Contacts of the helix formed by residues 131 - 155 (chain B) in PDB entry 2H3W
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 ASP 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE* 3.7 2.2 - - - -
130B VAL* 1.3 92.5 - - + +
132B LEU* 1.3 64.4 + - - +
133B GLN* 3.3 14.3 + - - +
134B GLY* 2.7 34.7 + - - -
135B GLN* 3.0 21.4 + - - +
333B GLU 5.9 1.3 - - - -
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Residues in contact with LEU 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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131B ASP* 1.3 75.0 - - - +
133B GLN* 1.3 66.6 + - - +
135B GLN* 3.1 13.2 + - - +
136B LEU* 3.0 44.8 + - + +
230B PHE* 6.3 0.2 - - + -
234B GLU* 5.6 4.5 - - + +
237B TRP* 3.5 60.8 - - + +
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Residues in contact with GLN 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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131B ASP* 3.2 13.1 + - - +
132B LEU* 1.3 84.5 - - + +
134B GLY* 1.3 58.0 + - - +
137B ARG* 2.9 52.0 + - - +
230B PHE* 3.7 22.5 - - + -
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 3.3 29.9 - - - +
131B ASP* 2.7 20.2 + - - -
133B GLN* 1.3 73.6 - - - +
135B GLN* 1.3 64.0 + - - +
137B ARG* 3.5 7.0 - - - +
138B PHE* 3.0 19.6 + - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 3.5 23.6 - - + -
131B ASP 3.0 9.9 + - - +
132B LEU* 3.1 26.9 + - + +
134B GLY* 1.3 77.0 - - - +
136B LEU* 1.3 65.6 + - + +
138B PHE* 3.5 2.8 + - - +
139B ALA* 3.1 22.3 + - - +
237B TRP* 3.9 19.2 - - - -
288B LEU* 4.3 5.3 - - + -
289B ASP 3.5 15.4 + - - +
331B VAL* 3.0 39.1 - - + +
332B ALA 3.4 9.1 - - - +
333B GLU* 3.9 18.7 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.0 41.7 + - + +
135B GLN* 1.3 75.9 - - + +
137B ARG* 1.3 61.6 + - - +
139B ALA* 3.2 2.4 + - - -
140B ALA* 2.8 31.4 + - - +
230B PHE* 3.6 17.9 - - + -
233B LEU* 3.5 17.5 - - + +
234B GLU* 3.9 39.5 - - + +
237B TRP* 4.0 16.4 - - + -
288B LEU* 3.9 33.4 - - + -
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 2.9 37.5 + - - +
134B GLY* 3.5 8.7 - - - +
135B GLN 3.3 0.2 - - - -
136B LEU* 1.3 76.1 - - - +
138B PHE* 1.3 63.9 + - - +
140B ALA* 3.2 6.2 + - - +
141B LYS* 3.0 25.9 + - + +
226B SER 6.2 0.2 - - - -
227B ASP* 3.6 26.9 + - - +
230B PHE* 3.0 61.6 - - - +
366B GLU* 5.4 9.4 - - - +
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Residues in contact with PHE 138 (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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127B GLN* 3.5 46.4 - - + -
129B PHE* 3.9 19.1 - + + -
134B GLY 3.0 16.7 + - - +
135B GLN 3.9 2.2 - - - +
137B ARG* 1.3 73.4 - - - +
139B ALA* 1.3 63.0 + - - +
141B LYS* 3.1 6.0 + - + -
142B LEU* 2.8 56.7 + - + +
331B VAL* 4.1 12.1 - - + -
337B CYS* 3.9 23.6 - - + -
359B MET* 4.5 9.6 - - - -
362B THR* 4.0 30.3 - - + -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLN 3.1 18.1 + - - +
136B LEU* 3.2 6.7 + - - +
138B PHE* 1.3 75.3 - - - +
140B ALA* 1.3 57.7 + - - +
142B LEU* 3.4 8.8 + - - +
143B ILE* 3.0 33.4 + - - +
233B LEU* 3.8 15.5 - - + -
286B VAL* 4.7 5.8 - - + +
288B LEU* 4.0 22.4 - - + -
331B VAL* 4.1 15.7 - - + -
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Residues in contact with ALA 140 (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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136B LEU 2.8 17.6 + - - +
137B ARG* 3.5 6.1 - - - +
139B ALA* 1.3 77.6 - - - +
141B LYS* 1.3 57.4 + - - +
143B ILE* 3.4 4.2 + - - +
144B GLU* 3.0 25.8 + - - +
226B SER* 3.4 28.8 - - - +
229B ILE* 3.7 18.7 - - + +
