Contacts of the helix formed by residues 141 - 166 (chain D) in PDB entry 2UX1
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 141 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 4.2 17.0 - - + +
25D SER* 3.8 20.5 - - - +
79D ARG* 3.0 25.9 + - - -
83D LEU* 3.3 19.9 - - - +
136D SER* 2.8 15.4 + - - +
137D ASP* 5.6 0.4 - - - -
139D GLU 3.3 0.4 - - - -
140D GLY* 1.3 73.4 - - - +
142D SER* 1.3 56.8 + - - +
143D VAL 3.8 0.9 + - - -
144D THR* 2.7 29.2 + - - -
145D ASN* 3.0 27.5 + - - +
152F LYS* 5.2 2.3 + - - +
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ASP* 6.4 0.2 - - - +
140D GLY 3.4 7.8 + - - -
141D ASP* 1.3 71.4 + - - +
143D VAL* 1.3 64.6 + - - +
145D ASN* 3.6 10.2 - - - +
146D ASP 3.1 13.3 + - - -
130F GLN* 4.8 4.6 + - - -
133F PHE* 3.3 41.0 - - - -
149F ASN* 2.7 36.6 + - - -
152F LYS* 4.5 12.0 + - - +
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Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ARG* 3.4 37.5 - - - +
141D ASP* 3.3 1.2 + - - -
142D SER* 1.3 74.3 + - - +
144D THR* 1.3 66.0 + - - +
146D ASP* 3.2 6.6 + - - +
147D ILE* 3.2 27.4 + - + +
149F ASN* 3.8 15.3 - - - +
152F LYS* 3.7 24.2 - - + +
153F ALA* 3.4 44.2 - - + +
156F GLU* 3.9 5.4 - - - +
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D SER* 4.9 4.5 - - - -
29D LEU* 3.9 22.4 - - + -
79D ARG* 3.2 18.0 + - - +
83D LEU* 3.9 2.3 - - - +
136D SER* 4.0 9.2 - - - -
141D ASP* 2.7 33.9 + - - +
143D VAL* 1.3 77.6 - - - +
145D ASN* 1.3 63.7 + - - +
147D ILE* 3.1 21.0 + - + +
148D PHE* 3.1 41.0 + - + -
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Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 2.8 64.3 + - - +
136D SER* 3.1 15.5 + - - +
137D ASP* 3.4 24.5 + - - +
141D ASP 3.0 15.8 + - - +
142D SER* 3.6 11.6 - - - +
144D THR* 1.3 77.4 - - - +
146D ASP* 1.3 63.0 + - - +
148D PHE* 3.3 1.0 + - - +
149D ASN* 3.1 20.4 + - - +
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Residues in contact with ASP 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D SER 3.1 6.1 + - - -
143D VAL* 3.2 9.6 + - - +
145D ASN* 1.3 78.9 + - - +
147D ILE* 1.3 65.3 + - - +
149D ASN* 3.2 10.2 + - - +
150D VAL* 3.0 39.5 + - - +
146F ASP* 4.1 14.1 - - - +
149F ASN* 3.6 22.7 - - - +
150F VAL* 5.6 8.6 - - - +
146K ASP* 4.8 8.8 - - - +
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Residues in contact with ILE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 5.3 1.8 - - + -
72D TYR* 5.5 0.3 - - - -
75D GLU* 3.8 41.3 - - + +
76D MET* 3.6 33.9 - - + -
79D ARG* 3.7 41.1 - - + -
143D VAL* 3.2 19.3 + - + +
144D THR* 3.1 11.0 + - + +
146D ASP* 1.3 79.1 - - - +
148D PHE* 1.3 64.0 + - + +
150D VAL* 3.6 5.5 + - - +
151D ALA* 3.2 22.5 + - - +
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Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL* 4.1 16.8 - - + -
29D LEU* 3.8 23.8 - - + -
32D ALA* 4.3 6.5 - - + -
76D MET* 3.7 23.3 - - + -
128D LEU* 4.8 2.2 - - + -
129D PHE* 3.5 50.7 - + - +
132D GLY* 3.4 32.5 - - - -
133D PHE* 3.9 5.4 - - - +
136D SER* 4.4 0.4 - - - -
144D THR* 3.1 46.1 + - + -
145D ASN 3.8 4.7 - - - +
147D ILE* 1.3 74.7 - - + +
149D ASN* 1.3 60.6 + - - +
151D ALA* 3.4 1.4 + - - +
152D LYS* 2.9 32.4 + - - +
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Residues in contact with ASN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 3.8 14.9 - - + -
145D ASN* 3.1 15.0 + - - +
146D ASP* 3.2 13.6 + - - +
148D PHE* 1.3 77.1 - - - +
150D VAL* 1.3 57.8 + - + +
