Contacts of the helix formed by residues 143 - 172 (chain B) in PDB entry 4D1Q
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 143 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 4.3 0.9 - - - -
141B LEU 3.9 0.2 + - - -
142B PRO* 1.3 76.9 - - - +
144B PRO* 1.3 67.8 - - - +
145B ILE* 3.1 14.0 - - - +
146B THR* 2.8 37.1 + - - +
147B LEU* 3.2 10.7 + - - +
6D G 2.9 41.9 + - - -
7D T 4.8 5.2 - - - -
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Residues in contact with PRO 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.8 35.0 - - + +
110A SER* 4.0 11.0 - - - +
112A VAL* 4.1 1.5 - - + -
113A SER* 3.7 33.9 - - - +
142B PRO 3.9 1.1 - - - +
143B SER* 1.3 87.8 - - - +
145B ILE* 1.3 65.3 + - + +
147B LEU* 2.9 20.1 + - + +
148B SER* 2.9 11.3 + - - -
6C A 5.1 1.1 - - - +
7C C 6.5 0.9 - - + -
7D T 5.9 1.8 - - + -
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 3.1 20.2 - - - +
144B PRO* 1.3 81.7 - - + +
146B THR* 1.3 64.3 + - - +
148B SER* 3.9 8.4 - - - +
149B ARG* 3.0 62.6 + - + +
7C C 4.7 20.4 - - + -
8C A 4.0 20.2 - - - +
9C A 4.2 4.7 - - - +
6D G 4.0 8.1 - - - +
7D T 3.7 27.6 - - + +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.9 21.7 - - + +
142B PRO* 3.3 34.1 - - + -
143B SER* 2.8 19.3 + - - +
145B ILE* 1.3 78.9 - - - +
147B LEU* 1.3 59.7 + - + +
149B ARG* 3.2 18.3 + - - +
150B LYS* 2.9 27.0 + - - +
5D T 3.7 23.4 + - - -
6D G 3.2 13.3 + - - +
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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
----------------------------------------------------------
95A ILE* 4.2 7.6 - - + +
98A CYS* 3.6 11.2 - - + -
99A ALA* 3.3 39.7 - - + +
102A VAL* 4.6 6.5 - - + -
109A PHE* 3.9 25.1 - - + +
112A VAL* 3.3 44.2 - - + -
142B PRO* 4.3 11.2 - - + -
143B SER 3.2 8.0 + - - +
144B PRO* 2.9 6.6 + - + +
146B THR* 1.3 74.0 - - + +
148B SER* 1.3 68.1 + - - +
150B LYS* 2.9 6.4 + - - +
151B VAL* 2.9 25.3 + - - +
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.6 31.8 - - - -
144B PRO 2.9 10.7 + - - -
145B ILE* 3.9 11.9 - - - -
147B LEU* 1.3 76.8 - - - +
149B ARG* 1.3 67.1 + - - +
151B VAL* 3.1 3.3 + - - +
152B THR* 3.1 26.2 + - - -
593B THR* 4.1 8.5 + - - +
7C C 2.9 26.7 + - - -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 3.0 52.5 + - + +
146B THR* 3.4 13.1 + - - +
148B SER* 1.3 79.2 - - - +
150B LYS* 1.3 61.7 + - - +
152B THR* 3.5 7.1 + - - -
153B SER* 3.1 21.5 + - - -
8C A 5.8 0.4 + - - -
9C A 4.4 3.0 + - - +
10C C 5.5 1.6 - - - +
5D T 3.8 31.6 + - - +
6D G 2.8 44.9 + - - -
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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
----------------------------------------------------------
92A LYS* 6.2 3.1 - - - -
95A ILE* 3.3 35.4 - - + -
96A GLU* 4.1 24.2 - - - +
99A ALA* 3.9 19.5 - - + -
146B THR 2.9 14.1 + - - +
147B LEU* 2.9 9.6 + - - +
149B ARG* 1.3 72.2 - - - +
151B VAL* 1.3 55.7 + - - +
153B SER* 2.7 21.1 + - - -
154B ASP* 2.6 70.9 + - - +
157B GLU* 5.2 2.8 + - - -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA* 4.2 16.8 - - + +
102A VAL* 4.9 1.1 - - + -
103A VAL* 3.7 23.1 - - + -
109A PHE* 4.3 12.6 - - + -
147B LEU 2.9 15.5 + - - +
148B SER* 3.5 10.1 - - - +
150B LYS* 1.3 76.1 - - - +
152B THR* 1.3 64.6 + - - +
154B ASP* 4.4 5.2 - - - -
155B ALA* 2.9 25.5 + - - +
593B THR* 5.5 0.9 - - + -
