Contacts of the helix formed by residues 159 - 183 (chain B) in PDB entry 2PY5
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 THR 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LYS* 4.2 9.2 - - - +
156B TYR* 3.6 13.7 - - + +
157B LYS 4.3 3.8 - - - +
158B ILE* 1.3 74.8 - - - +
160B PRO* 1.3 75.4 - - + +
161B GLU* 3.5 14.0 + - - +
162B GLU* 2.7 45.2 + - - +
163B TYR* 2.9 22.6 + - - +
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Residues in contact with PRO 160 (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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158B ILE 4.5 0.9 - - - +
159B THR* 1.3 87.1 - - + +
161B GLU* 1.3 65.5 + - - +
163B TYR* 3.3 9.1 + - + +
164B ALA* 2.8 35.6 + - - +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASP 5.7 0.2 - - - +
159B THR* 3.2 20.3 - - - +
160B PRO* 1.3 91.8 - - - +
162B GLU* 1.3 57.6 + - + +
164B ALA* 3.4 7.7 + - - +
165B TYR* 3.0 27.4 + - - +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TRP* 3.9 16.8 - - + -
146B ILE* 4.0 21.3 - - + -
150B LYS* 3.6 7.3 + - - +
152B ARG* 3.0 19.1 + - - -
156B TYR* 2.7 32.5 + - - -
158B ILE* 3.5 12.1 - - + +
159B THR* 2.7 43.0 + - - +
161B GLU* 1.3 73.7 - - + +
163B TYR* 1.3 59.7 + - - +
165B TYR* 3.2 7.5 + - - +
166B ILE* 2.9 36.3 + - + +
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Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 3.3 33.2 + + - -
39B LYS* 5.5 0.3 - - - -
40B ILE* 3.4 52.1 + - + +
158B ILE* 3.6 13.6 - - + +
159B THR 2.9 13.1 + - - +
160B PRO* 3.4 13.0 - - + +
162B GLU* 1.3 77.1 - - - +
164B ALA* 1.3 58.4 + - - +
166B ILE* 3.4 3.3 + - - -
167B LYS* 2.9 39.2 + - + +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PRO 2.8 16.9 + - - +
161B GLU* 3.6 8.3 - - - +
162B GLU 3.3 0.2 - - - -
163B TYR* 1.3 79.0 - - - +
165B TYR* 1.3 56.3 + - - +
167B LYS* 3.5 5.8 + - - +
168B ASN* 2.9 38.9 + - - +
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Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 3.3 25.6 - - - -
143B LYS* 3.0 27.2 + - + -
144B GLY* 3.6 41.5 - - - -
145B ASP* 3.7 20.4 + - - +
146B ILE* 3.4 40.7 - - + +
148B TYR* 4.1 9.7 + - - -
161B GLU 3.0 14.3 + - - +
162B GLU* 3.5 8.5 - - - +
164B ALA* 1.3 75.8 - - - +
166B ILE* 1.3 62.1 + - + +
168B ASN* 3.4 6.9 + - + +
169B ASP* 3.0 43.5 + - - +
7L T 3.9 7.3 + - - -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 5.2 5.2 - - + +
14B GLU* 3.7 27.4 - - + +
25B TRP* 4.7 3.6 - - + -
26B ALA* 3.5 31.6 - - + -
27B TYR 4.5 0.7 - - - -
28B GLY* 4.2 19.1 - - - +
40B ILE* 3.8 30.3 - - + -
146B ILE* 5.4 0.4 - - + -
158B ILE* 4.4 6.3 - - + -
162B GLU 2.9 26.4 + - - +
163B TYR 3.7 3.1 - - - +
165B TYR* 1.3 78.4 - - + +
167B LYS* 1.3 65.5 + - - +
169B ASP* 3.2 7.1 + - - +
170B ILE* 3.1 27.5 + - + +
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Residues in contact with LYS 167 (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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30B MET* 4.1 11.7 - - + -
35B HIS 5.8 0.4 - - - -
38B TYR* 3.1 49.2 + - + +
40B ILE* 3.6 11.8 - - + +
163B TYR* 2.9 26.0 + - + +
164B ALA* 3.8 6.3 - - - +
166B ILE* 1.3 76.4 - - - +
168B ASN* 1.3 61.9 + - - +
