Contacts of the helix formed by residues 136 - 163 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A THR* 3.6 2.6 - - + +
135A THR* 1.3 80.9 + - - +
137A ASP* 1.3 58.8 + - - +
138A ASP* 3.2 13.0 + - - +
139A VAL* 3.0 43.6 + - + +
140A ARG* 2.9 33.2 + - - +
188A VAL* 4.8 2.4 - - - +
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Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR 3.4 4.1 + - - +
136A ASP* 1.3 74.6 + - - +
138A ASP* 1.3 66.4 + - - +
140A ARG* 2.8 34.2 + - - +
141A SER* 2.9 29.1 + - - -
516A SER* 3.8 12.4 - - - -
517A PRO* 5.8 3.0 - - + +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP* 3.2 10.0 + - - +
137A ASP* 1.3 78.3 - - - +
139A VAL* 1.3 60.0 + - - +
141A SER* 3.4 1.0 + - - -
142A LEU* 3.0 36.6 + - - +
188A VAL* 4.1 22.7 - - + +
516A SER* 2.8 25.6 + - - -
518A ASN* 3.0 38.6 + - - +
519A VAL* 4.4 7.0 - - + -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 3.7 8.5 - - + -
136A ASP* 3.0 31.4 + - + +
138A ASP* 1.3 72.6 - - - +
140A ARG* 1.3 61.6 + - - +
142A LEU* 4.0 0.6 - - - +
143A ARG* 2.9 65.0 + - - +
186A LEU 4.9 9.0 - - - +
188A VAL* 4.2 17.3 - - + +
191A LEU* 3.9 21.5 - - + +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.8 10.6 + - - +
131A VAL* 3.3 30.7 - - - +
132A MET* 3.7 28.5 + - - +
134A THR* 3.1 34.7 + - + +
135A THR* 3.1 20.0 + - - +
136A ASP 2.9 18.4 + - - +
137A ASP* 2.8 32.4 + - - +
139A VAL* 1.3 76.4 - - - +
141A SER* 1.3 63.1 + - - +
143A ARG* 3.7 1.5 - - - +
144A TRP* 3.0 40.0 + - + +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.5 5.2 - - - -
137A ASP 2.9 19.4 + - - -
138A ASP 3.6 4.7 - - - -
140A ARG* 1.3 75.9 - - - +
142A LEU* 1.3 57.6 + - - +
144A TRP* 3.8 0.9 - - - +
145A LEU* 2.9 29.4 + - - +
514A PHE 2.6 29.0 + - - +
515A LEU* 3.5 4.3 - - - +
516A SER* 3.1 27.8 + - - -
519A VAL* 3.5 13.0 - - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP 3.0 21.9 + - - +
139A VAL 4.1 1.6 - - - +
141A SER* 1.3 72.6 - - - +
143A ARG* 1.3 67.9 + - - +
145A LEU* 3.7 8.6 - - + +
146A ILE* 2.9 31.3 + - - +
188A VAL* 3.9 27.8 - - + +
191A LEU* 3.8 30.5 - - + -
192A VAL* 3.9 21.3 - - + -
195A THR* 3.6 21.3 - - + +
519A VAL* 3.8 30.7 - - + -
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Residues in contact with ARG 143 (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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42A LYS* 5.7 0.9 - - - +
134A THR* 3.1 33.7 + - - +
139A VAL* 2.9 42.7 + - + +
140A ARG 3.7 3.4 - - - +
142A LEU* 1.3 78.1 - - - +
144A TRP* 1.3 60.9 + - + +
146A ILE* 3.6 5.1 + - - +
147A THR* 2.7 37.0 + - - +
180A LYS 5.0 0.6 + - - -
181A THR* 3.0 43.1 + - - +
182A LEU* 3.8 8.4 - - - +
183A ASP 3.3 25.7 + - - -
184A ASP* 2.9 31.7 + - - +
191A LEU* 4.5 11.5 - - + +
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Residues in contact with TRP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.7 16.4 - - + +
35A ASP* 5.5 7.4 - - - -
38A ILE* 4.3 15.9 - - + -
42A LYS* 3.8 19.3 - - - -
129A VAL 4.8 6.3 - - - -
130A GLY* 4.1 8.0 + - - -
131A VAL* 3.6 48.2 + - + +
134A THR* 4.5 7.7 + - - -
140A ARG* 3.0 40.1 + - + +
141A SER 4.2 1.1 - - - +
143A ARG* 1.3 79.7 - - + +
