Contacts of the helix formed by residues 136 - 163 (chain B) in PDB entry 1UPX
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 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.5 2.6 - - + +
135B THR* 1.3 83.0 + - - +
137B ASP* 1.3 59.2 + - - +
138B ASP* 3.1 14.2 + - - +
139B VAL* 3.0 44.0 + - + +
140B ARG* 2.9 32.2 + - - +
188B VAL* 4.8 2.1 - - - +
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B THR 3.5 5.0 + - - +
136B ASP* 1.3 75.3 + - - +
138B ASP* 1.3 64.8 + - - +
140B ARG* 2.9 35.8 + - - +
141B SER* 3.0 27.4 + - - -
516B SER* 3.8 10.9 - - - -
517B PRO* 6.0 1.6 - - + -
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP* 3.1 9.4 + - - +
137B ASP* 1.3 77.9 - - - +
139B VAL* 1.3 65.9 + - - +
141B SER* 3.3 1.6 + - - -
142B LEU* 3.0 30.9 + - - +
188B VAL* 3.9 22.2 - - + +
516B SER* 2.8 25.2 + - - -
518B ASN* 2.7 41.7 + - - +
519B VAL* 4.3 7.9 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.7 7.9 - - + -
136B ASP* 3.0 32.2 + - + +
138B ASP* 1.3 75.0 - - - +
140B ARG* 1.3 57.5 + - - +
142B LEU* 4.1 0.6 - - - +
143B ARG* 2.9 62.3 + - - +
186B LEU 4.8 10.3 - - - +
188B VAL* 4.3 13.7 - - + +
191B LEU* 3.9 23.8 - - + -
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 4.1 10.5 + - - +
131B VAL* 3.1 37.8 - - - +
132B MET* 3.9 28.0 - - - +
134B THR* 3.0 35.1 + - + +
135B THR* 3.2 11.9 + - - +
136B ASP 2.9 20.1 + - - +
137B ASP* 2.9 40.1 + - - +
139B VAL* 1.3 77.5 - - - +
141B SER* 1.3 62.8 + - - +
144B TRP* 3.1 38.8 + - + +
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 4.4 5.4 - - - -
137B ASP 3.0 18.1 + - - -
138B ASP 3.6 4.9 - - - -
139B VAL 3.3 0.2 - - - -
140B ARG* 1.3 77.0 - - - +
142B LEU* 1.3 56.6 + - - +
144B TRP* 3.8 0.7 - - - +
145B LEU* 2.9 29.7 + - - +
514B PHE 2.6 28.8 + - - +
515B LEU* 3.4 4.0 - - - +
516B SER* 3.0 27.8 + - - -
519B VAL* 3.6 11.9 - - - +
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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
----------------------------------------------------------
138B ASP 3.0 22.1 + - - +
139B VAL 4.1 1.6 - - - +
141B SER* 1.3 72.6 - - - +
143B ARG* 1.3 66.8 + - - +
145B LEU* 3.7 9.0 - - + +
146B ILE* 2.9 31.8 + - + +
188B VAL* 3.8 33.0 - - + +
191B LEU* 3.8 31.0 - - + +
192B VAL* 4.1 16.4 - - + -
195B THR* 3.7 21.1 - - + +
519B VAL* 3.7 30.5 - - + -
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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
----------------------------------------------------------
42B LYS* 5.6 0.9 - - - +
134B THR* 2.9 35.5 + - - +
139B VAL* 2.9 39.7 + - + +
140B ARG 3.8 3.4 - - - +
142B LEU* 1.3 76.9 - - - +
144B TRP* 1.3 67.2 + - + +
146B ILE* 3.7 4.5 - - - +
147B THR* 2.8 32.1 + - - +
180B LYS 4.9 0.8 + - - -
181B THR* 2.9 46.1 + - - +
182B LEU* 3.8 5.2 - - - +
183B ASP 3.3 26.1 + - - -
184B ASP* 2.8 30.9 + - - +
191B LEU* 4.7 10.3 - - + +
