Contacts of the helix formed by residues 170 - 192 (chain F) in PDB entry 3A68
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 TYR 170 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F GLU* 4.4 6.5 - - - -
94F HIS* 2.8 53.7 + + + -
97F LYS* 3.3 22.6 - - + +
98F LEU* 3.3 24.2 + - + +
147F LEU* 3.9 33.9 - - + +
165F PHE* 3.6 26.9 - + - -
166F VAL* 3.0 27.1 + - + +
168F THR 3.5 0.6 - - - -
169F GLU* 1.3 92.5 - - + +
171F LEU* 1.3 60.7 + - - +
172F GLY 3.5 1.8 - - - -
173F GLU* 3.4 7.4 + - - +
174F GLN* 2.9 31.4 + - - +
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ASN* 4.3 9.8 - - - +
147F LEU* 3.8 29.6 - - + -
148F LEU* 3.9 23.6 - - + -
151F HIS* 4.3 6.5 - - + -
166F VAL* 3.2 18.2 + - + +
167F GLU* 3.4 23.4 + - + +
170F TYR* 1.3 74.5 - - - +
172F GLY* 1.3 66.4 + - - +
174F GLN* 3.3 4.3 + - - +
175F VAL* 3.2 18.7 + - - +
160O VAL* 3.5 32.8 - - + -
161O GLN* 3.6 27.4 - - + +
164O ASP* 5.5 0.4 - - - +
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Residues in contact with GLY 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F GLU 3.9 5.9 + - - -
170F TYR 3.5 0.2 - - - -
171F LEU* 1.3 74.5 - - - +
173F GLU* 1.3 70.8 + - - +
175F VAL* 3.2 4.2 + - - +
176F GLU* 3.0 30.2 + - - +
215F CA 4.6 4.9 - - - -
161O GLN* 3.7 22.5 - - - +
164O ASP* 5.2 2.6 + - - -
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Residues in contact with GLU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F HIS* 5.8 9.6 - - + +
168F THR 3.5 3.1 - - - +
169F GLU* 3.3 29.8 - - - +
170F TYR* 3.6 6.8 - - + +
172F GLY* 1.3 78.7 + - - +
174F GLN* 1.3 57.2 - - - +
176F GLU* 3.2 10.9 + - - +
177F ALA* 2.9 28.6 + - - +
215F CA 2.6 29.0 - - - -
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Residues in contact with GLN 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F HIS* 5.7 1.6 - - - -
140F GLU* 2.7 57.7 + - - +
143F THR* 3.9 10.3 - - - +
144F ASN* 3.4 34.8 - - + +
147F LEU* 3.8 19.8 - - + +
170F TYR 2.9 17.8 + - - +
171F LEU* 3.7 6.1 - - - +
172F GLY 3.2 0.4 - - - -
173F GLU* 1.3 74.2 - - - +
175F VAL* 1.3 61.1 + - - +
177F ALA* 3.3 5.3 + - - +
178F ILE* 3.0 30.0 + - + +
214F CA 4.1 8.0 - - - -
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Residues in contact with VAL 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ASN* 5.2 11.7 - - - +
171F LEU 3.2 12.6 + - - +
172F GLY* 3.2 8.7 + - - +
174F GLN* 1.3 77.0 - - - +
176F GLU* 1.3 63.7 + - + +
178F ILE* 3.3 8.5 + - + +
179F LYS* 3.0 21.8 + - - +
101O TYR* 5.3 1.8 - - + -
104O LYS* 3.9 39.5 - - + +
105O ARG* 3.8 22.9 - - - +
161O GLN* 3.6 29.6 - - + +
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Residues in contact with GLU 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F GLY* 3.0 21.2 + - - +
173F GLU* 3.5 9.9 - - - +
175F VAL* 1.3 77.2 - - - +
177F ALA* 1.3 57.7 + - - +
179F LYS* 3.3 6.3 + - - +
180F ARG* 2.9 29.7 + - - +
104O LYS* 2.9 42.7 + - - +
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Residues in contact with ALA 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F GLU* 4.2 21.5 - - + +
173F GLU 2.9 16.1 + - - +
174F GLN* 3.7 8.1 - - - +
175F VAL 3.3 0.2 - - - -
176F GLU* 1.3 76.6 - - - +
178F ILE* 1.3 62.8 + - - +
180F ARG* 3.4 10.6 + - - +
181F ILE* 3.1 33.8 + - + +
