Contacts of the helix formed by residues 136 - 160 (chain A) in PDB entry 1O9I
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 ASN 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER* 3.0 11.7 + - - +
135A GLY* 1.3 74.9 - - - +
137A LEU* 1.3 60.6 + - - +
138A VAL* 2.9 21.6 + - - +
139A ALA* 2.9 17.3 + - + +
140A ASP* 2.9 29.1 + - - -
200A VAL* 4.2 9.2 - - - +
201A PRO* 4.2 15.2 - - - +
261C LEU 5.6 0.7 - - - +
262C HIS* 2.9 25.4 + - - +
263C ASN* 5.3 0.4 - - - +
264C HIS* 3.8 25.8 + - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN* 4.3 12.1 - - + +
49A SER* 4.2 12.8 - - - +
55A TYR* 4.2 21.1 - - + -
59A LEU* 4.0 25.1 - - + -
135A GLY* 5.4 2.0 - - - -
136A ASN* 1.3 71.7 - - - +
138A VAL* 1.3 61.0 + - - +
139A ALA 3.3 0.4 - - - -
140A ASP* 3.6 20.6 - - + +
141A MET* 2.8 37.5 + - + +
192A LEU* 3.6 14.7 - - + +
264C HIS 2.8 14.1 + - - +
265C GLN* 3.8 36.6 - - + +
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASN* 2.9 10.3 + - - +
137A LEU* 1.3 78.2 - - - +
139A ALA* 1.3 63.8 + - - +
141A MET* 4.2 1.8 - - - +
142A ARG* 3.2 27.7 + - - +
189A GLN* 4.6 3.0 - - + +
192A LEU* 3.9 24.0 - - + +
193A GLU* 3.9 30.3 - - + +
196A TYR* 3.9 28.3 - - + -
197A GLY 4.3 6.1 - - - +
200A VAL* 3.4 23.3 - - + -
264C HIS* 3.8 8.4 + - + +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER* 4.3 5.2 - - - +
136A ASN* 2.9 21.3 + - + +
138A VAL* 1.3 77.6 - - - +
140A ASP* 1.3 63.5 + - - +
142A ARG* 3.2 11.5 + - - +
143A PHE* 3.0 23.9 + - - +
200A VAL* 4.0 22.6 - - + +
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN* 3.7 23.8 - - - +
132A THR* 3.6 16.3 - - - +
133A SER* 3.4 7.6 + - - -
134A SER* 2.7 45.8 + - - -
135A GLY 3.9 3.5 + - - -
136A ASN 2.9 19.4 + - - +
137A LEU* 3.5 11.2 + - + +
138A VAL 3.4 0.4 - - - -
139A ALA* 1.3 77.6 - - - +
141A MET* 1.3 59.8 + - - +
143A PHE* 3.1 7.0 + - - +
144A ASN* 2.8 35.8 + - - +
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Residues in contact with MET 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 4.0 23.6 - - + -
58A LEU* 4.4 8.5 - - + -
59A LEU* 3.9 27.1 - - + -
137A LEU* 2.8 28.8 + - + +
138A VAL 4.2 0.7 - - - +
140A ASP* 1.3 72.9 - - - +
142A ARG* 1.3 65.1 + - - +
144A ASN* 3.2 10.1 + - - +
145A VAL* 3.0 29.0 + - - +
185A PHE* 3.5 28.1 - - - +
188A ALA* 3.9 21.8 - - + -
189A GLN* 4.0 23.3 - - + +
192A LEU* 3.8 13.0 - - + -
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.2 18.7 + - - +
139A ALA* 3.2 11.1 + - - +
141A MET* 1.3 76.2 - - - +
143A PHE* 1.3 64.4 + - - +
145A VAL* 3.2 5.5 + - - +
146A VAL* 3.0 26.5 + - + +
189A GLN* 3.6 26.5 - - - +
193A GLU* 2.8 34.1 + - - +
198A ILE* 2.7 35.0 + - - +
199A ILE* 5.1 0.2 - - - +
200A VAL* 3.5 27.5 - - - +
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Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.7 35.2 - + - -
37A THR* 4.7 0.2 - - + -
41A SER* 3.6 25.6 - - - -
45A GLN* 3.9 7.4 - - - -
130A TYR 3.8 19.5 - - - -
132A THR* 3.7 34.8 - - + -
139A ALA 3.0 13.5 + - - +
140A ASP* 3.1 10.5 + - - +
142A ARG* 1.3 76.8 - - - +
