Contacts of the helix formed by residues 141 - 165 (chain B) in PDB entry 1L8I
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 5.4 5.6 - - + +
25B GLU* 4.2 12.7 + - + -
29B THR* 3.8 17.3 + - - +
83B ARG* 2.6 36.0 + - - -
87B LEU* 4.1 9.0 - - + +
139B ALA* 3.5 1.1 - - - +
140B LYS* 1.3 76.2 - - - +
142B ASP* 1.3 69.0 + - - +
143B ASP* 3.5 4.3 + - - +
144B THR* 2.7 28.5 + - - +
145B ALA* 2.9 19.7 + - - +
133H ARG* 4.4 11.0 - - - +
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS 3.3 9.4 + - - +
141B ASP* 1.3 73.0 + - - +
143B ASP* 1.3 64.3 + - - +
145B ALA* 3.0 10.4 + - - +
146B ASP* 3.0 20.6 + - - +
133H ARG* 4.2 9.7 - - + +
136H ILE* 4.1 39.4 - - + +
137H GLY* 4.4 9.5 + - - -
149H THR* 4.4 5.4 - - - +
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Residues in contact with ASP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 3.0 39.6 + - - +
141B ASP* 3.3 3.0 + - - -
142B ASP* 1.3 77.6 - - - +
144B THR* 1.3 65.6 + - - +
146B ASP* 3.0 6.6 + - - +
147B ILE* 3.0 25.5 + - - +
133H ARG* 4.2 3.1 - - - -
136H ILE* 3.5 15.7 - - - +
149H THR* 3.5 26.7 - - - +
152H SER* 2.9 21.4 + - - -
153H ARG* 3.7 20.8 + - - +
156H ASP* 3.6 2.1 - - - +
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 3.3 22.3 - - + +
32B LEU* 5.2 2.7 - - + -
33B LEU* 3.4 33.0 - - + -
83B ARG* 3.5 9.5 + - - +
139B ALA* 4.5 7.6 - - + -
141B ASP* 2.7 33.3 + - - -
143B ASP* 1.3 79.4 - - - +
145B ALA* 1.3 63.6 - - - +
147B ILE* 3.2 11.7 + - - +
148B LEU* 3.0 33.1 + - + +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.9 23.8 - - + +
139B ALA* 4.2 17.9 - - - +
141B ASP 2.9 11.3 + - - +
142B ASP* 3.3 13.9 - - - +
144B THR* 1.3 75.6 - - - +
146B ASP* 1.3 51.7 + - - +
148B LEU* 3.2 7.9 + - - +
149B THR* 2.8 38.0 + - - +
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Residues in contact with ASP 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASP 3.0 10.0 + - - +
143B ASP 3.0 10.5 + - - +
145B ALA* 1.3 74.6 - - - +
147B ILE* 1.3 66.7 + - - +
149B THR* 2.8 19.7 + - - -
150B ALA* 2.9 13.0 + - - +
310B TRS 2.6 47.5 + - - -
146H ASP* 4.2 4.5 - - - +
149H THR* 3.8 22.0 - - + +
153H ARG* 3.1 19.7 + - - +
146K ASP* 4.2 5.2 - - - +
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 5.2 1.8 - - + -
76B HIS* 4.7 3.6 + - - +
79B THR* 4.0 19.5 - - + +
80B MET* 3.7 30.3 - - + -
83B ARG* 3.6 41.1 - - + -
143B ASP 3.0 11.8 + - - +
144B THR* 3.4 9.6 - - + +
146B ASP* 1.3 76.1 - - - +
148B LEU* 1.3 60.4 + - + +
150B ALA* 3.5 3.9 + - - +
151B ALA* 3.0 26.1 + - + +
153H ARG* 3.4 42.4 - - + +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.4 7.6 - - + -
33B LEU* 4.6 7.9 - - + -
36B GLN* 4.1 18.2 - - + -
80B MET* 4.0 25.8 - - + -
132B VAL* 4.1 15.0 - - + +
135B ALA* 3.7 30.3 - - + +
136B ILE* 3.9 14.2 - - + +
139B ALA* 4.0 15.3 - - + -
144B THR* 3.0 28.8 + - + +
145B ALA* 3.4 6.3 - - - +
147B ILE* 1.3 72.2 - - - +
149B THR* 1.3 61.0 + - - +
151B ALA* 3.3 4.2 + - - +
152B SER* 2.7 31.7 + - - -
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.5 22.8 - - + +
145B ALA 2.8 21.6 + - - -
146B ASP* 2.8 17.6 + - - -
148B LEU* 1.3 68.9 - - - +
150B ALA* 1.3 60.3 + - - +
152B SER 3.2 0.2 + - - -
153B ARG* 2.8 33.7 + - - +
310B TRS 6.4 0.2 - - - -
142K ASP* 4.5 5.2 - - + +
143K ASP* 3.6 19.6 - - - +