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Residues in contact with ILE 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F LEU* 3.8 16.5 - - + +
140F GLU* 3.9 35.9 - - + +
141F LYS* 4.1 7.4 - - + +
144F ASN* 3.9 15.7 - - + +
174F GLN* 3.0 22.6 + - + +
175F VAL* 3.8 8.1 - - + +
176F GLU 3.3 0.2 - - - -
177F ALA* 1.3 74.3 - - - +
179F LYS* 1.3 59.9 + - - +
181F ILE* 4.9 0.2 - - - -
182F SER* 2.8 33.3 + - - -
37O ALA* 3.6 34.3 - - + +
39O GLN* 3.6 24.5 - - + +
104O LYS 5.8 0.7 - - - +
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Residues in contact with LYS 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ASP* 3.0 47.3 + - - -
73C ASP* 3.9 17.5 - - + +
175F VAL 3.0 16.0 + - - +
176F GLU* 3.8 5.4 - - - +
178F ILE* 1.3 76.8 - - - +
180F ARG* 1.3 62.8 + - - +
182F SER* 3.3 5.9 + - - -
183F GLU* 2.9 52.9 + - - +
37O ALA* 4.3 4.7 - - - +
100O GLU 5.3 0.4 + - - -
103O ASN* 3.8 20.5 - - - +
104O LYS* 3.8 30.9 - - + +
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Residues in contact with ARG 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F PHE* 3.5 30.2 - - - -
86F GLU* 5.9 1.0 + - - -
87F SER* 5.5 0.4 + - - -
176F GLU 2.9 18.3 + - - +
177F ALA* 3.6 11.2 - - - +
178F ILE 3.3 0.2 - - - -
179F LYS* 1.3 77.8 - - - +
181F ILE* 1.3 63.7 + - - +
183F GLU* 3.3 15.4 + - - +
184F TYR* 2.8 58.0 + - + +
204F LEU* 5.1 1.4 - - - +
207F GLU* 4.1 7.5 + - - -
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Residues in contact with ILE 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F TYR* 3.9 9.6 - - - +
83F PHE* 4.3 23.8 - - + -
133F MET* 3.5 32.3 - - - +
136F ALA* 4.1 10.5 - - + +
137F LEU* 3.6 18.4 - - + +
140F GLU* 3.4 34.5 - - + -
177F ALA* 3.1 17.2 + - + +
178F ILE 4.1 2.5 - - - +
180F ARG* 1.3 76.2 - - + +
182F SER* 1.3 66.9 + - - +
184F TYR* 3.0 8.6 + - + +
185F VAL* 2.9 21.4 + - + +
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Residues in contact with SER 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ASP* 3.5 29.4 - - - -
137F LEU* 3.4 16.8 - - - +
178F ILE 2.8 23.9 + - - -
179F LYS 3.5 5.2 - - - -
181F ILE* 1.3 76.5 - - - +
183F GLU* 1.3 56.0 + - - +
185F VAL* 3.2 2.6 + - - -
186F ALA* 2.9 24.9 + - - +
36O LEU* 3.5 17.8 - - - +
37O ALA* 3.3 22.3 + - - -
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Residues in contact with GLU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ASP* 4.6 3.1 - - - +
72C ARG 5.2 0.5 - - - +
73C ASP* 3.7 25.6 - - - +
76C ALA* 4.1 10.4 - - + -
78C ARG* 4.7 22.5 - - - +
179F LYS* 2.9 48.8 + - - +
180F ARG* 3.5 16.7 - - - +
181F ILE 3.2 0.2 - - - -
182F SER* 1.3 75.0 - - - +
184F TYR* 1.3 58.6 + - + +
186F ALA* 3.3 1.9 + - - +
187F GLN* 2.9 46.1 + - - +
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Residues in contact with TYR 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ARG* 6.1 0.4 - - - -
83F PHE* 3.8 25.8 - + - -
133F MET* 3.6 31.2 - - + -
180F ARG* 2.8 48.3 + - + +
181F ILE* 3.0 12.2 + - - +
183F GLU* 1.3 78.5 - - + +
185F VAL* 1.3 65.5 + - - +
187F GLN* 3.2 12.8 + - - +
188F LEU* 2.9 30.1 + - - +
200F PHE* 3.6 27.3 - + + -
203F MET* 4.8 1.3 - - + -
204F LEU* 3.4 16.4 - - + +
207F GLU* 2.6 35.1 + - - -
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Residues in contact with VAL 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LEU* 3.9 13.4 - - + +
133F MET* 3.8 35.0 - - + +
134F GLU* 4.0 13.5 - - + +
