Contacts of the helix formed by residues 180 - 206 (chain E) in PDB entry 4PHZ
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 GLY 180 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E HIS 3.2 1.6 + - - -
179E TYR* 1.3 83.2 - - - +
181E ILE* 1.3 62.2 + - - +
182E SER* 3.2 3.7 - - - +
183E ARG* 3.2 21.3 + - - +
184E VAL* 3.3 14.0 + - - +
171F ALA* 4.7 10.5 - - - +
172F PHE* 3.8 19.7 - - - -
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Residues in contact with ILE 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E GLU 3.8 22.7 - - - +
178E HIS* 3.4 17.2 + - - +
179E TYR 3.3 0.4 - - - -
180E GLY* 1.3 76.2 - - - +
182E SER* 1.3 61.6 + - - +
184E VAL* 3.4 10.6 + - - +
185E TYR* 3.3 48.6 + - + +
120F PRO* 4.4 2.5 - - + -
121F ILE* 4.0 20.6 - - + +
122F SER* 3.6 42.2 - - - +
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Residues in contact with SER 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E HIS 4.6 2.4 + - - -
180E GLY 3.2 2.0 - - - +
181E ILE* 1.3 74.3 - - - +
183E ARG* 1.3 55.3 + - - +
184E VAL 3.2 0.2 + - - -
185E TYR* 3.3 11.1 + - - +
186E ALA* 2.8 34.9 + - - +
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Residues in contact with ARG 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E GLY* 3.5 12.3 - - - +
182E SER* 1.3 79.2 - - - +
184E VAL* 1.3 62.6 + - + +
186E ALA* 3.2 10.3 + - + +
187E TRP* 3.0 24.5 + - + +
249E VAL* 5.2 4.4 - - - +
250E THR* 3.5 25.4 - - + +
253E THR* 3.5 28.5 + - - +
254E PHE* 3.4 33.0 - - - -
167F PRO 3.9 21.0 - - - +
168F ALA* 5.4 2.2 - - - +
171F ALA* 4.2 11.2 - - - +
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Residues in contact with VAL 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E GLY 3.3 13.8 + - - +
181E ILE* 3.5 11.0 - - - +
182E SER 3.1 0.6 - - - -
183E ARG* 1.3 75.5 - - + +
185E TYR* 1.3 59.8 + - - +
187E TRP* 3.1 5.5 + - - +
188E HIS* 2.8 32.3 + - + +
106F TRP* 3.6 30.3 - - + -
121F ILE* 4.8 4.5 - - + +
125F PHE* 3.8 29.2 - - + -
168F ALA* 3.8 30.5 - - + +
172F PHE* 4.1 13.5 - - + -
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Residues in contact with TYR 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E ILE* 3.3 36.1 + - + +
182E SER* 3.6 8.3 - - - +
184E VAL* 1.3 77.0 - - + +
186E ALA* 1.3 62.8 + - - +
188E HIS* 4.4 2.0 - - - +
189E LEU* 3.0 52.8 + - + +
190E PRO* 3.5 4.3 - - - +
106F TRP* 3.7 33.9 - + - -
110F TYR* 3.7 23.5 - + - -
121F ILE* 3.5 23.8 - - + +
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Residues in contact with ALA 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E SER 2.8 17.7 + - - +
183E ARG* 3.2 15.7 + - + +
185E TYR* 1.3 73.0 - - - +
187E TRP* 1.3 59.7 + - - +
190E PRO* 2.9 25.7 - - - +
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Residues in contact with TRP 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E ARG 3.0 12.0 + - - +
184E VAL 3.6 6.1 - - - +
186E ALA* 1.3 80.7 - - - +
188E HIS* 1.3 79.0 + + + +
189E LEU 3.5 0.2 - - - -
190E PRO* 3.8 3.1 - - + +
191E TRP* 3.2 66.2 + + - -
242E ALA* 3.8 22.0 - - + -
243E THR* 4.7 7.0 - - - -
246E GLY* 4.0 22.2 - - - -
128F ALA* 4.8 4.2 - - + +
163F PRO 5.2 0.2 - - - -
164F ASN* 2.8 34.8 + - + -
167F PRO* 3.7 33.7 - - + +
168F ALA* 4.3 12.3 - - + +
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Residues in contact with HIS 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E VAL* 2.8 25.8 + - + +
185E TYR* 4.6 0.2 - - - -
187E TRP* 1.3 82.3 - + - +
189E LEU* 1.3 68.1 + - + +
191E TRP* 3.4 6.8 + - - +
192E MET* 3.1 25.7 + - - +
102F LEU* 4.6 5.3 - - + +
106F TRP* 2.9 46.8 + + + +
125F PHE* 4.5 2.6 - + - -
126F PRO* 3.1 31.3 + - + -