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Residues in contact with TRP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.8 13.9 - - + +
35B ASP* 5.4 7.4 - - - -
38B ILE* 4.1 17.5 - - + -
42B LYS* 3.7 20.0 - - - -
129B VAL 4.8 6.3 - - - -
130B GLY* 4.0 8.4 + - - -
131B VAL* 3.5 49.6 + - + +
134B THR* 4.6 6.3 + - - -
140B ARG* 3.1 39.6 + - + +
141B SER 4.2 0.7 - - - +
143B ARG* 1.3 81.9 - - + +
145B LEU* 1.3 61.3 + - - +
147B THR* 3.8 24.2 - - + -
148B PHE* 2.8 71.6 + + + -
151B LYS* 5.6 1.8 - - - -
514B PHE* 5.0 0.7 - - + -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER 2.9 19.1 + - - +
142B LEU* 3.7 14.8 - - + +
144B TRP* 1.3 76.6 - - - +
146B ILE* 1.3 57.1 + - - +
148B PHE* 3.8 1.6 - - - +
149B GLY* 3.0 24.6 + - - -
195B THR* 3.7 32.8 - - + +
491B VAL* 4.1 14.6 - - + -
494B LEU* 6.0 3.6 - - + -
495B LEU* 4.3 14.9 - - + +
514B PHE* 3.7 33.3 - - + -
515B LEU* 4.2 20.2 - - + -
519B VAL* 4.8 2.5 - - + -
523B LEU* 4.7 11.2 - - + -
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU 2.9 23.5 + - - +
143B ARG* 3.7 4.0 - - - +
145B LEU* 1.3 72.1 - - - +
147B THR* 1.3 61.4 + - - +
149B GLY* 3.2 2.6 + - - -
150B LEU* 2.8 46.2 + - + +
177B ALA* 4.7 1.6 - - + -
181B THR* 3.9 13.5 - - + -
191B LEU* 3.6 34.3 - - + +
194B LEU* 3.9 20.0 - - + -
195B THR* 3.4 33.9 - - - +
198B THR* 3.8 19.0 - - - +
495B LEU* 5.3 1.3 - - - -
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Residues in contact with THR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.3 7.9 - - + -
42B LYS* 3.1 33.0 + - - +
70B LEU* 5.1 1.1 - - + +
143B ARG 2.8 22.9 + - - -
144B TRP* 3.6 31.1 - - + -
146B ILE* 1.3 76.0 - - - +
148B PHE* 1.3 57.3 + - + +
150B LEU* 3.2 12.6 + - - +
151B LYS* 3.0 42.3 + - + +
178B LEU* 5.0 6.5 - - + -
181B THR* 4.1 4.2 - - - +
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B CYS* 6.2 0.2 - - - -
7B TYR* 4.0 12.6 - + - -
8B GLN* 3.4 42.6 - - + -
131B VAL* 5.2 1.8 - - + -
144B TRP* 2.8 59.4 + + + +
145B LEU 3.8 3.1 - - - +
147B THR* 1.3 76.1 - - - +
149B GLY* 1.3 63.8 + - - +
151B LYS* 3.2 19.5 + - - -
152B GLY 3.2 9.9 + - - -
488B GLN* 3.4 26.4 - - + +
491B VAL* 4.3 12.6 - - + -
514B PHE* 3.5 43.1 - + - -
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Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU 3.0 15.3 + - - -
146B ILE 3.2 3.8 + - - -
148B PHE* 1.3 75.4 - - - +
150B LEU* 1.3 56.7 + - - +
152B GLY 3.2 2.3 + - - -
153B MET* 2.9 23.6 + - - +
198B THR* 4.3 2.0 - - - -
491B VAL* 3.8 14.2 - - - +
492B ILE* 3.4 23.0 - - - +
495B LEU* 4.2 14.1 - - - -
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.9 14.4 - - + +
146B ILE* 2.8 30.8 + - + +
147B THR* 3.2 9.6 + - - +
149B GLY* 1.3 73.0 - - - +
151B LYS* 1.3 60.3 + - - +
153B MET* 3.6 16.1 - - + +
154B ALA* 2.8 30.5 + - - +
173B PHE* 4.0 18.2 - - + -
174B MET* 4.1 17.2 - - + +
177B ALA* 3.7 33.0 - - + -
178B LEU* 3.8 30.1 - - + +
181B THR* 5.0 0.9 - - + -
198B THR* 4.1 4.2 - - + +
