Contacts of the helix formed by residues 159 - 183 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LYS* 4.7 7.2 - - - +
156A TYR* 3.7 20.4 - - + +
157A LYS* 4.2 4.3 - - - +
158A ILE* 1.3 75.0 - - - +
160A PRO* 1.3 75.5 - - + +
161A GLU* 3.5 13.3 + - - +
162A GLU* 2.9 37.1 + - - +
163A TYR* 2.9 22.8 + - - +
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Residues in contact with PRO 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ILE 4.5 1.3 - - - +
159A THR* 1.3 88.9 - - - +
161A GLU* 1.3 68.8 + - - +
163A TYR* 3.5 8.1 + - + +
164A ALA* 3.0 29.6 + - - +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A THR* 3.2 20.0 + - - +
160A PRO* 1.3 82.5 - - + +
162A GLU* 1.3 65.2 + - + +
164A ALA* 3.4 7.6 + - - +
165A TYR* 3.1 36.5 + - + -
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TRP* 3.7 24.5 - - + -
146A ILE* 4.0 14.3 - - + +
147A ASP 6.2 0.2 - - - +
150A LYS* 4.4 3.6 + - - +
152A ARG* 3.0 21.7 + - - +
156A TYR* 2.7 35.2 + - - -
158A ILE* 3.5 11.3 - - + -
159A THR* 2.9 34.3 + - - +
161A GLU* 1.3 75.7 - - + +
163A TYR* 1.3 63.5 + - - +
165A TYR* 3.2 5.4 + - + +
166A ILE* 3.0 30.5 + - - +
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Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.0 35.8 + + - -
39A LYS* 5.6 0.2 - - - -
40A ILE* 3.5 49.2 + - + +
158A ILE* 3.7 14.5 - - + +
159A THR 2.9 18.6 + - - +
160A PRO* 3.5 9.9 - - + +
162A GLU* 1.3 75.5 - - - +
164A ALA* 1.3 61.0 + - - +
166A ILE* 3.3 5.9 + - - -
167A LYS* 2.9 34.1 + - + +
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 3.5 18.5 - - + +
160A PRO 3.0 17.7 + - - +
161A GLU* 3.6 7.6 - - - +
162A GLU 3.3 0.2 - - - -
163A TYR* 1.3 80.3 - - - +
165A TYR* 1.3 56.5 + - - +
167A LYS* 3.8 6.6 - - - +
168A ASN* 2.9 30.1 + - - +
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 5.5 0.2 - - - -
142A LEU* 4.0 25.6 - - + -
143A LYS 2.6 24.5 + - - -
144A GLY* 3.4 27.6 - - - -
145A ASP* 3.6 21.3 + - - -
146A ILE* 3.7 29.2 - - + -
161A GLU* 3.1 31.0 + - + -
162A GLU* 3.2 7.4 + - + +
164A ALA* 1.3 77.7 - - - +
166A ILE* 1.3 56.9 + - - +
168A ASN* 3.3 3.4 + - - +
169A ASP* 2.9 40.2 + - - +
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 5.0 7.9 - - + +
13A PHE 6.4 0.2 - - - -
14A GLU* 3.7 29.8 - - + +
25A TRP* 4.6 1.8 - - + -
26A ALA* 3.5 30.3 - - + -
27A TYR* 4.4 1.1 - - - +
28A GLY* 4.1 19.3 - - - +
40A ILE* 4.0 31.2 - - + -
146A ILE* 4.2 4.5 - - + -
158A ILE* 4.5 6.5 - - + -
162A GLU 3.0 22.6 + - - +
163A TYR 3.7 3.6 - - - +
165A TYR* 1.3 75.1 - - - +
167A LYS* 1.3 63.5 + - - +
169A ASP* 3.3 6.5 + - - +
170A ILE* 3.1 27.3 + - + +
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Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A MET* 4.2 11.2 - - + -
35A HIS 5.6 0.7 - - - -
38A TYR* 3.2 53.4 + - + +
40A ILE* 3.7 10.5 - - + +
163A TYR* 2.9 24.4 + - + +
164A ALA* 3.8 7.4 - - - +
166A ILE* 1.3 76.3 - - - +