127F SER 4.1 4.3 - - - -
128F ALA* 3.9 24.4 + - + +
165F ASN* 4.9 0.8 + - - -
168F ALA* 4.1 24.3 - - + +
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Residues in contact with LEU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E TYR* 3.0 43.7 + - + +
188E HIS* 1.3 84.1 - - + +
190E PRO* 1.3 74.0 - - + +
192E MET* 3.2 20.0 + - + +
193E ALA* 2.8 24.6 + - - +
106F TRP* 4.9 9.2 - - + -
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Residues in contact with PRO 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E TYR 3.5 5.2 - - - +
186E ALA* 2.9 29.8 - - - +
187E TRP* 3.8 4.7 - - + +
189E LEU* 1.3 89.8 - - + +
191E TRP* 1.3 54.7 + - + +
193E ALA* 3.1 9.8 + - + +
194E VAL* 2.7 40.6 + - + +
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Residues in contact with TRP 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E TRP* 3.2 63.8 + + - +
188E HIS* 3.4 9.0 + - - +
189E LEU 3.3 0.8 - - - -
190E PRO* 1.3 80.8 - - + +
192E MET* 1.3 57.9 + - - +
194E VAL* 3.2 28.2 + - + +
195E GLY 2.8 25.6 + - - -
239E THR* 3.6 32.5 - - + -
242E ALA* 4.0 21.8 - - + -
243E THR* 4.1 7.0 - - - -
130F ILE* 3.6 36.9 - - + +
131F VAL* 3.5 31.3 - - + +
134F ILE* 4.2 3.1 - - + -
164F ASN* 5.6 3.1 - - - -
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Residues in contact with MET 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E HIS* 3.1 19.0 + - - +
189E LEU* 3.2 19.7 + - + +
191E TRP* 1.3 75.6 - - - +
193E ALA* 1.3 58.2 - - - +
195E GLY 3.3 0.5 + - - -
196E ALA* 2.9 29.6 + - - +
99F LEU* 3.7 17.9 - - + +
102F LEU* 3.9 9.4 - - + -
103F ILE* 3.3 46.2 - - + +
106F TRP* 3.6 32.1 - - + -
130F ILE* 3.8 16.2 - - + -
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Residues in contact with ALA 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E LEU 2.8 13.8 + - - +
190E PRO* 3.2 13.2 - - + +
192E MET* 1.3 74.6 - - - +
194E VAL* 1.3 57.8 + - + +
196E ALA* 3.2 8.0 + - - +
197E ALA* 2.8 29.8 + - - +
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Residues in contact with VAL 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E PRO* 2.7 22.1 + - + +
191E TRP* 3.5 36.6 - - + +
193E ALA* 1.3 70.2 - - + +
195E GLY* 1.3 66.3 + - - +
197E ALA* 3.1 9.6 + - - +
198E TRP* 3.0 25.0 + - + +
235E VAL* 5.8 6.3 - - + -
239E THR* 5.5 2.2 - - - +
134F ILE* 4.4 10.3 - - + -
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Residues in contact with GLY 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E TRP 2.8 17.9 + - - -
192E MET 3.7 3.6 - - - -
194E VAL* 1.3 76.9 - - - +
196E ALA* 1.3 60.7 + - - +
198E TRP* 3.2 5.6 + - - +
199E ILE* 3.1 23.9 + - - +
95F VAL* 3.7 21.2 - - - +
99F LEU* 4.3 4.5 - - - -
130F ILE* 4.5 12.1 - - - -
134F ILE* 5.6 1.6 - - - -
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Residues in contact with ALA 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E MET 2.9 13.5 + - - +
193E ALA* 3.6 8.7 - - - +
195E GLY* 1.3 72.2 - - - +
197E ALA* 1.3 66.5 + - - +
198E TRP 3.2 0.2 + - - -
199E ILE* 3.2 4.5 + - - +
200E PHE* 2.8 46.2 + - + -
99F LEU* 3.8 19.7 - - + +
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Residues in contact with ALA 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E ALA 2.8 16.9 + - - +
194E VAL* 3.4 13.2 - - - +
196E ALA* 1.3 72.7 - - - +
198E TRP* 1.3 51.1 + - - +
200E PHE* 3.1 6.8 + - - +
201E PHE* 2.7 36.1 + - - +
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Residues in contact with TRP 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E VAL* 3.0 13.8 + - + +
195E GLY* 3.5 9.0 - - - +
196E ALA 3.2 0.2 - - - -
197E ALA* 1.3 71.9 - - - +
199E ILE* 1.3 67.5 + - - +
201E PHE* 3.5 7.6 + + - +