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Residues in contact with LYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 2.8 30.6 + - - +
34B GLN* 5.3 0.2 + - - -
38B ILE* 4.1 15.2 - - - +
70B LEU* 3.9 27.9 - - + +
71B PHE* 5.1 0.3 - - - -
73B THR* 3.0 36.1 + - - +
74B ILE* 3.5 30.6 - - + +
144B TRP* 5.6 1.8 - - - -
147B THR* 3.0 24.3 + - - +
148B PHE* 3.2 23.2 + - + +
150B LEU* 1.3 77.0 - - - +
152B GLY* 1.3 61.0 + - - +
154B ALA* 3.3 2.8 + - - +
155B ALA 3.0 18.4 + - - -
488B GLN* 4.1 7.0 - - + -
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Residues in contact with GLY 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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74B ILE* 4.6 0.4 - - - -
148B PHE 3.2 8.1 + - - -
149B GLY 3.2 2.4 + - - -
151B LYS* 1.3 78.8 - - - +
153B MET* 1.3 62.3 + - - +
155B ALA* 3.2 4.5 + - - +
156B TYR* 3.2 26.7 + - - -
488B GLN 3.5 21.4 + - - -
489B LYS* 3.8 13.5 - - - +
492B ILE* 3.6 12.1 - - - -
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Residues in contact with MET 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY 2.9 12.2 + - - +
150B LEU* 3.6 13.0 - - + +
152B GLY* 1.3 76.8 - - - +
154B ALA* 1.3 56.4 + - - +
156B TYR* 3.3 4.9 + - - +
157B ALA* 2.9 29.8 + - - +
170B LEU* 3.7 23.3 - - + -
173B PHE* 3.9 15.5 - - + -
174B MET* 4.0 13.2 - - + -
198B THR* 3.2 45.5 - - + +
201B PHE* 3.7 11.2 - - + +
202B GLY* 3.7 8.5 - - - +
205B ALA* 3.9 23.1 - - + +
492B ILE* 3.8 12.6 - - + +
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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
----------------------------------------------------------
67B THR* 3.9 15.7 - - - +
70B LEU* 3.7 26.2 - - + -
71B PHE 4.9 0.7 - - - +
150B LEU 2.8 18.4 + - - +
151B LYS 3.5 5.2 - - - +
153B MET* 1.3 74.9 - - - +
155B ALA* 1.3 59.7 + - - +
157B ALA* 3.7 1.3 - - - +
158B LYS* 2.8 32.8 + - - +
174B MET* 3.4 22.4 - - + +
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Residues in contact with ALA 155 (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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71B PHE* 3.6 39.2 - - + -
74B ILE* 4.0 3.4 - - + -
151B LYS 3.0 12.3 + - - +
152B GLY 3.2 8.9 + - - +
154B ALA* 1.3 77.8 - - - +
156B TYR* 1.3 62.8 + - - +
158B LYS* 3.2 3.5 + - - +
159B HIS* 3.1 29.5 + - + -
489B LYS* 3.8 22.0 - - + -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY 3.2 11.2 + - - -
153B MET* 3.8 6.3 - - - +
155B ALA* 1.3 77.8 - - - +
157B ALA* 1.3 61.4 + - - +
159B HIS* 3.3 8.0 + + - +
160B ALA* 3.1 22.2 + - - +
202B GLY 5.3 0.2 - - - -
205B ALA* 4.3 15.7 - - + +
206B MET* 3.7 31.9 - - + -
209B LEU* 3.8 21.7 - - + +
240B HIS* 5.7 0.4 - + - -
452B CYS* 3.1 24.9 - - - -
453B ASN* 3.4 36.9 + - + -
489B LYS* 3.5 34.4 - - + +
492B ILE* 3.7 23.1 - - + -
493B VAL* 3.6 8.8 - - + +
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR* 4.6 7.0 - - + -
153B MET 2.9 18.1 + - - +
