Contacts of the helix formed by residues 136 - 164 (chain A) in PDB entry 3OTB
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 SER 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.8 8.6 - - - -
84A ARG* 4.9 2.7 - - - +
134A TYR 3.4 0.5 - - - +
135A PRO* 1.3 81.9 - - - +
137A ASN* 1.3 65.7 + - - +
138A GLN* 3.7 9.4 + - - +
139A THR* 2.6 55.3 + - - +
140A LEU* 3.0 12.0 + - - +
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Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.2 19.4 + - - +
84A ARG* 2.9 40.6 + - - +
136A SER* 1.3 73.9 - - - +
138A GLN* 1.3 52.5 + - - +
140A LEU* 3.3 2.9 + - - +
141A LYS* 2.8 45.0 + - - +
265A LEU* 4.0 25.4 - - + +
266A ASP* 5.6 4.4 + - - -
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Residues in contact with GLN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 3.1 8.9 - - - +
137A ASN* 1.3 80.3 - - - +
139A THR* 1.3 57.2 + - + +
141A LYS* 3.4 18.3 + - - +
142A ASP* 2.4 61.6 + - - +
8B TYR* 5.1 2.9 - - - +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.8 18.4 - - - +
135A PRO* 3.6 11.8 - - + +
136A SER* 2.6 52.2 + - - +
138A GLN* 1.3 73.3 - - + +
140A LEU* 1.3 59.3 + - - +
142A ASP* 3.2 3.1 + - - +
143A TYR* 2.8 26.9 + - - +
8B TYR* 4.0 20.4 - - + +
9B VAL* 3.8 4.8 - - - +
12B PHE* 4.2 20.0 - - + -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.4 46.2 - - + +
25A VAL* 3.7 29.8 - - + -
69A VAL* 6.3 0.2 - - + -
70A ILE* 5.8 0.7 - - + -
81A VAL* 3.7 23.8 - - + -
134A TYR* 4.0 11.2 - - + +
136A SER 3.0 13.0 + - - +
137A ASN 3.5 7.2 - - - +
139A THR* 1.3 74.2 + - - +
141A LYS* 1.3 60.0 + - - +
143A TYR* 2.8 34.2 + - + +
144A LEU* 3.0 16.1 + - + +
258A TRP* 6.1 0.2 - - + -
265A LEU* 4.6 16.6 - - + -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASN* 2.8 25.6 + - - +
138A GLN* 3.6 20.1 + - - +
140A LEU* 1.3 73.2 - - - +
142A ASP* 1.3 61.2 + - - +
144A LEU* 3.1 12.0 + - - +
145A SER* 2.9 33.2 + - - +
252A ILE 4.7 2.6 - - - +
253A ILE 6.0 1.3 - - - +
255A ASP* 6.1 0.4 - - - -
258A TRP* 3.5 54.6 - - + +
265A LEU* 3.6 25.9 - - + +
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Residues in contact with ASP 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLN* 2.4 53.4 + - - +
139A THR 3.3 5.2 - - - +
141A LYS* 1.3 76.7 - - - +
143A TYR* 1.3 58.0 + - - +
145A SER* 3.7 1.4 - - - -
146A TRP* 2.8 29.5 + - - +
5B LYS 4.9 0.7 - - - +
6B PHE* 3.7 29.2 - - + -
8B TYR* 2.8 39.1 + - + +
9B VAL* 3.7 9.4 - - + +
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.8 22.7 - - + -
27A ARG* 2.7 41.9 + - - +
79A SER* 2.9 20.3 + - - -
81A VAL* 5.4 0.9 - - + -
132A VAL* 6.0 2.5 - - + -
134A TYR* 3.3 39.3 - + + -
139A THR 2.8 12.8 + - - +
140A LEU* 2.8 19.7 + - + +
142A ASP* 1.3 76.7 - - - +
144A LEU* 1.3 73.8 - - + -
146A TRP* 3.0 45.8 + + - +
147A ARG* 3.0 22.8 + - + +
9B VAL* 3.8 8.7 - - + +
13B GLU* 6.0 0.4 - - - -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 4.4 15.5 - - + -
71A ALA 5.7 0.9 - - - -
72A TYR* 3.9 31.6 - - + -
79A SER* 5.3 2.2 - - - -
81A VAL* 4.9 13.0 - - + -
140A LEU* 3.0 21.7 + - + +
141A LYS* 3.4 8.5 - - - +
143A TYR* 1.3 92.5 - - + +
145A SER* 1.3 59.2 + - - +
147A ARG* 2.6 27.3 + - + +
148A GLN* 2.8 12.6 + - - +
252A ILE* 4.0 19.8 - - + +
258A TRP* 3.7 33.9 - - + -
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 2.9 19.0 + - - +
142A ASP 3.7 0.4 - - - -
144A LEU* 1.3 75.6 - - - +
146A TRP* 1.3 58.2 + - - +
148A GLN 4.5 0.2 - - - +
149A ALA* 2.8 37.7 + - - +
252A ILE* 4.4 2.9 + - - +
253A ILE* 3.6 38.8 + - - +