230B PHE* 3.7 20.4 - - + +
233B LEU* 3.7 2.0 - - + +
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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
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137B ARG* 3.0 18.7 + - + +
138B PHE* 3.7 9.2 - - + +
140B ALA* 1.3 71.7 - - - +
142B LEU* 1.3 60.8 + - - +
144B GLU* 3.2 19.1 + - - +
145B GLY* 2.9 25.5 + - - -
226B SER* 4.2 9.4 - - - +
361B TYR* 3.6 14.3 + - + +
362B THR* 3.1 44.6 + - + +
363B LYS 4.5 0.2 - - - -
364B LYS 2.9 28.1 + - - -
366B GLU* 3.1 40.1 - - + +
369B ARG* 5.2 1.3 - - - +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 5.3 3.8 - - + -
138B PHE* 2.8 44.8 + - + +
139B ALA* 3.6 6.7 - - - +
141B LYS* 1.3 74.0 - - - +
143B ILE* 1.3 71.7 + - + +
145B GLY* 3.0 2.8 + - - -
146B VAL* 3.0 35.2 + - + +
284B PHE* 5.0 2.0 - - + -
286B VAL* 5.0 3.4 - - + -
329B PHE* 3.7 40.8 - - + -
330B ILE 5.5 2.2 - - - +
331B VAL* 4.4 13.2 - - + -
337B CYS* 5.6 0.2 - - + -
338B GLY 5.8 0.2 - - - +
358B VAL* 3.7 13.7 - - + +
359B MET* 4.2 10.1 - - + -
362B THR* 4.0 13.0 - - + +
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Residues in contact with ILE 143 (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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139B ALA 3.0 22.3 + - - +
140B ALA 3.6 6.1 - - - +
141B LYS 3.3 0.2 - - - -
142B LEU* 1.3 77.0 - - + +
144B GLU* 1.3 63.2 + - - +
146B VAL* 3.1 13.5 + - - +
147B LEU* 3.1 17.5 + - + +
203B ILE* 3.7 18.4 - - + -
214B LEU* 4.9 0.2 - - + -
216B VAL* 4.0 19.3 - - + -
229B ILE* 3.6 37.2 - - + -
233B LEU* 4.3 14.8 - - + -
284B PHE* 4.1 17.5 - - + -
286B VAL* 3.8 27.8 - - + -
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Residues in contact with GLU 144 (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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140B ALA 3.0 14.3 + - - +
141B LYS* 3.4 13.1 - - - +
143B ILE* 1.3 77.2 - - - +
145B GLY* 1.3 61.6 + - - +
147B LEU* 3.2 10.5 + - + +
148B ASP* 3.0 20.6 + - - +
224B LEU 4.6 6.6 - - - +
225B THR* 3.9 8.3 - - - +
226B SER* 3.0 40.1 + - - +
229B ILE* 4.3 10.1 - - + -
361B TYR* 3.0 36.7 + - + +
368B VAL* 5.7 1.9 - - - +
369B ARG* 4.5 7.4 + - - -
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Residues in contact with GLY 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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141B LYS 2.9 12.2 + - - -
142B LEU 3.0 4.6 + - - -
144B GLU* 1.3 77.6 - - - +
146B VAL* 1.3 60.1 + - - +
148B ASP* 3.3 2.9 + - - +
149B PHE* 3.1 22.3 + - - +
357B HIS* 3.8 5.4 + - - -
358B VAL* 3.8 11.8 - - - +
361B TYR* 3.6 32.2 - - - -
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Residues in contact with VAL 146 (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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142B LEU* 3.0 20.5 + - + +
143B ILE 3.1 5.8 + - - +
145B GLY* 1.3 76.3 - - - +
147B LEU* 1.3 58.0 + - - +
149B PHE* 3.2 5.6 + - - +
150B LYS* 2.8 26.0 + - + +
177B LEU* 4.1 18.8 - - + +
283B ILE* 5.3 1.1 - - + -
284B PHE* 3.4 38.4 - - + -
329B PHE* 4.0 24.5 - - + -
354B LEU* 4.6 10.8 - - + -
358B VAL* 3.6 19.3 - - + -
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Residues in contact with LEU 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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143B ILE* 3.1 21.3 + - + +
144B GLU* 3.2 11.9 + - + +
146B VAL* 1.3 78.3 - - - +
148B ASP* 1.3 61.8 + - - +
150B LYS* 3.0 9.3 + - + +
151B SER* 2.9 23.0 + - - -
216B VAL* 3.6 48.7 - - + +
217B TYR* 3.6 24.7 + - + +
223B PRO* 4.0 20.9 - - + -
224B LEU 4.5 8.1 - - - +
