Contacts of the helix formed by residues 133 - 157 (chain A) in PDB entry 1O9R
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 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.4 33.7 - - + +
18A VAL* 3.6 19.4 - - + +
72A ARG* 3.1 14.8 + - - -
76A LEU* 3.9 1.6 - - - +
128A SER 3.1 17.3 + - - +
129A ASP* 4.2 1.4 + - - -
131A ALA 4.8 1.1 - - - -
132A GLY* 1.3 78.6 - - - +
134A PRO* 1.3 62.0 - - - +
135A THR* 3.4 4.2 + - - -
136A THR* 2.5 39.4 + - - -
137A ALA* 3.0 21.0 + - - +
122C ARG* 5.7 0.3 + - - -
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Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASP* 5.1 9.6 - - - +
132A GLY* 3.3 10.1 - - - +
133A ASP* 1.3 90.6 - - - +
135A THR* 1.3 57.6 + - - +
137A ALA* 3.7 10.3 - - + +
138A ASP* 2.9 28.6 + - - +
122C ARG* 5.8 5.2 - - + +
125C ILE* 4.0 26.0 - - + -
126C ASP* 3.6 24.0 - - - +
141C THR* 4.1 5.7 - - - +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.4 35.2 - - - +
133A ASP* 3.2 2.9 + - - -
134A PRO* 1.3 77.9 - - - +
136A THR* 1.3 62.0 + - - +
138A ASP* 3.2 12.8 + - - +
139A ILE* 3.2 15.7 + - + +
122C ARG* 4.8 4.9 + - - +
125C ILE* 3.5 14.7 - - - +
141C THR* 4.3 7.1 - - - +
144C SER* 2.8 29.0 + - - +
145C ARG* 3.6 28.6 - - + +
148C ASP* 4.8 0.4 - - - -
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.4 23.6 - - + +
22A LEU* 4.0 11.4 - - + -
72A ARG* 2.8 25.7 + - + +
128A SER* 3.4 15.0 - - - +
133A ASP* 2.5 34.7 + - - -
135A THR* 1.3 75.7 - - - +
137A ALA* 1.3 63.5 + - - +
139A ILE* 3.0 17.3 + - + +
140A PHE* 3.1 24.7 + - + -
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.6 31.3 - - + +
128A SER* 3.8 10.7 - - - -
129A ASP* 4.0 11.0 - - + +
133A ASP 3.0 16.2 + - - +
134A PRO* 3.7 9.9 - - + +
136A THR* 1.3 76.0 - - - +
138A ASP* 1.3 57.5 + - - +
140A PHE* 3.2 4.7 + - - +
141A THR* 2.8 31.9 + - - +
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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
----------------------------------------------------------
134A PRO 2.9 8.4 + - - +
135A THR 3.4 10.1 - - - +
136A THR 3.2 0.2 - - - -
137A ALA* 1.3 74.6 - - - +
139A ILE* 1.3 59.8 + - - +
141A THR* 3.1 7.8 + - - -
142A ALA* 2.9 29.1 + - - +
138C ASP* 4.1 1.9 - - - +
141C THR* 3.4 26.7 - - + +
145C ARG* 3.0 23.6 + - - -
138E ASP* 4.1 4.0 - - - +
1164E TRS 2.6 47.5 + - - -
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 5.2 5.2 - - + -
65A HIS* 4.7 3.1 + - - +
68A THR* 3.6 28.3 - - + +
69A ILE* 4.0 26.0 - - + +
72A ARG* 3.8 40.6 - - + +
75A GLN* 5.4 2.5 - - - +
135A THR* 3.2 11.4 + - + +
136A THR* 3.0 9.3 + - + +
138A ASP* 1.3 77.1 - - - +
140A PHE* 1.4 64.3 + - + +
142A ALA* 3.5 3.2 + - - +
143A ALA* 3.1 21.2 + - + +
145C ARG* 3.5 37.0 - - + +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.7 25.1 - - + -
22A LEU* 3.6 22.2 - - + -
25A SER* 3.5 27.8 - - - -
69A ILE* 4.0 17.7 - - + -
121A ILE* 3.3 26.5 - - + +
124A ALA* 3.7 15.0 - - + -
125A ILE* 3.7 17.7 - - + +
128A SER* 3.4 27.6 - - - -
136A THR* 3.1 31.7 + - + -
137A ALA 3.7 6.1 - - - +
139A ILE* 1.4 77.8 - - + +
141A THR* 1.4 55.8 + - - +
143A ALA* 3.3 1.9 + - - -
144A SER* 2.8 26.3 + - - -
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.5 25.2 - - + +
137A ALA 2.8 18.8 + - - -
138A ASP* 3.1 10.6 + - - -
