 24.7 + - - +
159C LEU* 3.0 19.3 + - + +
238C ALA 4.2 11.9 - - - +
239C PHE* 5.6 0.4 - - + -
242C PRO* 5.3 9.4 - - + -
246C MET* 4.4 2.1 - - + +
499C PHE* 3.5 19.0 - - + -
503C TRP* 3.4 40.6 - - + -
2000C 0HK 4.3 4.9 - - - -
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Residues in contact with MET 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASN* 2.9 31.8 + - - +
153C ALA* 3.7 4.7 - - - +
155C VAL* 1.3 84.7 - - + +
157C ASN* 1.3 62.9 + - - +
159C LEU* 3.0 23.6 + - + +
160C VAL* 2.9 28.9 + - + +
190C LEU* 5.8 0.4 - - + -
191C ALA* 4.0 25.4 - - + +
194C ILE* 4.0 38.1 - - + -
195C SER* 3.8 13.5 - - - -
198C LEU* 5.6 1.3 - - - -
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Residues in contact with ASN 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C PHE* 3.5 12.1 - - - +
108C SER* 2.7 35.2 + - - -
109C LEU* 3.2 31.3 - - + +
112C ALA* 6.1 1.4 - - - +
153C ALA 2.9 16.2 + - - +
154C SER* 3.0 15.0 - - - +
156C MET* 1.3 75.8 - - - +
158C LEU* 1.3 59.9 + - - +
160C VAL* 3.1 13.2 + - - +
161C ILE* 3.0 26.7 + - - +
188C ILE* 4.7 10.3 - - - +
191C ALA* 5.5 5.0 - - - +
192C TRP* 4.9 3.2 - - - +
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 3.5 35.9 - - + -
154C SER* 3.0 14.3 + - - +
155C VAL* 2.9 8.6 + - - +
157C ASN* 1.3 74.8 - - - +
159C LEU* 1.3 64.1 + - - +
161C ILE* 3.2 9.8 + - + +
162C SER* 3.0 27.6 + - - +
246C MET* 3.4 17.5 - - + -
492C LEU* 5.5 0.3 - - - +
495C ILE* 3.8 19.7 - - + +
496C LEU* 5.4 4.7 - - + -
499C PHE* 3.6 48.5 - - + -
535C ASN* 5.9 0.2 - - - +
539C ASN* 6.0 0.9 - - - +
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 3.0 13.4 + - + +
156C MET* 3.0 36.1 - - + +
158C LEU* 1.3 77.1 - - - +
160C VAL* 1.3 59.9 + - + +
162C SER* 3.9 0.7 - - - -
163C PHE* 2.9 39.2 + - + +
241C MET* 6.2 0.9 - - - -
242C PRO* 3.6 38.4 - - + +
245C ILE* 4.5 12.1 - - + -
246C MET* 3.4 27.3 - - + -
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C PHE* 4.0 30.1 - - + -
156C MET* 2.9 25.4 + - + +
157C ASN* 3.4 11.2 - - - +
159C LEU* 1.3 74.8 - - + +
161C ILE* 1.3 64.0 + - + +
163C PHE* 4.2 3.7 - - - +
164C ASP* 2.9 27.4 + - + +
187C MET* 4.2 34.5 - - + +
188C ILE* 5.6 5.6 - - + -
191C ALA* 5.0 13.7 - - + -
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Residues in contact with ILE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ASN 5.9 0.2 - - - +
105C PHE* 3.6 28.5 - - + -
106C LEU* 3.8 18.2 - - + -
109C LEU* 3.5 32.5 - - + -
157C ASN* 3.0 15.0 + - - +
158C LEU* 3.4 13.0 - - + +
160C VAL* 1.3 76.0 - - - +
162C SER* 1.3 65.3 + - - +
164C ASP* 2.9 24.1 - - - +
165C ARG* 3.0 35.4 + - - +
492C LEU* 4.3 17.3 - - + -
495C ILE* 5.9 1.1 - - + -
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Residues in contact with SER 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU 3.0 15.5 + - - -
159C LEU 3.9 2.7 - - - -
161C ILE* 1.3 77.4 - - - +
163C PHE* 1.3 64.6 - - - +
165C ARG* 5.2 0.4 - - - -
166C TYR* 2.9 19.8 + - - +
246C MET* 3.9 27.6 + - - +
249C LEU* 4.3 19.1 - - - -
250C TYR 5.6 0.2 - - - -
253C ILE* 3.2 15.8 - - - +
492C LEU* 3.8 25.1 - - - +
496C LEU* 5.3 1.7 - - - +
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Residues in contact with PHE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 2.9 32.3 + - + +
160C VAL* 4.2 3.8 - - - +
162C SER* 1.3 75.5 - - - +
164C ASP* 1.3 63.6 + - - +
166C TYR* 3.3 4.1 + + - +
167C PHE* 2.9 58.9 + + + +
245C ILE* 3.9 24.5 - - + -
249C LEU* 3.8 19.0 - - + +
227D GLU* 3.8 8.7 - - - -
229D THR* 3.3 31.2 - - - -
230D ILE* 3.8 31.9 - - + -