6B PHE* 3.3 37.6 - - - -
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Residues in contact with TRP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 4.7 11.0 - - - -
134A TYR* 5.4 0.2 - - - -
142A ASP 2.8 15.8 + - - +
143A TYR* 3.0 30.3 - + - +
144A LEU 3.0 0.2 - - - -
145A SER* 1.3 75.2 - - - +
147A ARG* 1.3 89.9 + - - +
149A ALA* 4.0 2.4 - - + +
150A ASP* 3.0 29.8 + - + +
6B PHE* 3.8 21.0 - - + +
7B GLU* 3.5 54.2 + - + +
9B VAL* 3.6 19.5 - - + -
10B ARG* 4.0 37.7 - - + -
13B GLU* 4.8 3.6 - - - -
302B 3PO 4.8 8.7 - - - -
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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
----------------------------------------------------------
27A ARG* 4.4 5.8 - - - +
72A TYR* 3.7 21.3 - - + -
74A GLN* 3.0 11.6 + - - +
77A GLU* 3.1 37.2 + - - +
79A SER* 4.5 3.1 - - - +
143A TYR* 3.0 38.1 + - + +
144A LEU* 2.6 15.8 + - + +
146A TRP* 1.3 121.8 - - - +
148A GLN* 1.3 60.6 + - - +
150A ASP* 2.9 39.7 + - - +
151A CYS 2.8 24.6 + - - -
302B 3PO 4.9 9.5 + - - -
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.0 22.4 + - + +
144A LEU 2.8 15.1 + - - +
145A SER 4.1 2.0 - - - +
147A ARG* 1.3 73.4 - - - +
149A ALA* 1.3 52.0 + - - +
151A CYS* 2.9 6.2 - - - +
152A HIS* 2.8 34.4 + - + +
207A ARG 5.3 0.7 - - - +
208A LYS* 2.9 45.2 + - + +
250A CYS 3.2 23.2 + - - -
251A ASP* 3.0 15.5 - - - +
252A ILE* 2.9 39.5 + - + +
253A ILE* 3.3 12.3 - - + +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER 2.8 25.2 + - - +
146A TRP* 4.0 3.8 - - + +
148A GLN* 1.3 69.8 - - - +
150A ASP* 1.3 66.0 + - - +
152A HIS* 3.3 8.4 + - - +
153A ILE* 3.0 37.4 + - + +
253A ILE* 4.0 15.0 - - + +
6B PHE* 4.4 13.0 - - + -
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 2.7 22.9 - - - +
146A TRP* 3.0 20.5 + - + +
147A ARG* 2.9 35.8 + - - +
149A ALA* 1.3 75.6 - - - +
151A CYS* 1.3 57.1 + - - +
153A ILE* 3.2 9.3 + - - +
154A ASN* 2.3 54.0 + - - +
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Residues in contact with CYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.4 15.7 - - - +
74A GLN* 3.5 29.2 - - - +
147A ARG 2.8 4.9 + - - -
148A GLN 2.9 14.1 + - - +
150A ASP* 1.3 76.6 - - - +
152A HIS* 1.3 55.9 + - - -
154A ASN* 3.0 6.1 + - - +
155A ASN* 2.9 32.2 + - - +
205A MET 5.5 0.2 - - - -
206A TYR 3.9 15.7 - - - -
208A LYS 4.1 4.3 - - - -
209A GLY* 3.7 30.7 - - - -
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Residues in contact with HIS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLN* 2.8 18.4 + - + +
149A ALA* 3.3 8.9 + - - +
151A CYS* 1.3 74.2 - - - +
153A ILE* 1.3 70.1 + - + +
155A ASN* 4.8 0.9 - - - -
156A LEU* 3.3 42.2 + - + +
184A ALA* 6.1 3.1 - - + -
199A TYR* 3.9 27.1 + + - -
207A ARG* 3.9 21.1 - - + +
208A LYS* 5.3 10.8 - - - +
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ALA* 3.0 26.3 + - + +
150A ASP* 3.6 8.3 - - - +
151A CYS 3.2 0.2 - - - -
152A HIS* 1.3 87.7 - - + +
154A ASN* 1.3 67.5 + - - +
156A LEU* 4.3 4.0 - - - +
157A TYR* 3.4 19.3 + - - +
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Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 3.9 3.8 + - - -
75A SER* 6.3 0.2 - - - -
150A ASP* 2.3 55.3 + - - +
151A CYS* 3.0 6.9 + - - +
153A ILE* 1.3 85.1 - - - +
155A ASN* 1.3 54.6 + - - +
156A LEU 3.3 0.2 - - - -
157A TYR* 3.1 3.3 + - - +
158A ASN* 2.6 53.7 + - - +
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 4.5 3.8 - - - +
46A ASN* 3.0 29.7 + - - +
151A CYS* 2.9 15.0 + - - +
152A HIS 4.4 0.2 - - - +