168A ASN* 1.3 57.5 + - - +
170A ILE* 3.4 7.6 - - - +
171A GLN* 3.0 47.8 + - - +
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 3.0 31.5 + - - +
141A VAL* 3.4 8.2 - - - +
142A LEU* 2.9 42.3 + - + +
164A ALA 2.9 17.9 + - - +
165A TYR* 3.6 6.8 - - - +
166A ILE 3.2 0.2 - - - -
167A LYS* 1.3 74.8 - - - +
169A ASP* 1.3 62.9 + - - +
171A GLN* 3.2 6.8 + - - +
172A ILE* 2.9 44.6 + - - +
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Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 5.0 8.1 - - + -
14A GLU* 4.0 11.8 - - - +
130A VAL* 4.3 18.8 - - + +
131A LYS* 5.9 2.6 - - - -
141A VAL* 6.2 0.2 - - - +
165A TYR* 2.9 25.3 + - - +
166A ILE* 3.6 6.7 - - - +
168A ASN* 1.3 83.3 - - - +
170A ILE* 1.3 65.6 + - + +
171A GLN 3.4 0.2 + - - -
172A ILE* 3.5 8.8 + - - +
173A ILE* 3.5 23.6 + - - +
7J T 3.9 17.2 + - - -
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Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 2.8 33.9 + - - +
11A CYS 3.8 5.8 - - - +
12A ALA* 3.6 40.2 - - + +
28A GLY* 3.8 12.6 - - - +
29A TYR 3.7 35.9 - - - +
30A MET* 3.8 15.5 - - + -
38A TYR* 4.9 2.9 - - + -
40A ILE* 4.7 6.3 - - + -
166A ILE* 3.1 13.7 + - + +
167A LYS* 3.4 18.2 - - - +
169A ASP* 1.3 77.1 - - - +
171A GLN* 1.3 59.5 + - - +
173A ILE* 3.6 0.8 + - - -
174A ALA* 2.9 15.2 + - - +
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Residues in contact with GLN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A MET* 3.6 34.3 - - - +
35A HIS* 4.6 10.6 + - - +
167A LYS* 3.0 33.6 + - - +
168A ASN* 3.2 8.0 + - - +
170A ILE* 1.3 74.1 - - - +
172A ILE* 1.3 61.1 + - - +
174A ALA* 3.7 0.6 - - - +
175A GLU* 2.8 57.5 + - + +
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Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 3.7 38.4 - - + +
133A ILE* 4.1 10.3 - - + -
134A ALA* 3.8 28.9 - - + +
139A LEU* 3.5 14.1 - - + +
140A THR 3.5 20.6 - - - +
141A VAL* 4.0 9.2 - - + -
168A ASN* 2.9 43.7 + - - +
169A ASP* 3.8 6.3 - - - +
170A ILE 3.4 0.2 - - - -
171A GLN* 1.3 76.6 - - - +
173A ILE* 1.3 60.1 + - + +
175A GLU* 4.5 2.5 - - - +
176A ALA* 3.0 25.6 + - - +
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 3.5 18.4 - - - +
59A TYR* 5.1 3.4 - - + +
61A HIS* 3.6 31.4 - - + +
122A SER* 3.7 16.2 - - - +
126A LEU* 4.6 4.9 - - + -
130A VAL* 4.0 17.9 - - + -
133A ILE* 3.7 24.2 - - + -
169A ASP 3.5 12.3 + - - +
170A ILE* 4.1 0.9 - - - +
171A GLN 3.3 0.4 - - - -
172A ILE* 1.3 77.2 - - + +
174A ALA* 1.3 61.1 + - - +
176A ALA* 4.0 1.5 - - - +
177A LEU* 2.9 50.5 + - + +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 3.6 16.0 + - - -
30A MET* 4.2 7.2 - - + -
32A ILE* 3.6 18.1 - - - +
35A HIS* 3.6 25.8 + - + +
170A ILE 2.9 19.5 + - - +
171A GLN* 3.7 8.5 - - - +
173A ILE* 1.3 76.2 - - - +
175A GLU* 1.3 56.9 + - - +
178A LEU* 3.0 30.7 + - - +
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A HIS* 3.5 26.8 + - + +
139A LEU* 3.5 39.6 - - + +
