Contacts of the helix formed by residues 133 - 157 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.5 32.4 - - + +
18B VAL* 3.7 18.9 - - + +
72B ARG* 3.1 16.6 + - - -
76B LEU* 3.9 1.7 - - - +
128B SER 3.1 15.9 + - - +
129B ASP* 4.2 1.0 + - - -
131B ALA 4.9 0.9 - - - +
132B GLY* 1.3 77.9 - - - +
134B PRO* 1.3 57.9 - - - +
135B THR* 3.4 4.5 + - - -
136B THR* 2.5 36.5 + - - -
137B ALA* 2.9 25.5 + - - +
122D ARG* 5.6 0.5 + - - -
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Residues in contact with PRO 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 5.8 0.2 - - + -
129B ASP* 4.4 14.7 - - - +
132B GLY* 3.2 14.1 - - - +
133B ASP* 1.3 82.9 - - - +
135B THR* 1.3 60.4 + - - +
137B ALA* 3.6 9.1 - - + +
138B ASP* 2.9 29.5 + - - +
122D ARG* 5.7 5.6 - - + +
125D ILE* 4.0 26.7 - - + -
126D ASP* 3.6 24.5 - - - +
141D THR* 4.0 6.6 - - + +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG* 3.5 33.7 - - - +
133B ASP* 3.2 2.5 + - - -
134B PRO* 1.3 78.9 - - - +
136B THR* 1.3 61.6 + - - +
138B ASP* 3.3 5.7 + - - +
139B ILE* 3.3 21.0 + - + +
122D ARG* 4.9 5.1 + - - +
125D ILE* 3.6 11.6 - - - +
141D THR* 4.3 7.9 - - - +
144D SER* 2.7 33.3 + - - +
145D ARG* 3.6 29.2 - - + +
148D ASP* 4.3 1.1 - - - +
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.3 24.6 - - + +
22B LEU* 4.0 11.4 - - + -
72B ARG* 2.8 25.9 + - + +
76B LEU* 4.2 0.3 - - - +
128B SER* 3.5 14.1 - - - +
133B ASP* 2.5 34.9 + - - -
135B THR* 1.3 72.4 - - - +
137B ALA* 1.3 66.2 + - - +
139B ILE* 3.0 18.4 + - - +
140B PHE* 3.1 24.6 + - + -
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 3.7 28.1 - - + +
128B SER* 3.8 11.8 - - - -
129B ASP* 4.0 11.2 - - + +
133B ASP 2.9 16.9 + - - +
134B PRO* 3.2 11.0 + - + +
136B THR* 1.3 76.0 - - - +
138B ASP* 1.3 52.4 + - - +
140B PHE* 3.3 6.5 + - - +
141B THR* 2.8 35.5 + - - -
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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
----------------------------------------------------------
134B PRO 2.9 6.3 + - - +
135B THR 3.4 9.9 - - - +
136B THR 3.1 0.2 - - - -
137B ALA* 1.3 74.6 - - - +
139B ILE* 1.4 66.1 + - - +
141B THR* 3.5 9.1 - - - +
142B ALA* 2.9 23.4 + - - +
1164B TRS 2.6 49.1 + - - -
138D ASP* 4.1 1.6 - - - +
141D THR* 3.4 29.0 - - + +
145D ARG* 2.9 23.7 + - - -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 5.1 4.5 - - + -
65B HIS* 4.7 2.8 + - - +
68B THR* 3.6 29.8 - - + +
69B ILE* 4.0 27.6 - - + +
72B ARG* 3.7 40.2 - - + +
75B GLN* 5.5 2.2 - - - +
135B THR* 3.3 12.7 + - + +
136B THR* 3.0 9.0 + - + +
138B ASP* 1.4 78.1 - - - +
140B PHE* 1.4 63.1 + - + +
142B ALA* 3.4 3.3 + - - +
143B ALA* 3.1 22.2 + - + +
145D ARG* 3.6 32.3 - - + +
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 3.7 25.6 - - + -
22B LEU* 3.6 21.5 - - + -
25B SER* 3.5 27.8 - - - -
69B ILE* 4.0 17.5 - - + -
121B ILE* 3.2 26.2 - - + +
124B ALA* 3.7 15.3 - - + -
125B ILE* 3.7 20.4 - - + +
128B SER* 3.3 28.3 - - - -
136B THR* 3.1 32.2 + - + -
137B ALA 3.7 3.1 - - - +
139B ILE* 1.4 80.1 - - + +
141B THR* 1.4 56.5 + - - +
143B ALA* 3.3 2.6 + - + -
144B SER* 2.8 25.3 + - - -
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Residues in contact with THR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 3.5 28.6 - - + +
137B ALA* 2.8 22.8 + - - +
138B ASP* 3.1 12.7 + - - +
140B PHE* 1.4 71.5 - - - +
142B ALA* 1.3 66.6 + - - +