144A ASN* 1.3 71.0 + - - +
146A VAL* 3.1 10.6 + - + +
147A ARG* 2.8 36.7 + - + +
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Residues in contact with ASN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 3.2 22.6 - - + -
45A GLN* 2.8 42.4 + - - -
59A LEU* 3.4 19.0 - - - +
140A ASP 2.8 15.9 + - - +
141A MET* 3.2 17.2 + - - +
143A PHE* 1.3 79.2 - - - +
145A VAL* 1.3 66.3 + - - +
147A ARG* 3.2 3.1 + - - +
148A GLU* 3.1 27.7 + - - +
185A PHE* 3.6 23.6 - - + -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET 3.0 18.6 + - - +
142A ARG* 3.2 7.6 + - - +
144A ASN* 1.3 76.4 - - - +
146A VAL* 1.3 55.2 + - + +
148A GLU* 3.3 5.5 + - - +
149A SER* 2.7 45.7 + - - +
182A GLN* 4.0 6.5 - - + +
185A PHE* 3.6 20.9 - - + -
186A MET* 3.6 39.9 - - + +
189A GLN* 3.7 17.3 - - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.6 26.9 - - + -
142A ARG* 3.0 16.5 + - + +
143A PHE* 3.1 11.9 + - + +
145A VAL* 1.3 74.6 - - + +
147A ARG* 1.3 67.1 + - - +
149A SER* 3.1 6.1 + - - -
150A GLU* 2.8 38.2 + - + +
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 2.9 62.6 + - + +
34A GLY 3.0 13.6 + - - -
35A GLU* 3.0 22.8 + - - -
37A THR* 4.1 12.1 - - + -
38A GLY* 3.7 18.3 - - - +
42A PHE* 4.2 6.4 - - + -
66A GLU* 3.2 26.1 + - - -
143A PHE* 2.8 26.1 + - + +
144A ASN* 3.2 11.6 + - - +
146A VAL* 1.3 72.9 - - - +
148A GLU* 1.3 87.4 + - - +
150A GLU* 3.9 0.9 - - - +
151A ALA* 2.9 43.0 + - - +
178A GLU* 5.6 1.0 + - - +
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Residues in contact with GLU 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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42A PHE* 3.3 13.0 - - + -
66A GLU* 2.9 22.7 - - - +
144A ASN 3.1 17.2 + - - +
145A VAL 3.8 1.1 - - - +
147A ARG* 1.3 90.5 + - - +
149A SER* 1.3 58.5 + - - +
151A ALA* 4.0 3.2 - - - +
152A ARG* 3.0 23.2 + - - +
178A GLU* 3.4 27.9 - - - +
181A HIS* 3.3 32.5 + - + +
182A GLN* 3.2 32.2 + - + +
185A PHE* 4.0 9.0 - - + -
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Residues in contact with SER 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 VAL* 2.7 32.2 + - - +
146A VAL* 3.6 7.2 - - - -
148A GLU* 1.3 75.9 - - - +
150A GLU* 1.3 62.9 + - - +
152A ARG* 3.4 1.0 + - - +
153A LEU* 2.9 28.8 + - - +
182A GLN* 3.5 23.6 + - - +
186A MET* 5.6 0.3 - - - +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.5 45.9 + - + +
146A VAL* 2.8 32.2 + - + +
149A SER* 1.3 74.7 - - - +
151A ALA* 1.3 63.3 + - - +
153A LEU* 3.4 20.7 + - - +
154A GLN* 3.0 31.6 + - - +
111D VAL 5.6 1.6 - - - +
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.6 9.8 - - - +
34A GLY* 5.5 0.2 - - - -
35A GLU* 4.5 2.0 - - - +
147A ARG* 2.9 45.7 + - - +
148A GLU* 4.0 4.0 - - - +
150A GLU* 1.3 76.9 - - - +
152A ARG* 1.3 57.1 + - - +
154A GLN* 3.0 10.1 + - - +
155A VAL* 2.9 30.7 + - + +
178A GLU* 3.8 16.6 - - - +
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Residues in contact with ARG 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 GLU 3.0 20.2 + - - +
149A SER 4.0 0.9 - - - +