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Residues in contact with ASP 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 4.2 0.2 - - - +
102C ASN* 3.8 2.4 - - - +
105C PHE* 3.4 25.3 - - + -
160C VAL* 2.9 23.5 + - + +
161C ILE 2.9 5.0 - - - +
163C PHE* 1.3 76.8 - - - +
165C ARG* 1.3 89.0 + - - +
167C PHE* 3.0 4.6 + - - +
168C SER* 2.9 21.8 + - - -
175C TYR* 2.7 31.1 + - - +
179C ARG* 2.7 35.7 + - - -
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Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ASN* 2.9 48.9 + - - +
106C LEU* 5.5 6.5 - - - +
161C ILE* 3.0 36.9 + - - +
162C SER* 4.0 1.6 - - - +
164C ASP* 1.3 90.4 + - - +
166C TYR* 1.3 63.3 + - - +
168C SER* 3.0 9.6 + - - +
169C ILE* 3.0 31.7 + - + +
179C ARG* 5.3 1.1 - - - +
253C ILE* 3.7 27.8 - - + -
489C ALA 5.0 8.5 - - - +
490C GLN* 3.5 43.3 + - - +
491C THR* 5.6 1.2 - - - -
492C LEU* 5.1 10.5 - - - +
1001C MET* 6.5 0.4 - - + -
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Residues in contact with TYR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C SER 2.9 17.6 + - - +
163C PHE* 3.6 7.9 - + - +
165C ARG* 1.3 75.1 - - - +
167C PHE* 1.3 70.5 + + - +
169C ILE* 3.4 6.3 + - + +
170C THR* 2.9 59.3 + - + +
249C LEU* 4.2 25.1 - - + -
252C ARG* 3.6 52.4 + - + -
253C ILE* 3.2 21.1 - - + +
227D GLU* 3.6 32.2 + - - -
228D PRO* 5.5 2.9 - - - +
229D THR* 5.6 0.4 - - + +
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Residues in contact with PHE 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PHE* 2.9 37.2 + + + -
164C ASP 3.5 7.0 - - - +
166C TYR* 1.3 84.8 - + - +
168C SER* 1.3 60.5 + - - +
170C THR* 3.7 8.1 - - - -
171C ARG* 2.8 58.0 + - + +
175C TYR* 3.8 31.6 - + + -
227D GLU* 3.3 46.9 - - + -
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Residues in contact with SER 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ASP 2.9 14.5 + - - -
165C ARG* 3.1 14.2 + - - -
167C PHE* 1.3 76.6 - - - +
169C ILE* 1.3 64.8 + - - +
172C PRO* 3.9 9.5 - - - +
175C TYR* 3.5 14.2 - - - -
176C ARG* 3.9 31.1 - - - +
179C ARG* 3.0 29.2 + - - -
1001C MET* 4.4 14.7 - - - +
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Residues in contact with ILE 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ARG* 3.0 33.4 + - + +
166C TYR* 3.6 9.0 - - + +
168C SER* 1.3 80.7 - - - +
170C THR* 1.3 75.7 + - + +
171C ARG 3.3 0.2 + - - -
172C PRO* 3.7 12.8 - - - +
252C ARG 5.8 1.6 - - - +
253C ILE* 4.7 18.6 - - + -
256C GLU* 3.6 27.6 - - + +
257C THR* 4.7 11.9 - - + -
259C LYS* 4.5 26.4 - - + +
1001C MET* 4.1 30.4 - - + +
1068C ASN* 4.7 3.8 - - - +
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Residues in contact with THR 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C TYR* 2.9 60.3 + - + +
167C PHE* 3.7 6.6 - - - -
169C ILE* 1.3 82.4 - - + +
171C ARG* 1.3 75.7 + - - +
172C PRO* 3.5 3.0 - - - +
1064C GLU* 4.4 3.5 - - - +
1068C ASN* 3.3 28.9 + - - +
227D GLU* 4.9 1.0 + - - -
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Residues in contact with ARG 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C PHE* 2.8 46.1 + - + +
168C SER 4.0 0.2 - - - -
170C THR* 1.3 89.7 + - - +
172C PRO* 1.3 63.4 - - - +
174C THR* 4.9 7.6 - - - +
175C TYR* 3.1 28.3 + - + +
176C ARG 3.2 7.4 + - - -
1061C ASP* 6.1 3.0 - - - -
1064C GLU* 2.8 22.0 - - + +
1065C LYS* 5.9 4.8 - - - +
214D THR* 6.3 1.2 - - - +
226D SER* 3.9 32.1 + - - -
227D GLU* 4.0 21.0 + - - +
228D PRO* 5.9 0.2 - - - +
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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
------------------------------------------------------------
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