144B SER* 3.2 2.5 + - - -
145B ARG* 3.0 35.1 + - + +
1164B TRS 5.3 5.8 - - - +
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Residues in contact with ALA 142 (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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65B HIS* 3.6 18.6 + - + -
138B ASP 2.9 15.7 + - - +
139B ILE* 3.8 4.3 - - - +
141B THR* 1.3 79.1 - - - +
143B ALA* 1.3 60.8 + - - +
145B ARG* 3.3 15.9 + - - +
146B ASP* 3.4 11.3 + - - +
1164B TRS 4.4 19.0 + - - +
145D ARG* 4.4 15.3 - - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B HIS* 3.5 35.8 - - + +
69B ILE* 5.0 9.6 - - + -
121B ILE* 4.1 12.8 - - + -
139B ILE* 3.1 16.7 + - + +
140B PHE* 3.6 6.3 - - - +
141B THR 3.3 0.2 - - - -
142B ALA* 1.3 77.3 - - - +
144B SER* 1.4 56.8 + - - +
146B ASP* 3.2 4.0 + - - +
147B LEU* 2.8 38.1 + - + +
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Residues in contact with SER 144 (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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118B ALA 5.1 1.6 + - - -
121B ILE* 3.6 14.1 - - - +
122B ARG* 4.2 13.1 + - - +
125B ILE* 3.8 20.5 - - - +
140B PHE 2.8 22.1 + - - -
141B THR* 3.2 5.8 + - - -
143B ALA* 1.4 68.9 - - - +
145B ARG* 1.4 62.0 - - - +
147B LEU* 4.4 4.5 - - - +
148B ASP* 2.8 45.5 + - - +
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Residues in contact with ARG 145 (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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141B THR* 3.0 25.2 + - + +
142B ALA* 3.6 10.8 - - - +
143B ALA 3.2 0.6 - - - -
144B SER* 1.4 77.8 - - - +
146B ASP* 1.3 65.5 + - - +
148B ASP* 4.1 3.8 - - - +
149B LYS* 3.1 24.3 + - - +
1164B TRS 3.8 29.1 + - - -
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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
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61B GLN* 3.8 29.1 + - + +
65B HIS* 2.7 37.8 + - + +
142B ALA 3.4 4.1 + - - +
143B ALA 3.2 3.6 + - - +
145B ARG* 1.3 80.7 - - - +
147B LEU* 1.4 62.7 + - + +
149B LYS* 3.4 9.3 + - - +
150B SER* 2.8 34.5 + - - -
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Residues in contact with LEU 147 (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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29B VAL* 5.5 2.7 - - + -
32B LEU* 4.1 9.6 - - + -
62B LEU* 4.1 24.0 - - + -
65B HIS* 6.1 2.5 - - + -
114B TYR* 4.3 14.1 - - + +
117B VAL* 3.8 27.8 - - + +
118B ALA* 4.0 16.4 - - + +
121B ILE* 3.5 36.6 - - + -
143B ALA* 2.8 26.4 + - + +
144B SER* 4.0 3.8 - - - +
146B ASP* 1.4 79.1 - - + +
148B ASP* 1.3 57.7 + - - +
150B SER* 3.8 3.6 - - - +
151B LEU* 2.8 30.1 + - - +
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ALA* 3.6 12.0 - - - +
122B ARG* 2.9 44.3 + - - -
144B SER* 2.8 29.9 + - - +
145B ARG* 4.2 3.6 - - - +
147B LEU* 1.3 72.8 - - - +
149B LYS* 1.3 62.4 + - - +
151B LEU* 3.7 8.8 - - - +
152B TRP* 3.1 22.5 + - - +
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Residues in contact with LYS 149 (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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145B ARG 3.1 19.4 + - - +
146B ASP* 3.8 10.3 - - - +
148B ASP* 1.3 75.8 - - - +
150B SER* 1.3 60.0 + - - +
152B TRP* 3.3 25.2 + - + +
153B PHE* 2.9 59.5 + - + -