150A GLU 3.4 0.2 - - - -
151A ALA* 1.3 72.3 - - - +
153A LEU* 1.3 60.7 + - - +
155A VAL* 4.3 0.2 - - - -
156A SER* 2.8 42.3 + - - -
175A LEU* 2.9 45.6 + - + +
178A GLU* 3.1 26.8 + - + +
179A THR* 3.1 21.6 + - - +
182A GLN* 3.6 21.5 - - - +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A SER 2.9 18.5 + - - +
150A GLU* 3.5 23.6 - - - +
151A ALA 3.2 0.2 - - - -
152A ARG* 1.3 76.9 - - - +
154A GLN* 1.3 59.5 + - + +
156A SER* 3.3 9.7 + - - -
157A ARG* 3.0 73.7 + - + +
111D VAL 5.3 1.8 - - - +
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Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 3.5 31.4 + - + +
28A SER* 5.1 4.4 + - - +
32A GLN* 5.3 0.4 + - - +
33A TRP* 4.2 35.7 - - - +
34A GLY* 5.3 1.0 - - - -
150A GLU* 3.0 20.2 + - - +
151A ALA* 3.0 9.1 + - - +
153A LEU* 1.3 79.2 - - + +
155A VAL* 1.3 58.0 + - + +
157A ARG* 3.1 6.3 + - - +
158A LEU* 2.8 36.5 + - + +
110D LEU* 3.6 27.4 - - + +
111D VAL* 4.0 27.6 + - - +
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 4.7 14.1 - - - +
35A GLU* 6.0 0.9 - - - +
151A ALA* 2.9 20.7 + - + +
152A ARG 3.8 1.6 - - - +
153A LEU 3.3 0.2 - - - -
154A GLN* 1.3 75.7 - - + +
156A SER* 1.3 57.5 + - - +
158A LEU* 3.2 10.7 + - + +
159A TYR* 2.9 27.4 + - - +
171A LEU* 3.7 35.4 - - + +
174A LEU* 4.5 10.5 - - + -
175A LEU* 3.5 22.0 - - + +
178A GLU* 3.5 26.0 - - - +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG* 2.8 33.6 + - - +
153A LEU* 3.5 11.1 - - - -
155A VAL* 1.3 76.4 - - - +
157A ARG* 1.3 62.4 + - - +
159A TYR* 3.3 20.0 + - - +
160A SER* 3.6 8.3 + - - -
175A LEU* 3.4 18.4 - - - +
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.0 55.0 + - + +
154A GLN* 3.1 7.7 + - - +
156A SER* 1.3 77.4 - - - +
158A LEU* 1.3 62.1 + - - +
160A SER* 2.9 18.2 + - - -
161A MET* 3.2 25.7 + - + +
86D PHE* 5.6 2.4 - - + -
109D SER 3.7 9.3 + - - -
110D LEU* 3.0 35.5 + - + -
111D VAL 3.2 23.2 + - - -
112D HIS 4.2 1.2 - - - -
113D GLY* 3.5 24.3 - - - +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.6 24.4 - - + +
24A ARG* 3.7 33.4 - - + +
25A LEU* 3.9 14.6 - - + +
27A GLU* 5.9 0.2 - - + -
28A SER* 3.5 25.1 - - - +
154A GLN* 2.8 22.1 + - + +
155A VAL* 3.2 15.9 + - + +
157A ARG* 1.3 75.7 - - - +
159A TYR* 1.3 57.7 + - - +
161A MET* 2.9 27.7 + - - +
162A THR* 3.5 6.4 + - - +
171A LEU* 3.8 12.3 - - + -
110D LEU* 3.8 21.3 - - + -
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL 2.9 12.9 + - - +
156A SER* 3.3 15.0 - - - +
157A ARG 3.1 0.4 - - - -
158A LEU* 1.3 76.4 - - - +
160A SER* 1.3 63.7 + - - +
162A THR* 3.1 7.7 + - - +
165A GLU* 5.4 1.0 + - - -
168A ARG* 2.9 90.7 + - + +
171A LEU* 3.7 16.4 - - + +
172A LYS* 3.7 35.2 + - + -
175A LEU* 5.1 10.3 - - + -
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A SER 3.6 6.6 + - - -
157A ARG* 2.9 12.9 + - - -
159A TYR* 1.3 82.9 - - - +
161A MET* 1.3 58.3 + - - +
162A THR 3.5 2.5 - - - -
168A ARG* 4.4 6.1 + - - +
86D PHE* 4.6 15.4 - - - -
87D GLY* 3.7 7.4 - - - -
88D PRO* 3.4 14.2 - - - +
89D GLU 5.3 0.9 + - - -
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il