Contacts of the helix formed by residues 169 - 193 (chain B) in PDB entry 4EVI
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 ALA 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B CYS 4.5 1.6 - - - -
166B SER 5.4 0.8 + - - -
167B GLU 3.9 3.2 + - - -
168B ASP* 1.3 74.3 + - - +
170B ASN* 1.3 57.3 + - - +
172B SER* 3.4 6.9 + - - -
173B GLN* 2.8 33.6 + - - +
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Residues in contact with ASN 170 (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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124B HIS* 4.8 9.4 + - - -
168B ASP* 3.3 7.9 + - - +
169B ALA* 1.3 78.2 - - - +
171B PHE* 1.3 64.3 + - - +
173B GLN* 3.2 11.8 + - - +
174B LEU* 3.0 51.5 + - - +
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B CYS* 3.6 42.0 - - - -
124B HIS* 3.8 29.4 - + + +
126B HIS* 3.9 24.5 - + + -
127B LEU* 3.9 22.7 - - + -
152B PHE* 5.2 0.2 - + - -
161B VAL* 4.0 24.0 - - + -
164B VAL* 4.8 6.3 - - + -
165B CYS* 4.0 18.6 - - - -
168B ASP* 3.2 27.6 + - - +
170B ASN* 1.3 79.0 + - - +
172B SER* 1.3 65.3 + - - +
174B LEU* 3.2 11.1 + - + +
175B PHE* 3.1 23.7 + + - +
329B PHE* 5.9 0.2 - + - -
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B CYS* 3.4 46.5 + - - +
168B ASP 3.0 10.0 + - - -
169B ALA* 3.6 7.0 - - - -
171B PHE* 1.3 77.1 - - - +
173B GLN* 1.3 62.7 + - - +
175B PHE* 3.2 4.7 + - - +
176B SER* 3.1 28.4 + - - -
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Residues in contact with GLN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ALA* 2.8 21.4 + - - +
170B ASN* 3.6 11.4 - - - +
172B SER* 1.3 73.4 - - - +
174B LEU* 1.3 57.6 + - + +
176B SER* 3.9 4.8 - - - -
177B GLU* 2.9 59.9 + - + +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.5 30.0 - - - +
120B PHE* 3.9 39.5 - - + +
121B CYS* 3.8 22.6 - - + +
124B HIS* 4.8 8.5 - - + -
170B ASN* 3.0 44.1 + - - +
171B PHE* 3.2 12.5 + - - +
173B GLN* 1.3 78.7 - - + +
175B PHE* 1.3 57.6 + - - +
177B GLU* 4.4 4.0 - - - +
178B GLY* 2.9 26.3 + - - -
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 5.1 1.6 - - + -
121B CYS* 3.9 21.7 - - - -
161B VAL* 4.6 12.1 - - + -
162B TYR* 5.4 7.9 - + - -
165B CYS* 4.3 18.8 - - - -
171B PHE* 3.1 14.3 + + + +
172B SER* 3.5 11.0 - - - +
174B LEU* 1.3 76.5 - - - +
176B SER* 1.3 57.2 + - - +
178B GLY* 3.1 2.8 + - - -
179B MET* 2.9 58.9 + - + +
329B PHE* 3.8 35.4 - + - -
330B LEU* 5.1 4.3 - - + -
401B N7I 4.2 20.6 - + + -
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B SER* 3.1 19.8 + - - -
173B GLN* 3.9 5.8 - - - -
175B PHE* 1.3 75.8 - - - +
177B GLU* 1.3 60.6 + - - +
179B MET* 3.2 7.9 + - - +
180B ALA* 2.8 30.5 + - - +
211B THR* 6.4 2.0 - - - -
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN 5.6 0.7 - - - +
117B SER* 2.7 37.0 + - - +
173B GLN* 2.9 53.2 + - + +
174B LEU* 4.4 4.9 - - - +
176B SER* 1.3 78.1 - - - +
178B GLY* 1.3 56.7 + - - +
180B ALA* 3.7 7.0 - - - +
181B GLY* 3.0 25.6 + - - -
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Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN 6.2 0.2 - - - -
117B SER* 3.9 1.3 - - - -
118B LEU* 3.9 34.7 - - - +