596B SER* 3.8 18.4 - - - -
597B LEU* 3.8 28.0 - - + +
600B LEU* 3.4 9.5 - - + +
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Residues in contact with THR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B SER* 3.1 20.8 + - - -
149B ARG* 3.9 6.6 - - - -
151B VAL* 1.3 76.3 - - - +
153B SER* 1.3 63.2 + - - +
155B ALA* 3.2 14.9 - - - +
156B LYS* 3.3 23.5 + - - +
592B GLN* 4.1 29.2 - - + +
593B THR* 4.4 12.6 + - - +
596B SER* 3.8 18.4 - - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG 3.1 14.7 + - - -
150B LYS* 2.7 26.9 + - - -
152B THR* 1.3 68.6 - - - +
154B ASP* 1.3 69.4 + - - -
155B ALA 3.0 1.6 - - - -
156B LYS* 2.9 21.7 + - - +
157B GLU* 3.0 17.4 + - - +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 5.8 0.7 - - - +
99A ALA* 5.4 2.4 - - - +
100A GLN* 4.3 8.5 + - - +
150B LYS* 2.6 52.6 + - + +
151B VAL* 3.9 5.8 - - - +
153B SER* 1.3 73.9 + - - +
155B ALA* 1.3 63.9 + - - +
157B GLU* 3.5 21.3 - - - +
158B LYS* 3.0 36.3 + - - +
600B LEU* 4.0 11.2 - - + -
604B TYR* 3.3 20.4 + - - -
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL 2.9 13.9 + - - +
152B THR 3.2 11.9 - - - +
154B ASP* 1.3 82.3 - - - +
156B LYS* 1.3 56.6 + - - +
157B GLU 2.8 9.4 + - - -
158B LYS* 3.7 0.3 - - - +
159B LYS* 2.8 36.4 + - - +
596B SER* 3.5 23.1 - - - +
599B PHE* 4.3 6.0 - - + -
600B LEU* 3.5 19.7 - - + +
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B THR* 3.7 24.1 + - - +
153B SER* 2.9 11.5 + - - +
155B ALA* 1.3 78.8 - - - +
157B GLU* 1.3 62.3 + - - +
159B LYS* 4.1 16.4 - - - +
160B ALA* 3.3 21.1 + - - +
592B GLN* 5.2 5.1 + - - -
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LYS* 5.2 2.3 + - - -
153B SER* 3.0 16.0 + - - +
154B ASP* 3.5 26.5 - - - +
155B ALA 2.8 4.0 + - - -
156B LYS* 1.3 71.0 - - - +
158B LYS* 1.3 76.4 + - + +
160B ALA* 3.1 8.5 + - - +
161B LEU* 2.8 28.8 + - + +
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLN* 5.4 4.2 - - - +
154B ASP* 3.1 24.9 - - - +
155B ALA 2.9 4.9 + - - +
157B GLU* 1.3 83.4 + - + +
159B LYS* 1.3 67.4 + - - +
160B ALA 3.0 2.0 - - - -
161B LEU* 3.0 27.0 + - + +
162B ILE* 3.1 18.7 + - - +
599B PHE* 4.1 7.4 - - + -
600B LEU* 4.2 7.4 - - + -
603B PHE* 3.7 40.6 - - + -
604B TYR* 4.1 26.2 + - - -
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA* 2.8 25.3 + - - +
156B LYS* 4.1 25.2 - - - +
158B LYS* 1.3 72.9 - - - +
160B ALA* 1.3 62.5 + - - +
162B ILE* 3.9 0.7 - - - +
163B GLY* 3.5 11.8 + - - -
209B LEU 4.3 2.0 - - - +
212B LYS* 5.5 0.8 - - - +
234B GLN* 3.1 50.9 - - - +
235B PHE* 3.6 33.2 - - + -
595B ASP* 3.6 19.3 + - - +
596B SER* 5.1 1.4 + - - -
599B PHE* 3.3 42.1 - - + -
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LYS 3.3 12.6 + - - +
157B GLU* 3.1 10.6 + - - +
158B LYS 3.0 0.4 - - - -
159B LYS* 1.3 77.6 - - - +
161B LEU* 1.3 67.3 + - - +
163B GLY* 2.9 16.2 + - - -
164B ARG 4.5 0.3 + - - -
234B GLN 4.6 8.2 + - - +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU* 2.8 19.7 + - + +
158B LYS* 3.0 29.1 + - + +
160B ALA* 1.3 73.2 - - - +
162B ILE* 1.3 77.0 + - + +
163B GLY 2.9 5.7 + - - -
164B ARG* 3.7 10.7 + - - +
603B PHE* 5.1 5.8 - - + -
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LYS 3.1 10.9 + - - +
159B LYS 3.9 5.2 - - - +
161B LEU* 1.3 79.2 - - + +
163B GLY* 1.4 55.0 + - - +
164B ARG* 2.7 17.9 + - - -
165B GLU* 2.8 22.0 + - + +
166B ILE* 3.2 36.0 + - + +