229B ILE* 4.6 2.2 - - + -
283B ILE* 4.4 7.4 - - + -
284B PHE* 4.6 11.2 - - + -
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Residues in contact with ASP 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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144B GLU* 3.0 13.3 + - + +
145B GLY 3.5 8.7 - - - +
147B LEU* 1.3 76.8 - - - +
149B PHE* 1.3 59.6 + - - +
151B SER* 2.6 27.8 + - - -
152B MET* 3.8 6.4 + - - +
357B HIS* 2.8 28.8 + - + -
361B TYR* 3.9 25.4 + - + -
364B LYS* 4.6 5.1 + - - -
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Residues in contact with PHE 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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145B GLY 3.1 9.7 + - - +
146B VAL* 3.2 10.1 + - - +
148B ASP* 1.3 78.8 - - - +
150B LYS* 1.3 63.0 + - - +
152B MET* 3.2 27.1 + - + +
153B ILE* 3.5 35.1 + - + +
158B LEU* 4.0 17.9 - - + -
173B TYR* 3.8 31.4 - + - -
176B ILE* 4.8 0.2 - - + -
177B LEU* 5.3 0.4 - - + -
353B ALA* 4.1 9.9 - - + -
354B LEU* 3.8 46.2 - - + -
357B HIS* 3.6 34.9 - + + +
358B VAL* 5.2 0.4 - - + -
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Residues in contact with LYS 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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146B VAL* 2.8 14.6 + - + +
147B LEU* 3.0 12.5 + - + +
149B PHE* 1.3 75.8 - - - +
151B SER* 1.3 60.2 + - - +
153B ILE* 2.8 7.1 + - + +
154B ASP* 2.7 60.2 + - - +
177B LEU* 3.6 29.6 - - + -
178B SER* 4.6 1.3 - - - -
194B LEU* 4.3 14.1 - - + -
199B PRO* 6.3 0.8 - - - +
200B PRO 4.9 5.0 + - - -
217B TYR* 2.9 32.2 + - - +
283B ILE* 3.8 33.4 - - + +
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Residues in contact with SER 151 (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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147B LEU 2.9 11.1 + - - -
148B ASP* 2.6 26.1 + - - -
150B LYS* 1.3 76.0 - - - +
152B MET* 1.3 61.3 + - - +
154B ASP* 3.9 7.7 - - - +
155B ASN* 2.8 44.9 + - - +
217B TYR* 5.4 0.9 + - - -
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Residues in contact with MET 152 (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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148B ASP* 4.2 2.9 - - - +
149B PHE* 3.2 19.0 + - + +
150B LYS 3.0 0.8 - - - -
151B SER* 1.3 85.8 + - - +
153B ILE* 1.3 61.3 + - - +
156B GLU* 2.9 23.6 + - - -
157B THR* 2.9 29.6 + - - +
158B LEU* 3.5 35.5 + - + +
159B PRO* 4.1 16.8 - - + -
357B HIS* 3.5 36.1 - - + +
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Residues in contact with ILE 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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149B PHE* 3.5 38.1 + - + +
150B LYS* 2.8 8.4 + - + +
152B MET* 1.3 78.0 - - - +
154B ASP* 1.3 65.7 + - - +
156B GLU* 3.2 3.6 + - - +
158B LEU* 4.1 13.7 - - + -
173B TYR* 3.4 27.1 - - + +
174B TYR* 3.1 55.6 + - + -
176B ILE* 4.7 2.5 - - + -
177B LEU* 3.7 24.9 - - + -
194B LEU* 4.0 16.6 - - + -
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LYS* 2.7 50.2 + - - +
151B SER* 4.0 7.3 - - - +
153B ILE* 1.3 76.9 - - - +
155B ASN* 1.3 66.5 + - - +
156B GLU* 3.2 6.3 + - - +
194B LEU* 3.9 27.7 - - - +
217B TYR* 4.5 0.9 + - - -
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B SER* 2.8 34.6 + - - +
154B ASP* 1.3 80.9 - - - +
156B GLU* 1.3 72.1 + - - +
157B THR* 3.2 24.8 + - + +
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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
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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