145A LEU* 1.3 60.6 + - - +
147A THR* 3.8 24.0 - - + -
148A PHE* 2.8 71.9 + + + -
151A LYS* 5.6 1.8 - - - -
514A PHE* 4.8 0.9 - - + -
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Residues in contact with LEU 145 (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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141A SER 2.9 17.9 + - - +
142A LEU* 3.7 15.3 - - + +
144A TRP* 1.3 74.6 - - - +
146A ILE* 1.3 57.9 + - - +
148A PHE* 3.5 1.8 + - - +
149A GLY* 2.9 25.5 + - - -
195A THR* 3.7 31.4 - - + +
491A VAL* 4.0 14.5 - - + +
494A LEU* 5.9 4.9 - - + -
495A LEU* 4.3 14.6 - - + +
514A PHE* 3.8 34.1 - - + -
515A LEU* 4.2 21.3 - - + -
519A VAL* 4.6 5.6 - - + -
523A LEU* 5.2 8.3 - - + -
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Residues in contact with ILE 146 (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 2.9 23.1 + - - +
143A ARG* 3.7 4.0 - - - +
145A LEU* 1.3 74.8 - - - +
147A THR* 1.3 59.9 + - - +
149A GLY* 3.1 2.1 + - - -
150A LEU* 2.8 51.7 + - + +
177A ALA* 4.8 0.9 - - + +
181A THR* 3.8 13.9 - - + -
191A LEU* 3.5 36.8 - - + +
194A LEU* 3.9 27.1 - - + -
195A THR* 3.4 24.0 - - - +
198A THR* 3.8 19.2 - - - +
495A LEU* 5.2 1.6 - - - -
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Residues in contact with THR 147 (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 ILE* 4.3 9.4 - - + -
42A LYS* 3.1 32.9 + - - +
70A LEU* 5.1 1.0 - - + +
143A ARG 2.7 22.4 + - - -
144A TRP* 3.2 31.7 + - + -
146A ILE* 1.3 75.1 - - - +
148A PHE* 1.3 59.2 + - + +
150A LEU* 3.2 12.6 + - - +
151A LYS* 2.9 39.5 + - + +
178A LEU* 5.0 6.3 - - + -
181A THR* 4.0 4.9 - - - +
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Residues in contact with PHE 148 (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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7A TYR* 4.0 12.6 - + - -
8A GLN* 3.4 41.1 - - + -
131A VAL* 5.2 2.2 - - + -
144A TRP* 2.8 60.5 + + + +
145A LEU 3.9 2.9 - - - +
147A THR* 1.3 74.6 - - - +
149A GLY* 1.3 63.1 + - - +
151A LYS* 3.2 17.0 + - - -
152A GLY 3.1 17.0 + - - -
488A GLN* 3.4 26.7 - - + +
491A VAL* 4.2 13.0 - - + -
514A PHE* 3.5 44.6 - + - -
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Residues in contact with GLY 149 (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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145A LEU 2.9 15.9 + - - -
146A ILE 3.1 3.3 + - - -
148A PHE* 1.3 75.6 - - - +
150A LEU* 1.3 56.5 + - - +
152A GLY 3.2 1.7 + - - -
153A MET* 2.9 23.9 + - - +
198A THR* 4.3 2.0 - - - -
491A VAL* 3.8 14.0 - - - +
492A ILE* 3.4 30.7 - - - +
495A LEU* 4.2 6.5 - - - -
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Residues in contact with LEU 150 (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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70A LEU* 3.9 8.6 - - + +
146A ILE* 2.8 36.7 + - + +
147A THR* 3.4 9.6 - - - +
149A GLY* 1.3 74.1 - - - +
151A LYS* 1.3 57.6 + - - +
153A MET* 3.6 19.5 - - + +
154A ALA* 2.8 31.0 + - - +
173A PHE* 4.0 16.8 - - + -
174A MET* 4.2 13.1 - - + +
177A ALA* 3.8 27.6 - - + -
178A LEU* 3.7 35.2 - - + +
181A THR* 5.0 0.9 - - + -
198A THR* 4.1 4.5 - - + +