174B LEU 2.9 16.7 + - - -
175B PHE 3.5 4.0 - - - -
177B GLU* 1.3 73.8 - - - +
179B MET* 1.3 70.1 + - - +
181B GLY* 3.5 1.3 + - - -
182B ASP* 3.3 21.3 + - - +
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Residues in contact with MET 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.8 25.4 - - + -
175B PHE* 2.9 37.1 + - + +
176B SER* 3.7 9.2 - - - +
178B GLY* 1.3 74.6 - - - +
180B ALA* 1.3 66.3 + - - +
182B ASP* 3.3 4.5 + - - +
183B SER* 3.0 27.3 + - - +
267B LYS* 4.1 2.6 + - - +
268B TRP* 3.7 35.7 - - + +
401B N7I 3.8 26.7 - - + -
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Residues in contact with ALA 180 (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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176B SER 2.8 17.6 + - - +
177B GLU* 3.7 7.9 - - - +
179B MET* 1.3 76.4 - - - +
181B GLY* 1.3 62.1 + - - +
183B SER* 3.3 6.5 + - - -
184B TRP 3.1 9.5 + - - -
211B THR* 4.2 18.2 - - - +
213B ASN* 2.9 33.7 + - - +
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 5.1 0.8 - - - +
112B PRO 3.7 19.7 - - - -
113B TYR* 3.8 17.2 - - - +
114B ASN 4.6 8.3 - - - -
177B GLU 3.0 16.9 + - - -
178B GLY 4.0 1.8 - - - -
179B MET 3.2 0.2 - - - -
180B ALA* 1.3 77.2 - - - +
182B ASP* 1.3 61.2 + - - +
184B TRP* 3.3 17.0 + - - +
185B LEU* 3.6 4.7 + - - +
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Residues in contact with ASP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.4 0.2 - - - +
13A GLN* 2.9 29.3 + - - +
17A TRP* 3.7 3.8 - - + -
118B LEU* 5.6 3.4 - - + -
178B GLY 3.3 11.5 + - - +
179B MET 3.3 8.1 + - - +
181B GLY* 1.3 74.7 - - - +
183B SER* 1.3 58.6 + - - +
185B LEU* 3.2 4.3 + - - +
186B PHE* 2.8 26.9 + - - +
267B LYS* 2.7 26.0 + - - -
268B TRP* 3.3 18.5 - - + -
361B ARG* 2.7 42.4 + - - -
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 3.0 14.4 + - - +
180B ALA* 3.3 7.7 + - - -
182B ASP* 1.3 72.9 - - - +
184B TRP* 1.3 63.5 + - - +
186B PHE* 4.5 1.6 - - - +
187B SER* 2.8 32.8 + - - +
213B ASN* 3.8 17.0 - - - +
214B THR* 3.4 21.0 + - - -
267B LYS* 2.9 28.8 + - - +
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Residues in contact with TRP 184 (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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1A MET* 3.8 35.2 - - + -
112B PRO* 3.4 44.7 - - + +
113B TYR* 3.5 28.5 - + + -
180B ALA 3.1 12.2 + - - +
181B GLY 3.3 12.8 - - - +
182B ASP 3.2 0.4 - - - -
183B SER* 1.3 79.2 - - - +
185B LEU* 1.3 68.0 + - + +
187B SER* 3.3 4.8 + - - -
188B ARG* 2.8 76.3 + - - +
213B ASN* 3.8 19.0 - - - +
241B GLN* 5.8 3.6 - - - -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA* 3.8 22.3 - - + +
9A LEU* 3.8 48.5 - - + +
10A LEU* 4.0 12.7 - - + +
13A GLN* 4.2 15.0 - - - +
106B LEU* 4.1 8.1 - - + -
113B TYR* 3.5 31.4 - - + -
181B GLY 3.6 2.8 + - - +
182B ASP 3.2 6.1 + - - +
184B TRP* 1.3 99.0 - - + +
186B PHE* 1.3 68.0 + - - +
187B SER 3.2 0.4 + - - -
188B ARG* 3.3 4.1 + - - +
189B ALA* 3.2 21.3 + - - +
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Residues in contact with PHE 186 (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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10A LEU* 3.7 21.9 - - + +