146K ASP* 3.7 37.9 - - + +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B HIS* 3.5 18.1 - - + -
146B ASP 2.9 9.8 + - - +
147B ILE* 3.6 11.0 - - - +
149B THR* 1.3 78.5 - - - +
151B ALA* 1.3 62.4 - - - +
153B ARG* 3.5 8.1 - - - +
154B ASP* 3.4 17.0 + - - +
310B TRS 4.5 24.0 + - - +
153H ARG* 4.9 9.0 - - - +
146K ASP* 5.4 0.2 - - - -
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Residues in contact with ALA 151 (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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40B PHE* 4.2 16.8 - - + -
76B HIS* 3.4 32.3 - - + +
80B MET* 5.0 6.3 - - + -
132B VAL* 4.7 3.1 - - + -
147B ILE* 3.0 18.6 + - + +
148B LEU* 3.6 8.5 - - - +
150B ALA* 1.3 74.7 - - - +
152B SER* 1.3 64.1 + - - +
154B ASP* 3.3 4.3 + - - +
155B LEU* 3.1 28.2 + - - +
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 4.0 21.6 - - - +
133B ARG* 3.8 16.3 - - - +
136B ILE* 3.7 11.0 - - - -
148B LEU 2.7 20.9 + - - -
151B ALA* 1.3 68.9 - - - +
153B ARG* 1.3 68.8 + - - +
155B LEU* 2.9 3.9 + - - +
156B ASP* 2.9 29.6 + - - +
143K ASP* 2.6 31.2 + - - -
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR 2.8 16.4 + - - +
150B ALA* 3.5 9.1 - - - +
152B SER* 1.3 77.3 - - - +
154B ASP* 1.3 61.3 + - - +
156B ASP* 3.7 4.2 + - - +
157B LYS* 3.5 18.0 + - - +
310B TRS 4.1 9.0 + - - -
79K THR* 3.6 20.4 - - - +
83K ARG* 5.1 2.9 - - - +
86K GLN* 4.6 4.8 + - - +
143K ASP* 3.5 27.8 + - + +
146K ASP* 3.2 26.3 + - - -
147K ILE* 3.5 45.5 - - + +
150K ALA* 4.9 10.1 - - - +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 3.9 10.6 - - - +
76B HIS* 2.6 37.1 + - + +
150B ALA 3.4 4.6 + - - +
151B ALA 3.3 4.4 + - - +
152B SER 3.1 0.4 - - - -
153B ARG* 1.3 78.6 - - - +
155B LEU* 1.3 61.6 + - + +
157B LYS* 3.1 12.2 + - - +
158B PHE* 2.9 55.4 + - + -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.5 31.0 - - + -
43B LEU* 4.1 15.5 - - + -
73B LEU* 4.2 15.5 - - + -
76B HIS* 5.2 1.6 - - + -
125B TYR* 4.3 9.3 - - + +
128B VAL* 3.6 32.3 - - + -
129B ALA* 3.8 25.1 - - + +
132B VAL* 4.9 1.3 - - + -
151B ALA 3.1 26.3 + - - +
152B SER* 2.9 9.0 + - - +
154B ASP* 1.3 76.4 - - + +
156B ASP* 1.3 62.6 + - - +
158B PHE* 3.1 7.1 + - + +
159B LEU* 2.8 31.8 + - - +
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 3.8 12.8 - - - +
133B ARG* 2.6 35.3 + - - -
152B SER* 2.9 18.0 + - - +
153B ARG 4.1 1.3 - - - +
155B LEU* 1.3 76.5 - - - +
157B LYS* 1.3 60.7 + - - +
159B LEU* 3.8 6.6 - - - +
160B TRP* 3.2 22.2 + - - +
19K ASN* 3.3 19.7 + - - +
83K ARG* 2.7 42.6 + - - +
86K GLN* 3.9 9.6 - - - +
143K ASP* 3.5 2.6 - - - +
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Residues in contact with LYS 157 (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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153B ARG 3.5 10.0 + - - +
154B ASP* 3.1 16.0 + - - +
155B LEU 3.0 0.6 - - - -
156B ASP* 1.3 77.2 - - - +
158B PHE* 1.3 74.7 + - + +
160B TRP* 3.2 13.4 + - + +
161B PHE* 2.9 54.6 + - + +
82K GLU* 4.2 20.3 + - - +
86K GLN* 3.6 23.0 - - - +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY 5.1 0.9 - - - -
69B PHE* 3.4 61.0 - + + -
72B ALA* 3.6 29.2 - - + -
73B LEU* 3.9 19.3 - - + -
125B TYR* 3.9 18.4 - + + -
154B ASP* 2.9 47.0 + - + -
155B LEU* 3.5 8.7 - - - +
157B LYS* 1.3 87.9 - - + +
159B LEU* 1.3 66.7 + - - +
161B PHE* 3.0 2.9 + - - +