202E TRP* 2.9 69.2 + + - -
231E ILE* 5.1 1.6 - - + -
232E GLY* 4.2 9.0 - - - -
235E VAL* 3.8 43.3 - - + -
91F PRO 3.5 25.6 + - - -
92F PHE* 3.6 17.0 - - + +
95F VAL* 4.0 26.4 - - + +
134F ILE* 5.6 9.0 - - + -
137F ASP* 4.4 5.1 + - + -
138F VAL* 3.7 28.5 - - + -
141F LEU* 4.2 6.7 - - + -
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Residues in contact with ILE 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E GLY 3.1 8.1 + - - +
196E ALA* 3.6 6.7 - - - +
198E TRP* 1.3 81.0 - - - +
200E PHE* 1.3 72.2 + - + +
202E TRP 3.3 0.7 + - - -
203E PHE* 3.0 19.2 + - + +
31F LEU* 4.5 19.7 - - + -
35F PHE* 4.9 4.9 - - + -
92F PHE* 3.8 38.4 - - + -
95F VAL* 4.0 11.9 - - + +
96F PHE* 3.7 36.1 - - + +
99F LEU* 3.8 28.0 - - + -
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Residues in contact with PHE 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E ALA* 2.8 49.2 + - + -
197E ALA* 3.6 7.4 - - - +
199E ILE* 1.3 78.2 - - + +
201E PHE* 1.3 70.3 + - - +
203E PHE* 3.3 11.4 + + - +
204E VAL* 3.0 27.8 + - + +
28F TRP* 3.6 39.7 - + - -
31F LEU* 4.9 8.5 - - + -
99F LEU* 6.2 0.7 - - + -
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Residues in contact with PHE 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E ALA 2.7 16.5 + - - +
198E TRP* 3.5 14.4 - + - +
199E ILE 3.2 0.2 - - - -
200E PHE* 1.3 77.0 - - - +
202E TRP* 1.3 113.5 + + - +
204E VAL* 2.9 16.2 + - + +
205E ARG* 3.0 54.6 + - + +
228E ASP* 5.9 0.2 - - - -
231E ILE* 3.7 33.0 - - + -
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Residues in contact with TRP 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E TRP* 2.9 74.2 - + - -
199E ILE 3.3 1.4 + - - -
201E PHE* 1.3 101.8 - + - +
203E PHE* 1.3 62.8 + - - +
204E VAL 3.1 0.9 + - - -
205E ARG* 4.6 1.6 - - - +
206E LYS* 3.1 42.8 + - + +
224E ILE* 3.8 17.0 - - + -
228E ASP* 3.7 45.5 - - + -
231E ILE* 4.5 5.6 - - + -
90F LEU* 3.8 7.2 - - + +
91F PRO* 3.6 28.5 - - + -
92F PHE* 3.7 20.4 - + + -
141F LEU* 4.1 11.9 - - + -
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Residues in contact with PHE 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E ILE 3.0 17.2 + - - +
200E PHE* 3.7 10.3 - + - +
201E PHE 3.2 0.4 - - - -
202E TRP* 1.3 77.3 - - - +
204E VAL* 1.3 68.2 + - + +
206E LYS 2.6 17.3 - - - +
207E GLY* 4.1 4.4 - - - -
208E ILE* 3.5 29.8 - - + -
24F GLN* 4.2 8.5 - - - -
27F ASP* 3.5 45.7 - - + +
28F TRP* 3.8 44.0 - + - -
31F LEU* 4.0 23.1 - - + -
90F LEU* 5.0 2.5 - - - -
92F PHE* 4.1 10.5 - + + -
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Residues in contact with VAL 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E PHE* 3.0 20.5 + - + +
201E PHE* 2.9 5.0 + - - +
203E PHE* 1.3 90.9 - - + +
205E ARG* 1.3 70.2 + - + +
206E LYS 2.8 16.2 + - - +
207E GLY* 5.0 0.3 - - - -
28F TRP* 5.6 5.4 - - + -
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Residues in contact with ARG 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E PHE* 3.0 59.7 + - + +
202E TRP* 4.6 2.0 - - + +
204E VAL* 1.3 80.7 - - + +
206E LYS* 1.3 83.3 + - + +
231E ILE* 4.7 8.3 - - - +
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Residues in contact with LYS 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E TRP* 3.1 31.0 + - + +
203E PHE 2.6 23.4 - - - +
204E VAL 3.4 4.2 - - - +
205E ARG* 1.3 103.7 - - + +
207E GLY* 1.3 62.8 + - - +
210E THR* 5.7 2.7 - - + -
211E SER* 3.3 19.7 - - - +
214E ARG* 5.4 7.4 - - - +
222E ASP 5.3 1.7 + - - +
223E VAL* 2.8 38.3 + - + +
224E ILE* 5.4 0.7 - - + -
228E ASP* 2.7 34.8 + - - -
90F LEU* 4.1 10.8 - - + -
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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