Contacts of the helix formed by residues 134 - 157 (chain B) in PDB entry 5XS0
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 SER 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.9 1.6 - - - -
132B LEU* 3.4 3.1 - - - +
133B LYS* 1.3 76.8 - - - +
135B LYS* 1.3 61.4 + - - +
136B ALA 3.6 0.3 + - - -
137B LEU* 3.1 38.5 + - - +
138B SER* 2.8 28.2 + - - -
130C GLU* 3.0 35.3 + - - -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 4.4 17.8 - - + +
103B PHE* 3.5 48.5 - - + -
105B VAL* 5.4 0.3 - - - +
134B SER* 1.3 71.6 - - - +
136B ALA* 1.3 63.6 + - - +
138B SER* 3.4 3.4 + - - -
139B LEU* 3.0 31.7 + - + +
95C PHE* 3.6 43.9 - - + +
97C ASP* 3.2 27.8 + - - +
130C GLU* 4.6 2.6 + - - +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 3.3 4.1 + - - +
135B LYS* 1.3 80.6 - - - +
137B LEU* 1.3 59.7 + - - +
139B LEU 3.3 0.7 + - - -
140B GLU* 2.9 25.6 + - - +
95C PHE* 3.3 25.7 - - + -
105C VAL 4.0 8.7 - - - +
106C GLY* 4.2 3.1 - - - -
126C TYR* 3.2 12.5 - - - -
128C VAL* 3.6 33.4 - - + -
130C GLU* 4.4 5.5 + - + +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 4.2 18.2 - - + +
134B SER* 3.1 32.4 + - - +
136B ALA* 1.3 73.6 - - - +
138B SER* 1.3 65.5 + - - +
140B GLU* 3.3 15.3 + - - +
141B LYS* 2.9 25.8 + - - +
58C GLY* 6.1 5.8 - - - +
128C VAL* 3.7 30.1 - - + -
130C GLU* 4.1 5.2 - - - +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.7 14.7 + - - +
105B VAL* 4.1 17.7 - - - -
129B SER* 3.3 25.8 + - - -
132B LEU* 3.2 22.1 - - - +
134B SER 2.8 21.5 + - - -
135B LYS 3.5 4.9 - - - -
137B LEU* 1.3 78.0 - - - +
139B LEU* 1.3 61.1 + - - +
141B LYS 3.4 0.2 + - - -
142B ALA* 2.9 26.5 + - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 4.3 13.0 - - + -
96B VAL* 4.1 18.8 - - + -
105B VAL* 3.8 25.8 - - + -
107B VAL* 4.7 1.8 - - + -
135B LYS* 3.0 20.3 + - + +
136B ALA 3.7 0.2 - - - +
138B SER* 1.3 76.5 - - - +
140B GLU* 1.3 61.3 + - - +
142B ALA* 3.3 2.8 + - - +
143B ARG* 2.9 39.8 + - + +
94C ASP* 3.7 15.9 - - + +
95C PHE* 3.6 28.5 - - + -
126C TYR* 3.2 31.0 - - + +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA 2.9 11.1 + - - +
137B LEU* 3.6 16.6 - - - +
138B SER 3.3 0.2 - - - -
139B LEU* 1.3 76.4 - - - +
141B LYS* 1.3 64.1 + - - +
143B ARG* 4.0 0.8 - - - +
144B LYS* 2.6 66.2 + - + +
126C TYR* 3.5 36.9 - - + +
128C VAL* 4.2 14.1 - - - +
149C ASP* 4.5 0.5 - - - +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 2.8 30.5 + - - +
129B SER* 3.7 16.9 - - - +
130B GLU 5.3 0.6 - - - +
132B LEU* 5.2 6.1 - - + -
137B LEU 2.9 17.9 + - - +
138B SER 3.8 3.1 - - - +
140B GLU* 1.3 78.8 - - + +
142B ALA* 1.3 57.4 - - - +
144B LYS* 4.1 2.6 - - - +
145B GLU* 2.9 57.6 + - + +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.8 16.4 - - + +
107B VAL* 3.8 18.4 - - + -
127B GLY* 3.3 34.2 - - - +
128B VAL 4.2 7.2 - - - +
138B SER 2.9 17.0 + - - +
139B LEU 3.9 1.6 - - - +
141B LYS* 1.3 77.8 - - - +
143B ARG* 1.3 56.9 + - - +
146B ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN* 2.4 59.6 + - - +
93B VAL* 3.3 29.7 - - - +
107B VAL* 3.9 14.4 - - + -
139B LEU* 2.9 22.7 + - + +
140B GLU* 4.0 2.9 - - - +
142B ALA* 1.3 76.0 - - - +
144B LYS* 1.3 63.9 + - + +