154B ALA* 3.7 8.1 - - - +
156B TYR* 1.3 75.4 - - - +
158B LYS* 1.3 57.2 + - - +
160B ALA* 3.3 7.7 + - - +
161B ASP* 2.9 28.6 + - - +
165B LYS 4.5 1.2 - - - +
166B HIS* 5.8 0.5 - - - +
170B LEU* 4.0 27.1 - - + -
171B ASP* 5.1 4.9 - - - +
174B MET* 4.3 10.1 - - + -
205B ALA* 4.5 3.4 - - + +
208B LEU* 5.3 2.1 - - + +
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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
----------------------------------------------------------
64B ARG* 3.0 37.0 + - - +
67B THR* 3.1 19.6 + - - +
68B GLY* 3.5 17.0 - - - +
71B PHE* 4.1 20.2 - - + -
154B ALA 2.8 18.3 + - - +
155B ALA 3.6 4.9 - - - +
156B TYR 3.2 0.4 - - - -
157B ALA* 1.3 77.4 - - - +
159B HIS* 1.3 57.6 + - + +
161B ASP* 3.1 11.3 + - + +
162B VAL* 2.9 34.6 + - + +
325B ILE* 4.5 4.7 - - + -
337B GLU* 3.2 50.9 + - - +
338B ILE* 5.1 0.8 - - - +
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Residues in contact with HIS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.6 15.5 - + - -
155B ALA* 3.1 28.7 + - + -
156B TYR* 3.8 9.0 - + - +
158B LYS* 1.3 75.6 - - + +
160B ALA* 1.3 61.8 + - - +
162B VAL* 3.4 16.3 + - - +
163B LEU* 3.4 19.4 + - + +
209B LEU* 3.6 26.0 - - + -
240B HIS* 4.0 14.4 + - + +
241B ASP* 2.9 41.8 + - + +
306B THR* 3.3 34.6 - - + +
453B ASN* 6.0 0.7 - - - -
489B LYS* 5.3 1.5 + - + -
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TYR 3.1 13.4 + - - +
157B ALA* 3.6 7.6 - - - +
158B LYS 3.2 0.2 - - - -
159B HIS* 1.3 75.6 - - - +
161B ASP* 1.3 58.0 + - - +
163B LEU* 3.0 15.8 + - - +
164B GLY 3.2 0.7 + - - -
165B LYS* 2.9 32.0 + - + +
208B LEU* 3.9 28.0 - - + +
209B LEU* 3.7 15.4 - - - +
212B ALA* 4.0 11.7 - - + -
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B HIS* 2.9 28.7 - - - -
64B ARG* 2.7 50.4 + - - +
67B THR* 5.4 1.2 + - - -
157B ALA 2.9 14.8 + - - +
158B LYS* 3.1 17.5 + - - +
160B ALA* 1.3 74.5 - - - +
162B VAL* 1.3 61.4 + - - +
164B GLY* 2.9 19.8 + - - -
165B LYS 3.2 10.1 + - - +
166B HIS* 3.8 10.2 + - + +
337B GLU 5.6 0.5 - - - +
338B ILE* 4.3 6.6 - - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LYS* 2.9 22.2 + - + +
159B HIS* 3.4 10.3 - - - +
161B ASP* 1.3 75.8 - - + +
163B LEU* 1.3 60.1 + - + +
164B GLY 3.6 0.5 + - - -
241B ASP* 3.6 21.3 - - - +
243B ARG* 3.6 34.5 + - + +
337B GLU 3.6 24.2 - - - +
338B ILE* 3.7 16.5 - - - +
339B GLY* 3.6 23.8 - - - +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B HIS* 3.4 12.8 + - + +
160B ALA 3.0 11.1 + - - +
162B VAL* 1.3 79.2 - - + +
164B GLY* 1.3 56.3 + - - +
165B LYS* 2.9 22.7 + - - -
209B LEU* 4.8 1.6 - - + -
212B ALA* 3.9 27.6 - - + +
213B ASN* 3.3 27.8 - - - +
216B THR* 4.0 17.4 + - + +
217B TYR* 3.6 34.3 - - + +
242B LEU* 5.4 2.5 - - + +
243B ARG* 3.8 19.7 - - + +
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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).
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