207B LEU* 4.3 5.4 - - + -
235B PHE* 4.0 3.4 - - + -
599B PHE* 3.9 26.2 - - + -
603B PHE* 3.2 30.3 - - + -
607B PHE* 3.4 31.6 - - + -
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LYS 3.5 7.5 + - - -
160B ALA 2.9 18.6 + - - -
162B ILE* 1.4 78.1 - - - +
164B ARG* 1.3 56.3 + - - +
166B ILE* 4.2 0.8 - - - +
167B LYS* 3.1 28.9 + - - +
235B PHE* 3.2 31.7 - - - +
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA 4.5 0.2 + - - -
161B LEU 3.7 9.1 + - - +
162B ILE 2.7 5.1 + - - -
163B GLY* 1.3 69.4 - - - +
165B GLU* 1.3 74.8 + - - +
166B ILE 2.9 1.9 + - - -
167B LYS* 3.0 6.2 + - - +
168B SER* 2.9 28.6 + - - -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 2.8 20.1 + - + +
164B ARG* 1.3 83.5 - - - +
166B ILE* 1.3 56.5 + - + +
168B SER* 3.2 8.0 + - - -
169B ALA* 3.1 27.1 + - + +
198B TYR* 2.8 31.0 + - + +
200B GLU* 3.6 27.0 - - - +
205B ARG* 3.6 18.9 + - - -
607B PHE* 4.1 14.9 - - + -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.2 31.5 + - + +
163B GLY 4.2 3.4 - - - +
164B ARG 3.0 0.8 - - - -
165B GLU* 1.3 74.7 - - + +
167B LYS* 1.3 67.4 + - - +
168B SER 3.0 1.6 - - - -
169B ALA* 3.4 5.8 + - - +
170B VAL* 3.0 27.3 + - + +
196B LEU* 4.1 17.0 - - + -
198B TYR* 4.2 20.2 - - + +
207B LEU* 4.5 5.4 - - + -
209B LEU* 4.2 12.6 - - + -
232B PHE* 5.4 4.3 - - + -
235B PHE* 3.3 37.0 - - + -
237B VAL* 3.9 19.5 - - + -
607B PHE* 5.9 0.4 - - + -
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLY 3.1 19.6 + - - +
164B ARG* 3.0 7.1 + - - +
166B ILE* 1.3 78.0 - - - +
168B SER* 1.3 66.2 - - - +
170B VAL* 3.5 2.8 + - - +
171B GLU* 3.0 54.7 + - + +
235B PHE 4.6 2.0 - - - +
236B ASN* 3.0 33.1 + - + +
237B VAL* 4.1 17.7 - - + +
238B GLU* 4.9 4.8 - - - +
239B ASP 6.1 0.4 - - - +
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 2.9 14.4 + - - -
165B GLU* 3.2 16.0 + - - +
166B ILE 3.0 0.2 - - - -
167B LYS* 1.3 72.9 - - - +
169B ALA* 1.3 59.0 + - - +
171B GLU* 2.5 36.7 + - - +
172B LYS* 2.8 33.3 + - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 3.1 12.2 + - + +
166B ILE 3.8 2.9 - - - +
168B SER* 1.3 81.5 + - - +
170B VAL* 1.3 62.3 + - - +
172B LYS* 3.4 12.5 + - - +
174B GLY* 3.2 26.6 + - - +
175B ALA* 4.0 2.9 - - + -
198B TYR* 3.6 43.3 - - + -
199B HIS 6.0 0.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 3.0 29.2 + - + +
167B LYS 3.6 4.9 - - - +
168B SER 2.7 2.6 + - - -
169B ALA* 1.3 75.7 - - - +
171B GLU* 1.3 68.1 + - + +
173B ASP* 3.5 6.6 + - - -
174B GLY 4.5 0.2 + - - -
175B ALA* 3.9 18.4 - - + -
196B LEU* 5.0 5.2 - - + -
232B PHE* 5.1 1.8 - - + -
237B VAL* 4.4 17.9 - - + -
239B ASP 4.1 16.2 - - - +
242B SER* 3.5 23.5 - - - +
243B ILE* 4.0 30.7 - - + -
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LYS* 3.0 54.5 + - + +
168B SER* 2.5 15.4 + - - +
170B VAL* 1.3 73.7 - - + +
172B LYS* 1.3 55.7 + - + +
173B ASP* 2.8 24.2 + - - +
242B SER* 5.0 3.4 + - - -
461B LEU* 4.8 3.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 2.8 36.9 + - - +
169B ALA* 3.8 9.4 - - - +
170B VAL 3.3 0.2 - - - -
171B GLU* 1.3 76.4 - - - +
173B ASP* 1.3 58.6 + - - +
174B GLY* 3.0 12.9 + - - +
461B LEU* 3.8 22.9 - - + +
464B ILE* 4.7 31.5 - - + +
560B SER* 5.7 0.7 - - - -
----------------------------------------------------------
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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