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Residues in contact with LYS 151 (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 GLN* 2.8 31.2 + - - +
34A GLN* 5.4 0.4 + - - -
38A ILE* 4.0 16.9 - - - +
70A LEU* 3.9 27.9 - - + +
71A PHE* 5.1 0.3 - - - -
73A THR* 2.9 36.0 + - - +
74A ILE* 3.5 28.8 - - + +
144A TRP* 5.6 1.4 - - - -
147A THR* 2.9 23.6 + - - +
148A PHE* 3.2 23.9 + - + +
150A LEU* 1.3 76.4 - - - +
152A GLY* 1.3 63.2 + - - +
154A ALA* 3.2 2.9 + - - +
155A ALA 3.0 17.8 + - - -
488A GLN* 4.1 6.7 - - + -
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Residues in contact with GLY 152 (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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74A ILE* 4.6 0.7 - - - -
148A PHE 3.1 8.3 + - - -
149A GLY 3.2 2.2 + - - -
151A LYS* 1.3 78.6 - - - +
153A MET* 1.3 62.7 + - - +
155A ALA* 3.2 12.0 + - - +
156A TYR* 3.2 18.9 + - - -
488A GLN 3.6 20.8 + - - -
489A LYS* 3.9 14.6 - - - +
492A ILE* 3.7 12.3 - - - -
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Residues in contact with MET 153 (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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149A GLY 2.9 11.7 + - - +
150A LEU* 3.6 10.5 - - + +
152A GLY* 1.3 76.0 - - - +
154A ALA* 1.3 57.5 - - - +
156A TYR* 3.3 4.1 + - - +
157A ALA* 2.9 27.2 + - - +
170A LEU* 4.7 7.2 - - + -
173A PHE* 4.0 14.8 - - + -
174A MET* 3.8 21.1 - - - +
198A THR* 3.2 46.0 - - + +
201A PHE* 3.7 20.9 - - + +
202A GLY* 3.6 8.7 - - - +
205A ALA* 3.8 23.0 - - + +
492A ILE* 3.9 12.4 - - + +
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Residues in contact with ALA 154 (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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67A THR* 3.9 20.8 - - - +
70A LEU* 3.7 29.6 - - + -
71A PHE 5.0 0.4 - - - +
150A LEU 2.8 18.2 + - - +
151A LYS 3.5 4.9 - - - +
153A MET* 1.3 75.5 - - - +
155A ALA* 1.3 59.2 + - - +
157A ALA* 3.7 2.8 - - - +
158A LYS* 2.8 31.6 + - - +
174A MET* 3.8 13.7 - - - -
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Residues in contact with ALA 155 (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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71A PHE* 3.6 39.9 - - + -
74A ILE* 4.0 2.9 - - + -
151A LYS 3.0 12.9 + - - +
152A GLY 3.2 8.9 + - - +
154A ALA* 1.3 76.4 - - - +
156A TYR* 1.3 62.6 + - + +
158A LYS* 3.2 3.6 + - - +
159A HIS* 3.1 29.8 + - - +
489A LYS* 3.9 21.8 - - + -
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Residues in contact with TYR 156 (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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152A GLY 3.2 9.7 + - - -
153A MET* 3.8 7.2 - - - +
155A ALA* 1.3 77.4 - - - +
157A ALA* 1.3 62.7 + - - +
159A HIS* 3.3 7.1 + - - +
160A ALA* 3.1 22.7 + - - +
202A GLY 5.2 0.4 - - - -
205A ALA* 4.3 16.2 - - + +
206A MET* 3.5 31.9 - - + -
209A LEU* 3.8 23.0 - - + +
240A HIS* 5.7 0.4 - + - -
452A CYS* 3.1 25.7 - - - +
453A ASN* 3.3 35.8 + - + -
489A LYS* 3.5 35.1 - - + +
492A ILE* 3.6 24.0 - - + -
493A VAL* 3.6 7.6 - - + +