182B ASP* 2.8 30.4 + - - +
183B SER 4.5 0.7 - - - +
185B LEU* 1.3 74.0 - - - +
187B SER* 1.3 60.5 + - - +
189B ALA* 3.2 2.6 + - - +
190B LEU* 2.8 42.7 + - + +
214B THR* 5.9 1.1 - - + -
267B LYS* 4.2 20.0 - - + -
301B ALA* 3.6 33.7 - - + -
357B VAL* 3.7 31.0 - - + -
358B GLY 4.1 1.6 - - - -
361B ARG* 3.6 48.0 - - + -
362B VAL 4.5 2.5 - - - -
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B SER 2.8 23.0 + - - -
184B TRP 3.3 2.8 + - - -
186B PHE* 1.3 79.3 - - - +
188B ARG* 1.3 60.3 + - - +
190B LEU* 3.3 9.9 + - - +
191B VAL* 3.1 34.7 + - - +
213B ASN 3.9 1.4 + - - -
214B THR* 3.9 27.4 - - - -
217B VAL* 3.2 33.9 - - - +
218B ILE* 5.5 0.7 - - - -
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Residues in contact with ARG 188 (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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1A MET* 5.1 8.8 + - - +
3A ALA* 4.9 3.6 - - - +
6A ALA* 3.9 19.2 - - + +
184B TRP* 2.8 84.8 + - - +
185B LEU 3.3 7.5 + - - +
187B SER* 1.3 83.3 + - - +
189B ALA* 1.3 59.2 + - - +
191B VAL* 3.6 10.4 - - + +
192B SER* 3.5 17.2 - - - -
213B ASN 5.3 0.2 + - - -
216B LYS* 6.3 0.4 - - - +
217B VAL* 3.2 36.0 - - + +
220B GLU* 5.0 6.7 + - - -
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Residues in contact with ALA 189 (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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6A ALA* 4.4 2.1 - - - +
7A VAL* 3.9 32.5 - - + +
10A LEU* 3.6 31.2 - - + -
185B LEU 3.2 9.8 + - - +
186B PHE 3.6 3.1 - - - +
188B ARG* 1.3 73.9 - - - +
190B LEU* 1.3 58.1 + - - +
192B SER* 3.2 0.9 + - - -
193B LYS* 2.7 38.8 + - - +
357B VAL* 3.7 9.2 - - + +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PHE* 2.8 38.8 + - + +
187B SER* 3.3 10.7 + - - +
189B ALA* 1.3 76.7 - - - +
191B VAL* 1.3 58.2 + - - +
194B CYS* 2.8 48.8 + - + +
198B PHE* 3.9 24.8 - - + -
214B THR* 4.8 14.6 - - + -
218B ILE* 5.0 5.4 - - + -
265B LEU* 5.0 8.1 - - + -
267B LYS* 5.9 0.4 - - + -
301B ALA* 4.8 7.0 - - + -
357B VAL* 3.8 25.7 - - + +
363B LEU* 4.2 18.2 - - + -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER 3.1 18.3 + - - +
188B ARG* 3.6 9.9 - - - +
190B LEU* 1.3 76.3 - - + +
192B SER* 1.3 60.9 + - - +
195B ARG* 3.4 27.9 + - - +
198B PHE* 4.2 12.1 - - + -
217B VAL* 4.0 16.8 - - + -
218B ILE* 4.1 25.4 - - + -
221B THR* 3.5 25.0 - - + +
222B PHE* 3.7 28.0 - - + -
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.1 33.4 - - - +
7A VAL* 5.2 3.1 - - - +
188B ARG 3.5 12.1 + - - -
189B ALA* 3.2 4.4 + - - -
190B LEU 3.1 0.2 - - - -
191B VAL* 1.3 80.3 - - - +
193B LYS* 1.3 69.3 + - - +
194B CYS 3.2 1.8 + - - -
195B ARG* 3.6 13.5 + - - +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.8 32.6 - - + +
189B ALA 2.7 23.2 + - - +
192B SER* 1.3 76.0 - - - +
194B CYS* 1.3 62.9 + - - +
195B ARG 3.8 0.7 + - - -
355B THR* 4.0 10.6 - - - +
356B PRO 3.8 18.8 - - - +
357B VAL* 3.7 28.5 - - - +
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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