154A ASN* 1.3 76.7 - - - +
156A LEU* 1.3 58.9 + - - +
158A ASN* 4.5 3.8 - - - +
159A THR* 2.6 46.6 + - - -
199A TYR* 3.4 21.8 + - - +
202A GLU* 5.2 3.4 - - - +
206A TYR* 2.7 45.4 + - - +
207A ARG* 3.4 3.9 - - - +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A HIS* 3.3 36.5 + - + +
153A ILE* 4.7 3.6 - - - +
155A ASN* 1.3 78.1 - - - +
157A TYR* 1.3 60.1 + - - +
159A THR* 4.3 0.6 - - - -
160A VAL* 3.3 21.8 + - - +
184A ALA* 4.3 28.0 - - + +
187A LYS* 3.9 15.4 - - + +
188A ASN* 4.4 23.3 - - - +
191A LEU* 4.9 3.3 - - + +
199A TYR* 3.5 45.7 + - + +
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE 3.4 18.0 + - - +
154A ASN* 3.1 6.1 + - - +
155A ASN 3.1 0.6 - - - -
156A LEU* 1.3 80.2 - - - +
158A ASN* 1.3 74.5 + - - +
160A VAL* 3.3 8.2 - - - +
161A PHE* 2.9 53.8 + + + +
176A GLN* 4.0 27.9 + - - +
179A LEU* 4.0 24.1 - - + +
180A GLN* 6.1 0.2 - - - +
187A LYS* 3.8 23.8 - - - +
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Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 3.7 20.7 + - + +
154A ASN* 2.6 42.4 + - - +
155A ASN* 4.2 3.2 - - - +
157A TYR* 1.3 85.9 - - - +
159A THR* 1.3 58.3 + - - +
161A PHE* 3.7 9.0 - - - -
162A TRP* 2.8 50.0 + - + +
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 3.7 25.9 - - + +
46A ASN* 4.6 0.7 + - - -
155A ASN* 2.6 36.6 + - - -
156A LEU 4.4 2.0 - - - -
158A ASN* 1.3 79.3 - - - +
160A VAL* 1.3 58.4 + - - +
162A TRP* 4.1 1.7 - - - +
163A ALA* 3.2 23.4 + - - +
191A LEU* 4.0 27.4 - - + -
197A ILE* 5.2 4.9 - - + -
199A TYR* 4.0 12.7 - - + -
202A GLU* 4.7 18.4 - - + +
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU 3.3 20.6 + - - +
157A TYR 3.3 7.2 - - - +
159A THR* 1.3 77.3 - - - +
161A PHE* 1.3 62.1 + - - +
163A ALA* 3.9 3.8 - - - +
164A LEU* 3.2 26.3 + - + +
179A LEU* 3.5 26.2 - - + -
187A LYS* 4.1 13.9 - - + +
190A ILE* 2.9 39.9 - - + -
191A LEU* 4.1 21.8 - - + -
195A PHE* 5.0 2.0 - - + -
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Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 2.9 48.0 + + + +
158A ASN* 3.0 14.1 + - - +
160A VAL* 1.3 79.9 - - - +
162A TRP* 1.3 87.9 + + - +
164A LEU 3.7 1.4 + - - -
165A ILE* 3.0 48.4 + - + +
172A PRO* 4.0 21.8 - - + -
175A ALA* 3.8 31.8 - - + +
176A GLN* 4.1 8.7 - - + -
179A LEU* 4.0 5.4 - - + -
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Residues in contact with TRP 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 3.5 55.8 - - + +
45A PRO* 3.9 19.6 - - + +
158A ASN* 2.8 33.2 + - + +
159A THR 4.4 2.0 - - - +
161A PHE* 1.3 96.4 - + - +
163A ALA* 1.3 59.1 + - - +
164A LEU 3.2 2.2 - - - -
165A ILE* 3.3 40.8 - - + -
166A GLN* 2.9 54.0 + - + +
167A GLN* 5.1 0.2 - - - -
172A PRO* 5.5 4.9 - - + -
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A THR 3.2 19.4 + - - +
160A VAL* 4.3 6.3 - - - -
161A PHE 3.4 0.4 - - - -
162A TRP* 1.3 78.4 - - - +
164A LEU* 1.3 57.1 + - - +
167A GLN* 3.3 19.7 + - - +
168A SER 3.0 22.2 + - - -
191A LEU* 4.6 0.9 - - + -
195A PHE* 3.1 40.2 - - + -
197A ILE* 4.4 13.0 - - + -
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 3.2 24.4 + - + +
161A PHE 3.9 0.7 - - - +
162A TRP 3.2 0.4 - - - -
163A ALA* 1.3 78.1 - - - +
165A ILE* 1.3 58.0 + - - +
168A SER* 3.2 16.4 - - - +
170A LEU* 2.8 41.7 + - + +
175A ALA* 3.9 38.1 - - + +
178A ARG* 4.3 15.9 - - + -
179A LEU* 4.3 13.0 - - + -
190A ILE* 4.6 9.6 - - + -
194A GLU* 4.5 5.2 - - + +
195A PHE* 3.3 27.8 - - + -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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