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Residues in contact with ALA 157 (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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67A THR* 4.5 4.7 - - + -
153A MET 2.9 18.1 + - - +
154A ALA 3.7 4.0 - - - +
156A TYR* 1.3 75.2 - - - +
158A LYS* 1.3 58.7 + - - +
160A ALA* 3.3 7.7 + - - +
161A ASP* 2.9 28.1 + - - +
165A LYS 4.5 1.2 - - - +
166A HIS* 6.0 0.2 - - - +
170A LEU* 3.8 37.2 - - + -
171A ASP* 5.1 1.8 - - - +
174A MET* 4.1 10.1 - - + -
205A ALA* 4.5 3.0 - - - +
208A LEU* 5.4 1.6 - - + +
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Residues in contact with LYS 158 (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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64A ARG* 3.1 27.9 + - - +
67A THR* 3.2 17.4 + - - +
68A GLY* 3.5 16.8 - - - +
71A PHE* 4.0 22.0 - - + -
154A ALA 2.8 18.3 + - - +
155A ALA 3.2 4.9 + - - +
157A ALA* 1.3 77.0 - - - +
159A HIS* 1.3 57.5 + - + +
161A ASP* 3.1 11.5 + - + +
162A VAL* 2.9 35.0 + - + +
325A ILE* 4.3 4.3 - - + -
337A GLU* 2.9 61.5 + - - +
338A ILE* 5.3 0.2 - - - +
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Residues in contact with HIS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.8 20.3 - + - -
155A ALA* 3.1 19.3 + - + -
156A TYR* 3.3 10.0 + + - +
158A LYS* 1.3 76.9 - - + +
160A ALA* 1.3 61.7 + - - +
162A VAL* 3.4 8.7 + - + +
163A LEU* 3.3 26.7 + - + +
209A LEU* 3.6 25.0 - - + +
240A HIS* 3.8 18.7 - + + +
241A ASP* 2.8 39.5 + - + +
306A THR* 3.2 34.5 - - + +
453A ASN* 5.8 0.8 + - - -
489A LYS* 5.3 2.0 - - + -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR 3.1 12.9 + - - +
157A ALA* 3.6 9.2 - - - +
158A LYS 3.2 0.2 - - - -
159A HIS* 1.3 76.6 - - - +
161A ASP* 1.3 57.0 + - - +
163A LEU* 3.0 15.8 + - - +
164A GLY 3.2 0.5 + - - -
165A LYS* 2.9 32.2 + - + +
208A LEU* 3.9 28.3 - - + +
209A LEU* 3.7 15.4 - - - +
212A ALA* 4.0 11.9 - - + -
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 2.8 28.8 + - + -
64A ARG* 2.7 48.3 + - - +
67A THR* 5.5 1.1 + - - +
157A ALA 2.9 14.2 + - - +
158A LYS* 3.1 16.6 + - - +
160A ALA* 1.3 73.4 - - - +
162A VAL* 1.3 64.6 + - - +
164A GLY* 2.9 14.4 + - - -
165A LYS 3.1 11.7 + - - +
166A HIS* 4.1 9.9 + - + +
337A GLU 5.4 0.7 - - - +
338A ILE* 4.4 8.1 - - - +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 2.9 21.7 + - + +
159A HIS* 3.4 10.8 - - + +
160A ALA 3.3 0.2 - - - -
161A ASP* 1.3 75.9 - - - +
163A LEU* 1.3 60.1 + - + +
164A GLY 3.6 0.2 + - - -
241A ASP* 3.6 22.4 - - - +
243A ARG* 3.6 29.6 + - + +
337A GLU 3.5 26.0 - - - +
338A ILE 3.8 10.3 - - - +
339A GLY* 3.6 32.7 - - - +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A HIS* 3.3 13.0 + - + +
160A ALA 3.0 10.9 + - - +
162A VAL* 1.3 77.4 - - + +
164A GLY* 1.3 58.8 + - - +
165A LYS* 3.5 5.9 + - - +
209A LEU* 4.8 2.2 - - + -
212A ALA* 3.9 27.0 - - + +
213A ASN* 3.2 27.8 - - - +
216A THR* 4.0 19.7 + - + +
217A TYR* 3.7 33.7 - - + +
242A LEU* 5.4 3.4 - - + +
243A ARG* 3.9 20.9 - - + +
----------------------------------------------------------
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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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