152D LYS* 3.4 6.5 + - - +
153D ALA* 2.9 29.5 + - - +
142K SER* 2.8 48.6 + - - -
143K VAL* 3.4 13.0 + - - +
146K ASP* 3.8 18.6 + - - +
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Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 4.9 9.9 - - + +
75D GLU* 5.8 3.4 - - - +
146D ASP* 3.0 37.3 + - - +
147D ILE* 3.9 5.6 - - - +
149D ASN* 1.3 72.5 - - + +
151D ALA* 1.3 70.2 + - - +
153D ALA* 3.3 14.7 + - - +
154D SER* 3.3 12.7 + - - -
146K ASP* 5.4 8.7 - - - +
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 3.6 34.7 + - + -
76D MET* 3.9 7.6 - - + -
129D PHE* 3.5 27.1 - - + -
147D ILE 3.2 15.2 + - - +
148D PHE 3.8 1.3 - - - +
150D VAL* 1.3 80.3 - - - +
152D LYS* 1.3 57.4 + - - +
154D SER* 3.1 4.5 + - - -
155D ILE* 3.0 31.9 + - - +
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Residues in contact with LYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ALA* 3.9 21.1 - - - +
129D PHE* 3.7 13.5 - - + +
130D GLN* 3.0 43.0 + - - +
133D PHE* 5.7 2.2 - - + -
148D PHE 2.9 17.9 + - - +
149D ASN* 3.6 7.4 - - - +
151D ALA* 1.3 73.8 - - - +
153D ALA* 1.3 66.8 + - - +
155D ILE* 4.6 3.1 - - - +
156D GLU* 3.0 65.9 + - + +
79K ARG* 4.4 5.5 - - - +
141K ASP* 5.4 1.4 + - - +
142K SER* 4.8 8.8 + - - +
143K VAL* 3.9 15.3 - - + +
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ASN 2.9 14.3 + - - +
150D VAL* 3.3 13.0 + - - +
152D LYS* 1.3 75.5 - - - +
154D SER* 1.3 57.5 + - - +
156D GLU* 4.0 2.2 - - - +
157D LYS* 3.2 26.3 + - - +
79K ARG* 5.0 1.9 + - - -
143K VAL* 3.5 35.1 - - + +
147K ILE* 6.3 0.4 - - + -
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Residues in contact with SER 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D GLU* 2.6 33.2 + - - -
72D TYR* 3.2 13.2 - - - -
150D VAL* 3.3 5.9 + - - -
151D ALA 3.1 2.9 + - - -
153D ALA* 1.3 76.7 - - - +
155D ILE* 1.3 69.3 + - - +
157D LYS* 3.2 10.0 + - - +
158D HIS* 3.0 30.0 + - - -
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D GLU* 3.9 16.8 - - - +
69D ILE* 4.2 18.4 - - + -
72D TYR* 4.0 10.3 - - + -
122D PHE* 3.3 53.2 - - + +
125D LEU* 4.5 3.6 - - + -
126D ALA* 4.3 7.6 - - + +
129D PHE* 3.9 20.4 - - + -
151D ALA 3.0 20.9 + - - +
152D LYS* 4.2 4.9 - - - +
154D SER* 1.3 76.4 - - - +
156D GLU* 1.3 56.4 + - - +
158D HIS* 3.1 14.7 + - + +
159D ILE* 3.0 28.3 + - + +
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Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ALA* 4.0 20.3 - - + +
152D LYS* 3.0 54.6 + - - +
153D ALA 4.0 1.1 - - - +
155D ILE* 1.3 78.3 - - - +
157D LYS* 1.3 60.8 + - - +
159D ILE* 3.3 9.2 + - - +
160D TRP 3.1 17.5 + - - -
172D LEU* 3.7 28.9 - - + +
79K ARG* 2.8 37.9 + - - +
82K THR* 3.5 11.7 - - + +
143K VAL* 4.0 2.6 - - - +
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Residues in contact with LYS 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ALA 3.2 15.5 + - - +
154D SER* 3.5 11.2 - - - +
156D GLU* 1.3 75.0 - - - +
158D HIS* 1.3 67.4 + - + +
160D TRP* 3.3 18.1 + - + +
161D MET* 3.2 46.0 + - + +
75K GLU* 6.2 3.0 - - - +
78K GLU* 4.2 18.0 + - + +
82K THR* 4.4 10.9 - - - +
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Residues in contact with HIS 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TYR* 3.6 34.2 + + + +
68D GLU* 2.7 35.7 + - - -
122D PHE* 3.7 23.8 - + + -
154D SER* 3.0 28.9 + - - -
155D ILE* 3.1 10.7 + - + +
157D LYS* 1.3 79.2 - - + +
159D ILE* 1.3 61.8 + - - +
161D MET* 3.1 15.2 + - - +
162D LEU* 2.8 35.2 + - - +
