Contacts of the helix formed by residues 137 - 167 (chain A) in PDB entry 5D0Y
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY 4.0 0.2 + - - -
136A THR* 1.3 77.4 + - - +
138A PHE* 1.3 81.5 + - - +
139A MET* 3.6 16.9 + - - +
140A VAL* 3.0 34.1 + - + +
141A ALA 3.3 8.7 + - - -
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Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.8 17.5 - - + -
124A GLY* 3.6 23.8 - - - -
127A THR* 3.6 19.7 - - + -
128A LEU* 3.8 23.6 - - + -
131A SER* 3.9 13.5 - - - +
136A THR 4.0 0.8 + - - -
137A ASN* 1.3 79.3 + - - +
139A MET* 1.3 79.8 + - + +
141A ALA* 3.3 4.5 + - - +
142A LEU* 2.7 46.0 + - + -
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Residues in contact with MET 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASN* 3.3 12.8 + - - +
138A PHE* 1.3 91.4 - - + +
140A VAL* 1.3 66.3 + - - +
142A LEU* 3.4 34.6 - - + +
143A SER* 2.9 24.8 + - - -
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 4.1 18.6 - - + -
137A ASN* 3.0 36.1 + - + +
139A MET* 1.3 76.7 - - - +
141A ALA* 1.3 62.2 + - - +
143A SER* 3.1 17.8 + - - +
144A SER* 3.0 17.1 + - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 5.9 0.9 - - - -
127A THR* 3.6 17.9 - - + +
130A VAL* 4.4 10.5 - - + -
131A SER* 3.9 16.8 - - - +
136A THR* 3.8 20.3 + - - +
137A ASN 3.3 2.0 + - - +
138A PHE 3.3 8.9 + - - +
140A VAL* 1.3 76.8 - - - +
142A LEU* 1.3 66.1 + - - +
143A SER 3.1 1.0 + - - -
144A SER* 3.1 15.4 + - - -
145A ARG* 3.2 17.9 + - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.9 34.5 - - + +
127A THR* 3.5 9.6 - - - +
138A PHE* 2.7 30.9 + - + +
139A MET* 3.4 39.5 - - + +
141A ALA* 1.3 72.8 - - - +
143A SER* 1.3 58.5 + - - +
145A ARG* 3.2 3.6 + - + -
146A ILE* 3.0 53.5 + - + +
149A GLU* 6.3 0.9 - - + -
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MET 2.9 16.5 + - - -
140A VAL* 3.1 11.8 + - - +
141A ALA 3.1 0.6 + - - -
142A LEU* 1.3 76.9 - - - +
144A SER* 1.3 66.6 + - - +
145A ARG 3.4 0.3 + - - -
146A ILE* 3.7 18.9 - - - +
147A LEU* 5.1 2.4 + - - +
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 4.8 12.1 - - - +
39A LEU* 3.5 13.9 - - - +
140A VAL* 3.0 17.3 + - - +
141A ALA* 3.5 7.3 + - - -
143A SER* 1.3 81.7 + - - +
145A ARG* 1.3 62.0 + - - +
146A ILE 4.0 0.2 + - - -
147A LEU* 5.2 3.6 + - - +
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 4.1 22.9 - - + -
39A LEU* 3.6 25.7 - - + +
122A TYR 3.0 13.1 + - - -
123A ILE* 4.7 0.4 - - - +
126A ASN* 3.8 7.5 - - - +
127A THR* 2.4 52.8 + - - +
130A VAL* 4.5 8.1 - - - +
141A ALA 3.2 17.5 + - - +
142A LEU* 4.1 4.7 - - + +
144A SER* 1.3 79.1 - - - +
146A ILE* 1.3 62.2 + - - +
147A LEU 3.4 2.5 - - - -
148A LYS* 3.3 12.9 + - - +
149A GLU* 3.2 28.1 + - + +
201A FOL 2.4 54.3 + - - -
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 4.4 22.2 - - + -
142A LEU* 3.0 40.2 + - + +
143A SER* 3.7 15.9 - - - +
144A SER 3.7 0.8 - - - -
145A ARG* 1.3 74.6 - - - +
147A LEU* 1.3 72.7 + - + +
149A GLU* 3.1 5.6 + - + -
150A MET* 3.0 48.0 + - + +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER 5.1 2.0 + - - +
144A SER 5.6 3.1 - - - +
145A ARG 3.4 0.8 - - - -
146A ILE* 1.3 83.8 - - + +
148A LYS* 1.3 62.8 + - - +
150A MET* 3.4 23.2 + - + +
151A ILE* 3.1 32.3 + - + +
151B ILE* 3.7 21.3 - - + -
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Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.9 36.3 - - + +