162B ILE* 2.8 29.8 + - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 3.5 29.2 - - - +
125B TYR* 4.3 7.7 - - + -
126B ALA* 4.1 23.8 - - + +
129B ALA* 4.3 12.3 - - + -
155B LEU 2.8 19.9 + - - +
156B ASP* 3.8 5.4 - - - +
158B PHE* 1.3 72.5 - - - +
160B TRP* 1.3 57.5 + - - +
162B ILE* 3.6 6.4 - - - +
163B GLU* 2.8 57.3 + - + +
17K THR* 4.4 2.9 - - - +
18K ARG 4.2 0.7 - - - -
19K ASN* 3.9 40.6 - - + +
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Residues in contact with TRP 160 (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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156B ASP 3.2 12.5 + - - +
157B LYS* 3.4 11.7 - - + +
158B PHE 3.2 0.4 - - - -
159B LEU* 1.3 81.2 - - - +
161B PHE* 1.3 85.9 + + - +
163B GLU* 3.9 7.7 - - - +
164B SER* 2.8 51.8 + - - -
17K THR* 5.8 1.6 - - - -
82K GLU* 3.8 42.2 - - + -
85K VAL* 3.5 23.3 - - + +
86K GLN* 3.6 33.7 - - + +
52L TRP* 3.8 21.7 + - - -
54L MET 5.0 2.2 + - - -
55L ARG* 4.3 16.6 - - - +
59L PHE* 4.2 15.3 - + - -
63L HIS* 3.9 12.1 - - - -
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET* 3.9 11.9 - - + -
69B PHE* 3.8 22.9 - + + -
157B LYS* 2.9 36.2 + - + +
158B PHE 3.0 6.5 + - - +
160B TRP* 1.3 111.6 - + - +
162B ILE* 1.3 68.0 + - - +
164B SER* 3.4 8.1 + - - -
165B ASN* 2.9 22.7 + - - +
82K GLU* 5.6 0.7 - - - -
59L PHE* 3.7 16.5 - + - -
60L ILE* 3.4 26.9 - - + -
63L HIS* 3.8 22.7 - + - -
64L GLU* 4.7 4.9 - - + -
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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
----------------------------------------------------------
65B MET* 4.5 9.4 - - + -
66B LEU* 5.0 4.7 - - + -
69B PHE* 3.7 17.0 - - + -
118B LEU* 3.5 39.4 - - + +
121B LEU* 4.4 7.9 - - + -
122B ALA* 3.9 12.3 - - + +
125B TYR* 3.5 52.3 - - + -
158B PHE 2.8 19.4 + - - +
159B LEU* 3.6 6.3 - - - +
161B PHE* 1.3 76.1 - - - +
163B GLU* 1.3 63.3 + - - +
165B ASN* 3.0 17.5 + - - +
166B ILE* 3.6 8.7 - - - +
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Residues in contact with GLU 163 (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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122B ALA* 4.3 4.0 - - + -
159B LEU* 2.8 35.7 + - + +
160B TRP* 3.9 7.2 - - - +
162B ILE* 1.3 73.3 - - - +
164B SER* 1.3 62.0 + - - +
166B ILE* 3.1 30.7 + - + +
16K TYR* 4.0 4.8 - - - +
17K THR* 3.0 29.7 + - - -
18K ARG* 2.7 61.0 + - - +
55L ARG* 4.9 11.1 + - - +
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B TRP* 2.8 42.2 + - - -
161B PHE 3.9 0.4 - - - -
162B ILE 3.2 0.6 - - - -
163B GLU* 1.3 75.6 - - - +
165B ASN* 1.3 57.3 + - - +
166B ILE 3.3 1.1 - - - -
54L MET 4.3 0.2 + - - -
55L ARG* 3.6 23.3 + - - +
56L GLY 2.8 33.5 + - - +
59L PHE* 3.1 35.5 - - - +
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Residues in contact with ASN 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 3.1 28.7 + - - +
62B VAL* 4.4 7.6 - - + -
65B MET* 3.7 15.0 - - - +
115B GLN* 2.8 25.3 + - - -
118B LEU* 3.4 21.3 - - + +
161B PHE 2.9 18.1 + - - +
162B ILE 3.0 7.0 + - - +
164B SER* 1.3 76.2 - - - +
166B ILE* 1.3 54.7 + - - +
167B GLU 3.6 0.2 + - - -
56L GLY 3.8 8.9 - - - +
57L ALA* 4.5 4.0 - - - -
59L PHE* 3.4 13.9 - - - +
60L ILE* 3.2 33.6 - - - +
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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