140A THR* 4.4 9.0 + - - +
171A GLN* 2.8 49.4 + - + +
172A ILE* 3.7 5.9 - - - +
174A ALA* 1.3 73.0 - - - +
176A ALA* 1.3 62.0 + - - +
178A LEU* 3.9 2.4 - - - +
179A ILE* 3.2 31.0 + - + +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.6 17.9 - - + +
133A ILE* 3.6 27.1 - - + -
137A PHE* 3.9 21.1 - - + -
139A LEU* 3.9 5.8 - - + +
172A ILE 3.0 17.5 + - - +
173A ILE* 4.0 1.6 - - - +
175A GLU* 1.3 75.5 - - - +
177A LEU* 1.3 64.8 + - - +
179A ILE* 3.4 5.3 + - - +
180A GLN* 3.0 22.2 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.8 24.5 - - + -
59A TYR* 3.8 22.7 - - + -
122A SER* 4.1 4.0 - - - -
125A LYS* 3.9 17.5 - - + -
126A LEU* 3.7 13.5 - - + -
173A ILE* 2.9 40.7 + - + +
174A ALA 4.1 2.0 - - - +
176A ALA* 1.3 75.7 - - - +
178A LEU* 1.3 58.4 + - - +
180A GLN* 3.2 21.9 + - - +
181A PHE* 2.8 56.7 + - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET* 5.2 2.7 - - + -
32A ILE* 3.4 32.0 - - + +
33A GLU* 4.5 24.0 - - + +
35A HIS* 4.1 12.1 - - + +
174A ALA 3.0 20.0 + - - +
175A GLU* 3.9 4.0 - - - +
176A ALA 3.3 0.2 - - - -
177A LEU* 1.3 76.7 - - - +
179A ILE* 1.3 56.9 + - + +
181A PHE* 3.3 7.9 + - + -
182A LYS* 2.8 71.7 + - + +
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 4.7 1.1 - - + +
139A LEU* 4.4 17.3 - - + -
175A GLU* 3.2 22.3 + - + +
176A ALA* 3.7 9.0 - - - +
177A LEU 3.3 0.2 - - - -
178A LEU* 1.3 75.5 - - + +
180A GLN* 1.3 64.0 + - - +
182A LYS* 3.3 6.9 + - + -
183A GLN* 3.0 39.3 + - - +
377A ALA* 3.8 34.8 - - + -
378A ILE* 4.5 7.4 - - + -
381A LEU* 4.0 13.0 - - + -
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LYS* 3.0 56.3 + - - +
126A LEU* 3.6 14.8 - - + +
176A ALA 3.0 12.3 + - - +
177A LEU* 3.2 17.4 + - - +
179A ILE* 1.3 76.1 - - - +
181A PHE* 1.3 63.2 + - + +
183A GLN* 3.1 14.4 + - - +
185A LEU* 3.2 39.0 + - + +
190A ALA* 5.3 0.8 - - - +
193A ASP* 4.1 6.5 + - - -
381A LEU* 3.8 32.0 - - + +
384A LEU* 3.9 6.5 - - - +
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Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET* 3.4 41.1 - - + -
32A ILE* 4.5 10.8 - - + -
59A TYR* 3.7 28.0 - + - -
125A LYS* 4.1 17.9 - - + -
177A LEU* 2.8 46.4 + - + +
178A LEU* 3.8 8.1 - - + +
180A GLN* 1.3 72.9 - - + +
182A LYS* 1.3 58.1 + - - +
184A GLY* 2.9 21.5 + - - -
185A LEU 3.6 19.9 + - - +
186A ASP* 3.8 25.3 - - + +
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 2.8 54.7 + - + +
179A ILE* 3.7 10.3 - - + +
180A GLN 3.3 0.2 - - - -
181A PHE* 1.3 76.5 - - + +
183A GLN* 1.3 69.0 + - - +
184A GLY 3.2 1.0 + - - -
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ILE* 3.0 33.4 + - - +
180A GLN 3.1 8.8 + - - +
182A LYS* 1.3 86.8 + - - +
184A GLY* 1.3 57.8 + - - +
185A LEU* 3.4 21.3 + - + +
367A TRP* 5.4 7.7 - - + -
378A ILE* 3.9 31.7 - - + +
381A LEU* 3.5 22.0 - - + -
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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