146B ALA* 3.3 1.6 + - - +
147B VAL* 3.0 21.6 + - - +
92C ASN* 5.2 3.0 + - - +
94C ASP* 2.8 34.3 + - - -
108C CYS* 3.5 28.3 - - - -
110C PHE* 4.4 4.9 - - - -
124C VAL* 4.4 9.6 - - + -
126C TYR* 3.7 23.1 - - + -
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 2.6 57.1 + - + +
141B LYS* 4.1 2.7 - - - +
143B ARG* 1.3 77.2 - - + +
145B GLU* 1.3 62.5 + - - +
147B VAL* 3.3 5.0 + - - +
148B THR* 3.0 28.0 + - - -
124C VAL* 4.4 10.1 - - + +
126C TYR* 4.1 12.1 - - + +
149C ASP* 2.7 35.4 + - - -
153C ARG* 3.3 43.6 + - - +
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Residues in contact with GLU 145 (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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126B TYR 3.9 4.6 - - - +
127B GLY* 4.0 5.1 - - - -
128B VAL* 3.3 28.4 + - - +
141B LYS* 2.9 46.9 + - + +
142B ALA 3.8 2.9 - - - +
144B LYS* 1.3 77.8 - - - +
146B ALA* 1.3 56.9 + - - +
148B THR* 3.3 5.4 + - - -
149B ASP* 2.9 32.4 + - + +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 3.2 37.5 - - + +
109B ALA* 3.9 15.0 - - + +
125B GLY* 3.5 8.8 - - - -
126B TYR* 3.4 15.3 - - - -
127B GLY* 3.5 1.9 - - - +
142B ALA 2.9 16.5 + - - +
143B ARG 3.3 5.1 + - - +
145B GLU* 1.3 76.7 - - - +
147B VAL* 1.3 56.4 + - - +
150B GLY* 2.9 24.8 + - - -
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Residues in contact with VAL 147 (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 HIS* 5.4 4.7 - - + +
88B ILE* 3.8 22.2 - - + -
91B GLN* 3.4 25.4 - - - +
109B ALA* 3.9 12.1 - - + -
111B VAL* 3.6 8.6 - - + +
143B ARG 3.0 10.7 + - - +
144B LYS* 3.8 4.5 - - - +
146B ALA* 1.3 76.9 - - - +
148B THR* 1.3 65.5 + - - +
150B GLY 3.2 1.6 + - - -
151B LEU* 3.0 21.7 + - + +
122C GLU 5.0 1.6 - - - +
123C ASP* 3.4 32.1 - - - +
124C VAL* 3.5 20.4 - - + -
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Residues in contact with THR 148 (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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68B GLY* 4.6 15.3 - - - -
144B LYS 3.0 17.6 + - - -
145B GLU* 3.9 5.6 - - - -
147B VAL* 1.3 76.4 - - - +
149B ASP* 1.3 63.4 + - - +
151B LEU* 3.2 9.7 + - + +
152B LYS* 3.0 39.7 + - + +
123C ASP* 5.4 2.0 + - - -
153C ARG* 3.8 13.2 + - - -
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Residues in contact with ASP 149 (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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140A GLU* 4.4 0.5 - - - +
144A LYS* 2.6 38.0 + - - -
125B GLY* 3.6 1.1 - - - -
126B TYR 3.2 18.7 + - - +
145B GLU* 2.9 18.0 + - + +
146B ALA 3.7 3.4 - - - +
148B THR* 1.3 78.6 - - - +
150B GLY* 1.3 56.7 + - - +
152B LYS* 3.3 20.6 + - - +
153B ARG* 2.9 39.0 + - - +
156B ARG* 5.6 0.7 + - - -
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Residues in contact with GLY 150 (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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109B ALA 4.7 0.7 - - - -
111B VAL* 3.7 16.9 - - - +
123B ASP* 4.5 3.5 - - - +
124B VAL 4.0 4.3 - - - -
125B GLY* 3.4 23.0 - - - -
146B ALA 2.9 13.4 + - - -
147B VAL 3.2 3.8 + - - -
149B ASP* 1.3 75.7 - - - +