170B ILE* 3.4 7.3 - - - +
171B GLN* 3.0 47.9 + - - +
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Residues in contact with ASN 168 (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 VAL* 3.9 27.6 - - + +
142B LEU 3.3 25.9 + - - +
143B LYS* 5.6 1.3 - - - -
144B GLY 5.3 2.7 - - - +
164B ALA* 2.9 23.4 + - - +
165B TYR* 3.6 7.7 - - + +
167B LYS* 1.3 82.2 - - - +
169B ASP* 1.3 58.5 + - - +
171B GLN* 3.1 6.7 + - - +
172B ILE* 2.8 38.0 + - + +
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 5.1 7.4 - - + -
14B GLU* 4.2 2.7 - - - +
130B VAL* 3.9 12.9 - - + +
143B LYS* 2.9 48.6 + - - +
165B TYR* 3.0 33.6 + - - +
166B ILE* 3.5 10.5 - - - +
168B ASN* 1.3 78.7 - - - +
170B ILE* 1.3 65.3 + - + +
172B ILE* 3.4 13.3 + - - +
173B ILE* 3.4 17.7 + - - +
7L T 3.7 9.7 + - - -
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER* 2.8 33.2 + - - +
11B CYS 3.8 6.3 - - - +
12B ALA* 3.6 39.3 - - + +
28B GLY* 3.9 10.8 - - - +
29B TYR 3.6 36.8 - - - +
30B MET* 3.7 15.3 - - + -
38B TYR* 4.7 2.5 - - + -
40B ILE* 4.7 6.5 - - + -
166B ILE* 3.1 10.3 + - + +
167B LYS* 3.4 18.6 - - - +
169B ASP* 1.3 75.0 - - - +
171B GLN* 1.3 59.7 + - - +
173B ILE* 4.9 0.2 - - - -
174B ALA* 2.9 18.7 + - - +
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Residues in contact with GLN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B MET* 3.6 32.4 - - - +
35B HIS* 4.9 12.3 + - - +
140B THR* 3.6 9.7 + - - -
141B VAL* 4.3 15.9 - - + +
167B LYS* 3.0 34.5 + - - +
168B ASN* 3.1 7.7 + - - +
170B ILE* 1.3 75.8 - - - +
172B ILE* 1.3 59.4 + - - +
175B GLU* 2.8 57.0 + - + +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.8 37.9 - - + +
133B ILE* 4.1 8.3 - - + -
134B ALA* 3.7 22.4 - - + +
139B LEU* 3.3 27.7 - - + +
141B VAL* 3.7 22.0 - - + +
142B LEU 3.9 5.6 - - - -
143B LYS* 3.9 22.9 - - + +
168B ASN 2.8 24.5 + - - +
169B ASP* 3.6 5.2 - - - +
171B GLN* 1.3 77.2 - - - +
173B ILE* 1.3 60.4 + - + +
175B GLU* 4.7 0.2 - - - -
176B ALA* 3.0 25.5 + - - +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER* 3.4 20.2 - - - +
59B TYR* 5.1 2.2 - - + +
61B HIS* 3.5 31.9 - - + +
122B SER* 3.7 16.2 - - - +
126B LEU* 4.5 5.4 - - + -
130B VAL* 4.1 16.8 - - + -
133B ILE* 3.7 23.8 - - + -
169B ASP 3.4 11.9 + - - +
170B ILE* 4.0 0.9 - - - +
171B GLN 3.3 0.4 - - - -
172B ILE* 1.3 77.9 - - + +
174B ALA* 1.3 60.2 + - - +
176B ALA* 3.9 1.7 - - - +
177B LEU* 2.9 52.3 + - + +
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Residues in contact with ALA 174 (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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10B SER* 3.6 15.3 + - - -
30B MET* 4.1 7.9 - - + -
32B ILE* 3.7 17.8 - - - +
35B HIS* 3.5 25.6 + - + +
170B ILE 2.9 19.4 + - - +
171B GLN* 3.6 8.7 - - - +
173B ILE* 1.3 76.5 - - - +
175B GLU* 1.3 60.7 + - - +
178B LEU* 3.1 26.5 + - - +
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B HIS* 3.6 26.0 + - + +
139B LEU* 3.5 19.6 - - + +
140B THR* 2.6 54.7 + - - +
141B VAL* 4.7 2.9 - - - -
171B GLN* 2.8 44.0 + - + +
172B ILE 3.8 3.4 - - - +
174B ALA* 1.3 72.0 - - - +
176B ALA* 1.3 63.5 + - - +
178B LEU* 3.5 2.1 + - - +
179B ILE* 3.2 32.0 + - + +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.6 25.5 - - + +