140A PHE* 1.4 71.1 - - - +
142A ALA* 1.3 67.2 + - - +
144A SER* 3.2 1.7 + - - -
145A ARG* 3.0 23.8 + - - +
134E PRO* 4.0 11.5 - - - +
135E THR* 4.1 10.5 - - - +
138E ASP* 3.5 38.4 - - + +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 3.6 18.2 + - + -
138A ASP 2.9 16.6 + - - +
139A ILE 3.8 4.0 - - - +
141A THR* 1.3 78.3 - - - +
143A ALA* 1.3 62.7 + - - +
145A ARG* 3.3 15.4 + - - +
146A ASP* 3.4 11.1 + - - +
145C ARG* 4.4 14.8 - - - +
1164E TRS 4.3 18.8 + - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 6.5 0.2 - - + -
65A HIS* 3.5 37.0 + - + +
69A ILE* 5.0 9.2 - - + -
121A ILE* 4.1 12.8 - - + -
139A ILE 3.1 12.3 + - - +
140A PHE* 3.6 9.2 - - - +
142A ALA* 1.3 78.4 - - - +
144A SER* 1.4 57.0 + - - +
146A ASP* 3.2 3.3 + - - +
147A LEU* 2.8 38.8 + - + +
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 5.1 1.6 + - - -
121A ILE* 3.7 12.0 - - - +
122A ARG* 4.2 11.3 + - - -
125A ILE* 3.8 10.9 - - - +
140A PHE 2.8 16.9 + - - -
141A THR 3.4 4.5 - - - -
143A ALA* 1.4 75.2 - - - +
145A ARG* 1.4 57.6 - - - +
147A LEU* 4.4 4.5 - - - +
148A ASP* 2.8 41.6 + - - +
135E THR* 2.7 29.9 + - - +
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Residues in contact with ARG 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 THR 3.0 16.4 + - - +
142A ALA* 3.6 10.3 - - - +
143A ALA 3.3 0.2 - - - -
144A SER* 1.4 76.5 - - - +
146A ASP* 1.3 66.1 + - - +
148A ASP* 4.1 2.6 - - - +
149A LYS* 3.1 24.9 + - - +
68E THR* 3.6 25.5 + - - +
75E GLN* 4.6 2.9 + - - +
135E THR* 3.7 23.1 - - + +
138E ASP* 2.9 41.6 + - - -
139E ILE* 3.5 26.5 - - + +
142E ALA* 4.4 9.9 - - - +
1164E TRS 3.7 14.9 + - - -
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Residues in contact with ASP 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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61A GLN* 3.8 31.2 + - + +
65A HIS* 2.7 37.5 + - + +
142A ALA 3.4 4.5 + - - +
143A ALA 3.2 3.5 + - - +
145A ARG* 1.3 82.3 - - - +
147A LEU* 1.3 60.6 + - + +
149A LYS* 3.9 9.2 - - - +
150A SER* 2.9 34.8 + - - -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 5.6 2.5 - - + -
32A LEU* 4.2 9.6 - - + -
62A LEU* 4.2 23.8 - - + -
65A HIS* 6.1 2.5 - - + -
114A TYR* 4.3 14.7 - - + +
117A VAL* 4.0 25.1 - - + +
118A ALA* 3.9 19.2 - - + +
121A ILE* 3.5 37.0 - - + -
143A ALA* 2.8 31.8 + - + +
144A SER* 3.9 3.8 - - - +
146A ASP* 1.3 73.3 - - + +
148A ASP* 1.3 58.7 + - - +
150A SER* 3.3 4.1 + - - -
151A LEU* 2.9 30.7 + - - +
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Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA* 3.6 12.1 - - - +
122A ARG* 2.8 40.5 + - - -
144A SER* 2.8 27.3 + - - +
145A ARG 4.1 1.1 - - - +
147A LEU* 1.3 74.0 - - - +
149A LYS* 1.3 62.1 + - - +
151A LEU* 3.5 7.0 + - - +
152A TRP* 3.1 22.7 + - - +
8E ASN* 3.1 13.5 - - - +
72E ARG* 2.8 34.6 + - - +
75E GLN* 3.7 9.8 - - + +
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Residues in contact with LYS 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 ARG 3.1 18.7 + - - +
146A ASP* 3.9 10.3 - - - +
148A ASP* 1.3 75.7 - - - +
150A SER* 1.3 61.3 + - - +
152A TRP* 3.3 14.2 + - + +
153A PHE* 2.9 60.5 + - + -
71E GLU* 2.9 37.3 + - - +
75E GLN* 3.8 18.3 + - - +
52F HIS* 5.8 0.2 + - - -