137F LEU* 4.3 12.1 - - + -
181F ILE 2.9 17.6 + - - +
182F SER 3.2 7.6 + - - +
184F TYR* 1.3 77.5 - - - +
186F ALA* 1.3 61.9 + - - +
188F LEU* 3.3 2.1 + - - +
189F ARG* 3.0 53.4 + - - +
28O VAL* 5.1 0.9 - - + -
36O LEU* 3.9 13.5 - - + -
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Residues in contact with ALA 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ASP 3.4 26.0 - - - +
74C ASN* 3.7 21.5 - - - +
75C VAL 4.7 2.0 - - - +
76C ALA* 3.8 8.3 - - + -
182F SER 2.9 8.0 + - - +
183F GLU 3.6 6.3 - - - +
185F VAL* 1.3 77.5 - - - +
187F GLN* 1.3 61.6 + - - +
189F ARG* 3.4 9.2 + - - +
190F ARG* 3.0 22.9 + - - +
36O LEU* 4.1 6.7 - - + -
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Residues in contact with GLN 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ALA* 3.9 22.3 - - + +
78C ARG* 3.1 33.6 + - - +
198C TRP* 2.8 35.6 + - + +
202C GLN* 4.2 0.2 - - - +
183F GLU* 2.9 36.7 + - - +
184F TYR* 3.8 18.8 - - - +
186F ALA* 1.3 73.0 - - - +
188F LEU* 1.3 61.4 + - - +
190F ARG* 3.1 7.4 + - - +
191F VAL* 3.0 36.1 + - - +
200F PHE* 3.9 12.1 - - + -
203F MET* 3.7 6.4 - - - +
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Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LEU* 5.5 0.4 - - + -
129F ALA* 3.8 35.0 - - + +
130F LEU* 4.0 18.9 - - + +
133F MET* 3.6 34.3 - - + -
184F TYR 2.9 18.3 + - - +
185F VAL 3.7 3.6 - - - +
187F GLN* 1.3 77.4 - - - +
189F ARG* 1.3 62.7 + - - +
191F VAL* 3.6 4.8 - - + +
192F GLY* 3.2 22.0 + - - -
197F VAL* 4.1 20.9 - - + +
200F PHE* 3.5 38.4 - - + -
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Residues in contact with ARG 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LEU* 3.9 19.8 - - + +
134F GLU* 2.9 28.5 + - - -
185F VAL* 3.0 31.2 + - - +
186F ALA* 3.6 8.7 - - - +
188F LEU* 1.3 76.9 - - - +
190F ARG* 1.3 61.6 - - - +
192F GLY* 3.9 6.8 + - - -
28O VAL* 3.5 15.6 + - - +
29O PRO 3.0 29.5 + - - -
30O THR* 3.9 21.9 + - - +
31O VAL 5.4 2.0 + - - -
32O PRO* 6.1 1.0 - - - +
36O LEU* 3.5 14.2 - - - +
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Residues in contact with ARG 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ASN 5.1 1.4 + - - -
75C VAL* 3.1 28.1 + - - +
76C ALA 5.3 1.0 + - - -
77C LEU* 3.6 27.4 - - - +
128C ASP* 3.1 38.4 + - - -
194C GLY* 3.3 46.2 - - - +
197C VAL* 3.8 11.7 - - - +
198C TRP* 4.1 18.2 - - + +
186F ALA 3.0 14.6 + - - +
187F GLN* 3.1 10.8 + - - +
189F ARG* 1.3 79.9 - - - +
191F VAL* 1.3 62.0 + - + +
192F GLY* 4.6 0.3 - - - -
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Residues in contact with VAL 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C HIS* 3.7 26.6 + - + +
198C TRP* 3.5 48.9 - - + -
187F GLN 3.0 23.7 + - - +
188F LEU* 3.6 12.8 - - + +
190F ARG* 1.3 77.6 - - - +
192F GLY* 1.3 65.5 + - - +
193F LYS 4.9 0.7 - - - +
196F GLY* 3.4 38.8 + - - +
197F VAL* 3.8 4.3 - - - +
200F PHE* 4.4 7.0 - - + -
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Residues in contact with GLY 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F LEU 3.2 14.2 + - - -
189F ARG 3.9 6.0 + - - -
190F ARG 3.4 2.6 - - - -
191F VAL* 1.3 79.2 - - - +
193F LYS* 1.3 67.7 + - - +
196F GLY* 3.7 0.5 - - - -
197F VAL* 3.1 27.7 + - - +
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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