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Residues in contact with SER 150 (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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58B PHE* 3.5 36.9 - - - +
61B GLN* 3.6 10.7 + - - -
114B TYR* 3.9 20.9 - - - -
146B ASP 2.8 18.3 + - - -
147B LEU* 3.8 5.2 - - - -
149B LYS* 1.3 73.3 - - - +
151B LEU* 1.4 66.1 + - - +
153B PHE* 3.2 4.6 + - - +
154B LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 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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111B ILE* 3.9 13.2 - - + +
114B TYR* 4.2 9.7 - - + -
115B GLY* 3.7 37.2 - - - +
118B ALA* 4.5 12.1 - - + -
119B ASN* 5.6 2.7 - - - +
122B ARG* 5.4 3.6 - - - +
147B LEU 2.8 18.7 + - - +
148B ASP* 3.7 10.5 - - - +
150B SER* 1.4 75.7 - - - +
152B TRP* 1.3 57.5 + - - +
154B LEU* 3.2 8.8 + - + +
155B GLU* 2.9 60.0 + - + +
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Residues in contact with TRP 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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148B ASP 3.1 15.7 + - - +
149B LYS* 3.6 26.9 - - + +
150B SER 3.3 0.2 - - - -
151B LEU* 1.3 74.6 - - - +
153B PHE* 1.3 93.6 + + - +
155B GLU* 3.2 8.9 + - - +
156B ALA* 2.7 45.8 + - + +
159B GLN* 4.8 7.6 - - - -
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Residues in contact with PHE 153 (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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54B LEU* 3.9 32.5 - - + -
58B PHE* 3.9 17.0 - + + -
149B LYS* 2.9 39.7 + - + +
150B SER* 3.2 8.5 + - - +
152B TRP* 1.3 118.2 - + - +
154B LEU* 1.3 59.5 + - - +
156B ALA* 3.6 9.0 + - + +
157B HIS* 2.8 26.7 + - - +
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Residues in contact with LEU 154 (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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51B VAL* 5.9 1.6 - - + -
54B LEU* 5.3 5.2 - - + -
55B LEU* 4.4 5.6 - - + -
58B PHE* 3.8 20.2 - - + -
107B LEU* 3.9 24.8 - - + +
110B LEU* 4.1 26.5 - - + +
111B ILE* 3.6 20.5 - - + +
114B TYR* 3.6 43.7 - - + -
150B SER 3.0 18.4 + - - +
151B LEU* 3.6 5.8 - - - +
153B PHE* 1.3 74.9 - - - +
155B GLU* 1.3 65.3 + - - +
157B HIS* 3.0 23.5 + - + +
158B VAL* 3.9 2.3 + - - +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 3.8 33.2 - - + +
151B LEU* 2.9 47.3 + - + +
152B TRP* 3.9 7.0 - - - +
154B LEU* 1.3 76.2 - - - +
156B ALA* 1.3 58.1 + - - +
158B VAL* 2.9 8.1 + - + +
159B GLN* 2.9 53.6 + - + +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TRP* 2.7 41.0 + - + +
153B PHE* 3.9 7.0 - - - +
154B LEU 3.2 0.2 - - - -
155B GLU* 1.3 72.5 - - - +
157B HIS* 1.3 62.0 + - + +
158B VAL 3.2 0.4 + - - -
159B GLN* 3.3 18.6 + - - +
160B GLU* 4.7 5.2 + - - +
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Residues in contact with HIS 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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47B GLN* 2.9 42.0 + - - +
50B ALA* 5.9 0.9 - - + -
51B VAL* 4.1 9.8 - - + +
54B LEU* 4.2 18.6 - - + +
107B LEU* 3.8 25.8 - - + +
153B PHE* 2.8 30.9 + - - +
154B LEU* 3.0 14.7 + - + +
156B ALA* 1.3 80.1 - - + +
158B VAL* 1.3 59.4 + - - +
160B GLU 3.6 11.8 - - - +
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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) + - + + + + + -
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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