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.5 38.1 - - - +
61A GLN* 3.5 13.9 + - - -
114A TYR* 3.9 16.6 - - - -
146A ASP 2.9 24.6 + - - -
147A LEU* 3.8 5.3 - - - -
149A LYS* 1.3 75.3 - - - +
151A LEU* 1.3 66.4 + - - +
153A PHE* 3.2 3.4 + - - +
154A LEU* 3.0 28.9 + - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.9 14.8 - - + +
114A TYR* 4.2 9.8 - - + -
115A GLY* 3.8 33.7 - - - +
118A ALA* 4.5 11.0 - - + -
147A LEU 2.9 17.3 + - - +
148A ASP* 3.7 6.7 - - - +
150A SER* 1.3 77.0 - - - +
152A TRP* 1.3 56.7 + - - +
154A LEU* 3.2 8.3 + - + +
155A GLU* 2.8 55.6 + - + +
6E THR* 4.1 5.8 - - - +
7E LYS* 4.3 1.3 - - + -
8E ASN* 3.7 36.8 - - + +
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Residues in contact with TRP 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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148A ASP 3.1 14.2 + - - +
149A LYS* 3.3 9.6 + - + +
151A LEU* 1.3 76.3 - - - +
153A PHE* 1.3 87.2 + + - +
155A GLU* 3.2 8.7 + - - +
156A ALA* 2.8 45.3 + - + +
159A GLN* 4.9 7.9 - - - -
71E GLU* 3.7 41.3 - - + -
74E VAL* 3.2 30.6 - - + +
75E GLN* 3.7 35.4 - - + +
41F TRP* 3.6 22.8 + - - -
44F LYS* 4.6 2.2 - - - +
48F PHE* 4.0 17.4 - + - -
52F HIS* 3.8 12.6 - + - -
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.9 21.8 - - + -
58A PHE* 3.9 16.8 - + + -
149A LYS* 2.9 44.1 + - + +
150A SER* 3.5 8.3 - - - +
152A TRP* 1.3 107.8 - + - +
154A LEU* 1.3 54.3 + - - +
156A ALA 3.6 3.6 + - - -
157A HIS* 2.7 32.2 + - - -
48F PHE* 3.5 22.3 - + + -
49F ILE* 3.7 23.3 - - + -
52F HIS* 3.8 24.2 - + - -
53F GLU* 5.4 1.8 - - - -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 5.9 1.1 - - + -
54A LEU* 5.3 5.2 - - + -
55A LEU* 4.4 6.7 - - + -
58A PHE* 3.9 17.9 - - + -
107A LEU* 3.8 24.5 - - + +
110A LEU* 4.1 27.8 - - + +
111A ILE* 3.6 23.3 - - + +
114A TYR* 3.6 45.5 - - + -
150A SER 3.0 18.3 + - - +
151A LEU* 3.6 6.1 - - - +
153A PHE* 1.3 76.0 - - - +
155A GLU* 1.3 63.1 + - - +
157A HIS* 3.1 23.7 + - - +
158A VAL* 3.9 1.6 + - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.7 27.0 - - + +
151A LEU* 2.8 34.2 + - + +
152A TRP* 3.9 6.9 - - - +
154A LEU* 1.3 74.5 - - - +
156A ALA* 1.3 56.7 + - - +
157A HIS 3.1 0.2 - - - -
158A VAL* 2.9 8.3 + - + +
159A GLN* 2.9 47.3 + - + +
5E LYS 4.2 2.1 - - - +
6E THR* 2.6 34.2 + - - -
7E LYS* 2.8 36.6 + - - +
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TRP* 2.8 33.0 + - - +
153A PHE 4.0 2.2 - - - +
154A LEU 3.2 0.4 - - - -
155A GLU* 1.3 71.8 - - - +
157A HIS* 1.3 51.9 + - - +
158A VAL 3.5 0.3 + - - -
159A GLN* 3.3 14.9 + - - +
44F LYS* 3.3 12.6 - - + +
45F GLY 2.7 31.5 + - - -
48F PHE* 3.6 36.3 - - + +
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Residues in contact with HIS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 4.3 4.8 + - - +
51A VAL* 4.1 20.4 - - + +
54A LEU* 4.2 12.3 - - + -
107A LEU* 3.8 21.9 - - + +
153A PHE 2.7 26.7 + - - -
154A LEU* 3.1 12.6 + - + +
155A GLU 3.1 1.6 - - - -
156A ALA* 1.3 77.8 - - - +
158A VAL* 1.3 60.3 + - - +
160A GLU 3.7 3.6 - - - +
45F GLY 3.3 22.7 - - - -
46F PRO* 3.3 30.5 - - - +
47F GLN* 4.6 0.8 - - - -
48F PHE* 3.7 12.1 + + + +
49F ILE* 3.4 43.2 + - + +
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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