40A GLN 4.0 6.1 - - - +
41A VAL* 4.0 11.2 - - + +
122A TYR* 4.1 7.7 - - - -
145A ARG 3.3 9.9 + - - +
146A ILE 3.3 0.4 - - - -
147A LEU* 1.3 78.6 - - - +
149A GLU* 1.3 84.4 + - - +
151A ILE* 3.1 2.8 + - - -
152A THR* 2.8 66.5 + - + -
156A HIS* 4.7 1.2 - - - -
201A FOL 2.7 49.0 + - - +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 3.7 9.2 - - + +
122A TYR* 3.4 21.3 - - - +
123A ILE* 3.7 31.5 - - + +
142A LEU* 6.3 0.9 - - + -
145A ARG* 3.2 41.9 + - + +
146A ILE* 3.1 8.8 + - + +
148A LYS* 1.3 107.8 + - - +
150A MET* 1.3 59.4 + - - +
152A THR* 4.2 2.1 + - - -
153A PRO* 3.2 22.1 - - - +
201A FOL 2.6 19.5 - - - +
154B TRP* 4.9 1.7 + - - -
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Residues in contact with MET 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 6.4 0.2 - - + -
146A ILE* 3.0 44.3 + - + +
147A LEU* 3.6 31.0 - - + +
148A LYS 3.1 0.2 - - - -
149A GLU* 1.3 82.6 - - - +
151A ILE* 1.3 60.4 + - - +
153A PRO* 3.6 2.8 - - - +
154A TRP* 3.2 13.7 + - - -
150B MET 3.4 2.7 - - - +
151B ILE* 3.6 34.3 - - + +
154B TRP* 3.0 42.3 + - + +
155B ILE* 4.3 11.2 - - + -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.1 22.6 + - + +
148A LYS* 4.0 3.4 - - - +
150A MET* 1.3 76.9 - - - +
152A THR* 1.3 69.2 + - + +
153A PRO* 3.1 3.4 - - - -
154A TRP* 3.0 23.9 - - - -
155A ILE* 3.5 13.6 - - + +
147B LEU* 3.7 27.8 - - + -
150B MET* 3.8 26.2 - - + -
151B ILE* 4.1 25.1 - - + -
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.7 13.2 - - + -
118A THR* 5.5 1.4 - - - +
122A TYR* 5.7 0.3 - - - -
148A LYS* 2.8 65.5 + - + +
149A GLU* 4.2 1.6 + - - -
151A ILE* 1.3 75.5 - - + +
153A PRO* 1.4 69.1 - - - +
155A ILE* 2.8 26.7 + - + +
156A HIS* 2.8 26.6 + - - +
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Residues in contact with PRO 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 3.9 19.3 - - + +
115A ILE* 5.8 0.9 - - + -
118A THR* 4.1 17.9 - - + +
149A GLU 3.2 26.2 - - - +
150A MET 3.6 3.6 - - - +
151A ILE 3.1 7.6 - - - +
152A THR* 1.4 94.3 - - - +
154A TRP* 1.3 51.2 + - - +
156A HIS* 3.0 5.9 + - + +
157A MET* 2.7 48.1 + - + +
154B TRP* 4.0 24.9 - - + -
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Residues in contact with TRP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A MET 3.2 8.2 + - - -
151A ILE 3.0 24.0 - - - +
152A THR 3.2 0.4 - - - -
153A PRO* 1.3 74.4 - - - +
155A ILE* 1.3 65.0 + - + +
157A MET* 3.3 23.2 + - + +
158A VAL* 3.1 31.5 + - + +
115B ILE* 4.0 33.0 - - + -
149B GLU 4.9 0.9 - - - -
150B MET* 2.9 51.3 + - + +
153B PRO* 4.0 22.9 - - + -
154B TRP* 3.1 39.3 - + - -
157B MET* 4.7 0.4 - - + -
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 5.6 1.6 - - + -
151A ILE* 3.5 32.8 - - + +
152A THR* 2.8 22.1 + - + +
154A TRP* 1.3 68.4 - - + +
156A HIS* 1.3 70.2 + - + +
158A VAL* 3.4 6.0 + - + +
159A VAL* 3.0 43.2 + - + +
150B MET* 4.6 10.5 - - - -
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Residues in contact with HIS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY 4.7 0.4 + - - -
45A PHE* 3.4 48.3 - + + -
96A TYR* 4.3 6.0 + - - +
114A VAL* 3.6 21.9 - - + +
118A THR* 4.8 1.8 + - - -
122A TYR* 3.7 37.8 + + - -
148A LYS* 5.7 0.2 - - - -
152A THR* 2.8 29.2 + - - +
153A PRO* 3.3 10.3 - - - +
155A ILE* 1.3 81.3 - - + +
157A MET* 1.3 53.9 + - - +
159A VAL* 3.6 1.7 - - - +
160A VAL* 2.7 41.1 + - + +
201A FOL 3.9 15.8 + - - -