151B LEU* 1.3 57.5 + - - +
153B ARG* 3.4 1.0 + - - +
154B ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 6.0 1.1 - - + -
72B ILE* 4.6 17.0 - - + -
84B TRP* 3.9 21.5 - - + -
86B HIS* 3.8 39.0 - - + +
111B VAL* 3.8 11.3 - - + +
113B VAL* 3.6 24.7 - - + -
147B VAL* 3.0 13.6 + - + +
148B THR* 3.2 11.9 + - + +
150B GLY* 1.3 76.9 - - - +
152B LYS* 1.3 65.5 + - + +
154B ALA* 3.3 0.8 + - - +
155B LEU* 3.0 30.4 + - + +
123C ASP* 5.7 2.0 - - - +
157C SER* 4.8 3.4 - - - +
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 6.1 0.6 - - - +
65B TYR* 4.8 12.9 - - - +
66B ILE* 3.6 26.9 + - + +
67B GLU* 5.4 0.2 - - - +
68B GLY* 4.3 12.8 - - - +
71B VAL* 4.2 32.6 - - + +
148B THR* 3.0 26.5 + - + +
149B ASP* 3.7 27.1 + - - +
151B LEU* 1.3 78.6 - - + +
153B ARG* 1.3 57.2 - - + +
155B LEU* 3.3 1.9 + - - +
156B ARG* 2.9 31.3 + - - +
162B LEU 4.8 2.4 - - - +
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Residues in contact with ARG 153 (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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144A LYS* 3.5 56.6 + - - +
148A THR* 3.8 18.6 + - - -
123B ASP* 3.0 40.7 + - + +
124B VAL 2.7 25.3 + - - +
149B ASP* 2.9 29.7 + - - +
150B GLY 4.0 2.2 - - - +
151B LEU 3.3 0.2 - - - -
152B LYS* 1.3 77.2 - - + +
154B ALA* 1.3 60.5 + - - +
156B ARG* 3.3 64.0 + - - +
157B SER* 3.8 5.5 + - - -
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Residues in contact with ALA 154 (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 VAL 3.7 13.5 - - - +
113B VAL* 3.6 23.8 - - + -
121B HIS* 3.6 37.3 - - - +
123B ASP* 3.8 10.6 - - - +
150B GLY 2.9 18.8 + - - +
151B LEU* 3.8 1.6 - - - +
152B LYS 3.3 0.2 - - - -
153B ARG* 1.3 75.2 - - - +
155B LEU* 1.3 63.3 + - - +
157B SER* 3.5 10.5 + - - -
158B PHE* 4.3 3.5 - - - -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.8 29.4 - - + +
72B ILE* 5.5 0.7 - - + -
75B ALA* 3.8 25.4 - - + -
79B PHE* 4.7 3.4 - - + -
84B TRP* 4.0 11.0 - - + -
113B VAL* 3.6 31.0 - - + -
151B LEU* 3.0 33.5 + - + +
152B LYS 3.9 3.4 - - - +
154B ALA* 1.3 72.1 - - - +
156B ARG* 1.3 66.8 + - - +
157B SER 3.1 3.5 + - - -
158B PHE* 3.2 28.2 + - + -
162B LEU* 3.4 30.1 - - + +
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.8 9.2 - - + -
148A THR* 6.0 0.2 + - - -
123B ASP* 5.9 0.8 + - - -
149B ASP* 5.6 0.6 + - - -
152B LYS* 2.9 15.3 + - - +
153B ARG* 3.3 61.0 - - - +
154B ALA 3.2 0.2 - - - -
155B LEU* 1.3 76.9 - - - +
157B SER* 1.3 58.9 + - - +
158B PHE 3.0 6.2 + - - -
159B GLY 3.4 17.5 + - - +
162B LEU 3.9 12.1 + - - +
163B GLY* 4.0 9.2 + - - +
164B ASN* 3.6 28.6 - - - +
166B ILE* 5.3 4.6 - - - +
167B LEU* 3.6 40.2 - - - +
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.3 29.3 - - - +
76A ASN* 3.1 17.2 + - - +
84A TRP* 3.6 11.1 - - - -
86A HIS* 3.8 15.3 - - - -
151A LEU* 5.0 1.2 - - - +
121B HIS* 3.7 31.6 + - - -
123B ASP* 4.4 4.9 + - - -
153B ARG 3.8 11.4 + - - -
154B ALA* 3.5 4.3 + - - -
155B LEU 3.1 1.6 - - - -
156B ARG* 1.3 75.6 - - - +
158B PHE* 1.3 59.0 + - - +
159B GLY 3.4 0.4 - - - -
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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