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Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D VAL* 4.3 8.5 - - + +
122D PHE* 3.7 40.2 - - + +
123D ARG* 3.9 23.8 - - + +
126D ALA* 4.2 6.5 - - + -
155D ILE* 3.0 22.3 + - + +
156D GLU* 3.3 11.6 + - - +
158D HIS* 1.3 75.5 - - - +
160D TRP* 1.3 63.9 + - - +
162D LEU* 4.5 6.3 - - - -
163D GLN* 2.8 37.0 + - + +
170D PRO* 3.8 22.4 - - + +
172D LEU* 3.9 21.5 - - + -
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Residues in contact with TRP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D GLU 3.1 8.8 + - - +
157D LYS* 3.5 26.9 - - + +
158D HIS 3.3 0.2 - - - -
159D ILE* 1.3 76.6 - - - +
161D MET* 1.3 74.5 + - + +
163D GLN* 3.8 1.2 - - - +
164D ALA* 2.8 36.0 + - + +
168D GLN 5.0 1.1 - - - +
170D PRO* 4.0 27.2 - - + +
47I HIS 5.0 0.4 - - - -
48I TRP 4.6 5.1 + - - -
50I MET 5.5 0.6 + - - -
55I PHE* 3.8 22.1 - + - -
59I HIS* 3.7 19.3 - + - -
107I TYR* 5.9 0.2 - - - -
78K GLU* 3.6 45.1 - - + -
81K ILE* 3.5 36.9 - - + +
82K THR* 3.5 27.6 - - + +
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Residues in contact with MET 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TYR* 5.4 0.7 - - - +
157D LYS* 3.2 32.7 + - - +
158D HIS* 3.1 18.6 + - - +
160D TRP* 1.3 96.7 - - + +
162D LEU* 1.3 60.8 + - - +
164D ALA* 3.3 3.3 + - - +
165D GLU* 3.0 25.8 + - - +
55I PHE* 3.6 27.8 - - + -
56I MET* 4.0 26.7 - - + +
59I HIS* 3.4 33.9 - - + +
78K GLU* 5.0 0.4 - - - +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D TRP* 3.7 29.6 - - + -
65D TYR* 3.8 15.7 - - + +
115D LEU* 4.0 27.5 - - + +
118D VAL* 3.6 27.6 - - + -
119D VAL* 3.6 22.2 - - + +
122D PHE* 3.8 19.7 - - + -
158D HIS 2.8 24.5 + - - +
159D ILE 3.9 1.8 - - - +
161D MET* 1.3 70.4 - - - +
163D GLN* 1.3 63.5 + - - +
165D GLU* 3.2 7.4 + - - +
166D LEU* 3.0 28.4 + - - +
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Residues in contact with GLN 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D VAL* 3.5 15.0 - - + +
123D ARG* 3.4 27.3 - - - +
159D ILE* 2.8 25.3 + - + +
160D TRP 3.8 2.9 - - - +
162D LEU* 1.3 76.0 - - - +
164D ALA* 1.3 62.8 + - - +
166D LEU* 3.0 29.5 + - - +
167D GLY 3.0 0.2 + - - -
168D GLN* 2.9 54.2 + - - +
169D ALA 2.9 33.7 + - - +
170D PRO* 3.9 6.7 - - + +
171D LYS* 3.5 3.8 - - - +
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D TRP* 2.8 27.2 + - + +
161D MET 3.4 6.1 - - - +
162D LEU 3.2 0.2 - - - -
163D GLN* 1.3 77.8 - - - +
165D GLU* 1.3 52.2 + - - +
167D GLY* 2.9 9.2 + - - -
168D GLN 3.6 8.7 + - - +
50I MET 4.0 7.4 - - - +
51I ARG* 3.5 6.6 - - + +
52I GLY 2.8 31.9 + - - -
55I PHE* 3.6 31.9 - - + -
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ILE* 6.0 0.2 - - - -
58D TRP* 3.5 35.7 + - + -
115D LEU* 3.8 15.0 - - + -
161D MET 3.0 14.1 + - - +
162D LEU 3.2 9.6 + - - +
164D ALA* 1.3 74.8 - - - +
166D LEU* 1.3 57.7 + - - +
167D GLY 3.2 1.2 + - - -
52I GLY 3.2 25.3 - - - -
53I ARG* 2.8 38.8 + - - +
54I GLY* 2.9 20.0 + - - -
55I PHE* 3.2 7.4 + - + +
56I MET* 3.0 29.3 + - - +
173I EPE 4.5 3.9 + - - -
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Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D GLU* 3.7 42.4 - - + +
115D LEU* 3.9 18.8 - - + -
116D ALA* 4.3 15.5 - - + +
119D VAL* 4.1 13.7 - - + -
162D LEU 3.0 17.3 + - - +
163D GLN* 3.0 31.2 + - - +
165D GLU* 1.3 77.4 - - + +
167D GLY* 1.3 60.4 + - - +
168D GLN* 3.5 25.5 + - - +
53I ARG* 5.1 3.1 - - - +
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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