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Residues in contact with MET 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 3.3 26.1 - - + +
111A ILE* 3.9 33.4 - - + +
114A VAL* 3.7 18.8 - - + -
115A ILE* 3.7 29.8 - - + -
153A PRO* 2.7 37.9 + - + +
154A TRP* 3.7 30.5 - - + +
155A ILE 3.2 0.4 - - - -
156A HIS* 1.3 74.1 - - - +
158A VAL* 1.3 59.0 + - + +
160A VAL 3.3 0.2 + - - -
161A TRP* 2.9 25.8 + - - +
154B TRP* 4.5 3.6 - - + -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TRP* 3.1 19.6 + - + +
155A ILE* 3.8 6.1 - - - +
157A MET* 1.3 73.4 - - + +
159A VAL* 1.3 70.0 + - + +
161A TRP* 3.1 16.7 + - + +
162A PHE* 3.1 41.2 + - + -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 6.6 0.2 - - + -
45A PHE* 3.6 29.6 - - + -
46A ILE* 4.1 9.2 - - + -
155A ILE* 3.0 31.6 + - + +
156A HIS 3.7 2.7 - - - +
158A VAL* 1.3 78.5 - - + +
160A VAL* 1.3 62.9 + - - +
162A PHE* 3.4 8.7 + - + -
163A ILE* 3.0 47.4 + - + +
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.7 8.7 - - + -
49A VAL* 4.0 28.9 - - + -
96A TYR* 4.3 1.8 - - + +
100A LEU* 4.5 7.4 - - + -
110A VAL* 3.6 24.5 - - + -
113A SER* 5.1 0.7 - - - +
114A VAL* 4.0 15.0 - - + -
156A HIS* 2.7 32.3 + - - +
157A MET 3.5 4.7 - - - +
158A VAL 3.2 0.2 - - - -
159A VAL* 1.3 72.4 - - - +
161A TRP* 1.3 66.6 + - - +
163A ILE* 3.7 6.1 - - - +
164A LEU* 3.0 39.6 + - + +
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Residues in contact with TRP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.7 27.0 - - + +
106A GLN 6.5 0.9 - - - -
107A ILE* 4.2 26.9 - - + -
110A VAL* 4.9 12.1 - - + -
157A MET 2.9 14.5 + - - +
158A VAL* 3.1 12.1 + - + +
160A VAL* 1.3 77.1 - - - +
162A PHE* 1.3 63.3 + + + +
164A LEU* 2.7 28.4 + - + -
165A GLU* 2.7 31.7 + - + +
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 3.1 40.0 + - + -
159A VAL* 4.0 8.1 - - + +
161A TRP* 1.3 89.5 - + + +
163A ILE* 1.3 62.4 + - + +
165A GLU* 4.0 17.5 - - - +
166A GLY* 2.9 26.9 + - - -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 6.4 0.2 - - + -
46A ILE* 3.7 29.8 - - + +
49A VAL* 4.7 11.2 - - + -
50A MET* 4.6 20.2 - - + -
53A TYR* 6.1 2.9 - - + -
159A VAL* 3.0 45.1 + - + +
160A VAL* 3.7 6.7 - - - +
162A PHE* 1.3 82.5 - - + +
164A LEU* 1.3 73.4 + - + +
166A GLY* 3.8 0.3 - - - -
167A LEU* 3.1 37.8 + - + +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 4.2 13.9 - - + -
53A TYR* 4.0 37.7 + - + -
100A LEU* 3.4 29.6 - - + +
105A ILE* 3.5 46.1 - - + +
106A GLN 5.3 0.2 - - - +
110A VAL* 4.9 7.4 - - + -
160A VAL* 3.0 41.3 + - + +
161A TRP* 2.7 13.2 + - + +
163A ILE* 1.3 75.4 - - + +
165A GLU* 1.3 66.8 + - - +
167A LEU 3.9 9.7 + - - -
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.8 16.7 - - + +
161A TRP* 2.7 34.6 + - + +
162A PHE* 4.0 17.7 - - + +
164A LEU* 1.3 75.0 - - - +
166A GLY* 1.3 75.8 + - - +
167A LEU 3.0 9.5 + - - +
----------------------------------------------------------
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE 2.9 19.7 + - - -
163A ILE 3.8 0.9 - - - -
165A GLU* 1.3 83.3 + - - +
167A LEU* 1.3 69.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 4.2 36.3 - - + -
53A TYR* 4.6 22.7 - - + -
54A LEU* 4.5 23.8 - - + -
163A ILE* 3.1 28.8 + - + +
164A LEU 4.1 6.5 - - - -
165A GLU 3.0 9.1 + - - +
166A GLY* 1.3 87.2 - - - +
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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