133B ILE* 3.7 20.2 - - + -
137B PHE* 4.0 20.3 - - + -
139B LEU* 4.1 4.2 - - + +
172B ILE 3.0 17.2 + - - +
173B ILE* 3.9 1.8 - - - +
175B GLU* 1.3 73.1 - - - +
177B LEU* 1.3 65.3 - - - +
179B ILE* 3.4 6.3 + - - +
180B GLN* 3.0 22.5 + - - +
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Residues in contact with LEU 177 (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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32B ILE* 3.7 31.0 - - + -
59B TYR* 3.9 22.2 - - + -
122B SER* 4.2 4.5 - - - -
125B LYS* 3.9 22.7 - - + -
126B LEU* 3.7 16.4 - - + -
173B ILE* 2.9 37.4 + - + +
174B ALA 4.2 2.0 - - - +
176B ALA* 1.3 73.3 - - - +
178B LEU* 1.3 56.5 + - - +
180B GLN* 3.1 22.7 + - - +
181B PHE* 2.7 51.1 + - + -
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Residues in contact with LEU 178 (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 MET* 5.9 0.9 - - + -
32B ILE* 3.4 29.3 - - + +
33B GLU* 4.4 17.9 - - + -
35B HIS* 3.8 8.3 - - + +
174B ALA 3.1 19.6 + - - +
175B GLU 3.8 4.0 - - - +
176B ALA 3.3 0.2 - - - -
177B LEU* 1.3 76.5 - - - +
179B ILE* 1.3 58.1 + - + +
181B PHE* 3.3 6.5 + - + +
182B LYS* 2.8 59.4 + - + +
9004B EDO 3.6 38.8 - - - +
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Residues in contact with ILE 179 (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 PHE* 5.7 0.4 - - + -
139B LEU* 4.1 16.8 - - + -
175B GLU* 3.2 18.4 + - + +
176B ALA* 3.7 7.2 - - - +
178B LEU* 1.3 76.7 - - + +
180B GLN* 1.3 63.0 + - - +
182B LYS* 3.3 11.6 + - + +
183B GLN* 3.1 25.0 + - + +
377B ALA* 3.6 31.2 - - + -
378B ILE* 4.3 15.9 - - + -
381B LEU* 3.9 16.8 - - + -
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Residues in contact with GLN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 3.0 44.6 + - - +
126B LEU* 3.4 18.0 - - - +
176B ALA 3.0 12.7 + - - +
177B LEU* 3.4 26.0 - - - +
179B ILE* 1.3 76.7 - - - +
181B PHE* 1.3 63.3 + - + +
183B GLN* 3.0 12.5 + - - +
185B LEU* 3.2 40.9 + - + +
190B ALA* 5.4 0.8 - - - +
193B ASP* 4.1 5.9 + - - -
381B LEU* 3.7 32.1 - - + +
384B LEU* 3.9 5.9 - - - +
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B MET* 4.3 32.8 - - + -
32B ILE* 5.3 2.5 - - + -
59B TYR* 3.6 27.8 - + - -
125B LYS* 4.5 12.3 - - + -
177B LEU* 2.7 55.7 + - + +
178B LEU* 3.9 9.4 - - + +
180B GLN* 1.3 72.9 - - + +
182B LYS* 1.3 58.0 + - + +
184B GLY* 3.0 19.2 + - - -
185B LEU 4.1 6.1 - - - +
186B ASP* 3.4 45.2 - - + +
187B ARG 5.2 0.4 - - - -
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 2.8 47.7 + - + +
179B ILE* 3.6 11.4 - - + +
181B PHE* 1.3 76.0 - - + +
183B GLN* 1.3 62.1 + - - +
184B GLY 3.2 1.2 + - - -
9004B EDO 3.2 25.6 + - - -
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Residues in contact with GLN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 3.1 15.7 + - + +
180B GLN 3.0 10.1 + - - +
182B LYS* 1.3 79.9 - - - +
184B GLY* 1.3 59.5 + - - +
185B LEU* 3.3 22.7 + - + +
367B TRP* 4.7 20.6 - - + -
370B ILE* 5.2 5.1 - - - +
378B ILE* 3.7 40.3 - - + +
381B LEU* 4.1 17.3 - - + -
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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