Contacts of the helix formed by residues 167 - 190 (chain B) in PDB entry 5FN4
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 ILE 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ILE* 1.3 85.4 + - + +
169B SER* 3.2 7.4 - - - +
170B SER* 2.5 34.2 + - - +
171B LEU* 2.9 24.5 + - + +
210B MET* 5.1 10.1 - - + -
214B HIS* 4.9 20.6 - - + +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 1.3 94.6 - - + +
169B SER* 1.3 57.4 + - - +
171B LEU* 3.2 19.8 + - + +
172B LEU* 2.9 29.1 + - + +
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE 3.2 4.9 - - - +
168B ILE* 1.3 77.7 - - - +
170B SER* 1.3 58.3 + - - +
172B LEU* 3.2 13.0 + - - +
173B LEU* 2.9 29.1 + - - +
7G ALA* 5.0 0.9 + - - -
10G ALA* 3.5 30.7 + - - +
11G ALA* 4.7 1.9 + - - -
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 2.5 33.9 + - - +
169B SER* 1.3 80.9 - - - +
171B LEU* 1.3 59.4 + - - +
173B LEU* 3.2 17.8 + - - +
174B LEU* 2.9 29.6 + - - +
210B MET* 4.6 10.3 - - - +
213B ILE* 5.8 3.4 - - - +
214B HIS* 5.7 3.5 - - - -
229B ILE* 5.1 1.4 - - - +
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Residues in contact with LEU 171 (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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167B ILE* 2.9 17.2 + - + +
168B ILE* 3.2 26.7 + - + +
170B SER* 1.3 80.8 + - - +
172B LEU* 1.3 79.1 + - + +
174B LEU* 3.2 3.7 + - - +
175B PHE* 2.9 56.7 + - + -
210B MET* 3.7 29.2 - - + -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE* 2.9 14.6 + - + +
169B SER* 3.4 14.6 - - - +
171B LEU* 1.3 84.6 - - + +
173B LEU* 1.3 64.2 + - - +
175B PHE* 3.2 3.8 + - - +
176B PHE* 2.8 48.7 + - + +
177B PHE* 4.5 13.0 - - + -
10G ALA 5.3 1.6 - - - +
14G ALA* 4.1 33.9 - - + +
17G ALA* 5.9 2.5 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER 2.9 11.9 + - - +
170B SER* 3.2 17.7 + - - +
172B LEU* 1.3 77.1 - - - +
174B LEU* 1.3 65.7 + - - +
177B PHE* 3.2 59.7 + - + +
178B SER 3.8 0.7 + - - -
229B ILE* 3.7 43.1 - - + +
232B LEU* 4.1 8.9 - - + +
233B MET* 3.5 31.0 - - + -
10G ALA* 5.5 8.1 - - + -
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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
----------------------------------------------------------
170B SER 2.9 13.2 + - - +
171B LEU* 3.4 9.4 - - - +
173B LEU* 1.3 77.1 - - - +
175B PHE* 1.3 59.1 + - + +
178B SER* 2.9 27.4 - - - -
205B PHE* 3.5 29.2 - - + +
206B GLY* 3.0 36.9 - - - +
209B GLY* 3.9 6.1 - - - -
210B MET* 3.5 31.9 - - + +
213B ILE* 5.3 3.8 - - + -
225B TYR* 4.7 4.3 - - + -
229B ILE* 3.4 29.2 - - + -
232B LEU* 4.5 0.2 - - - +
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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
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171B LEU* 2.9 50.7 + - + -
172B LEU* 3.2 6.4 + - - +
174B LEU* 1.3 77.0 - - + +
176B PHE* 1.3 64.5 + - + +
177B PHE 3.3 1.1 - - - -
178B SER* 3.2 4.9 + - - -
179B PHE* 2.9 29.6 + - - +
202B ILE* 3.7 39.3 - - + +
203B TRP* 4.1 25.4 - + - -
206B GLY* 4.1 11.2 - - - -
207B VAL* 4.1 22.9 - - + -
210B MET* 4.9 8.3 - - + -
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 4.8 19.1 - - + -
172B LEU* 2.8 27.7 + - + +
175B PHE* 1.3 77.1 - - + +
177B PHE* 1.3 99.7 + + - +
179B PHE* 3.2 15.9 + + - +
180B ILE* 2.9 54.4 + - + +
240B TYR* 5.2 4.3 - - - -
13G ALA 4.9 0.2 - - - -
17G ALA* 2.8 44.2 - - + -
20G ALA* 6.1 0.2 - - + -
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Residues in contact with PHE 177 (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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106B TYR* 4.8 1.0 + - - -
172B LEU* 4.5 10.5 - - + -
173B LEU* 3.2 55.1 + - + +
175B PHE 3.3 0.2 - - - -
176B PHE* 1.3 110.0 - + - +
178B SER* 1.3 55.9 + - - +
180B ILE* 3.2 12.8 + - + +
181B TYR* 2.9 29.3 + - - +
232B LEU* 4.3 12.7 - - + +
233B MET* 5.0 5.2 - - - -
236B VAL* 3.8 34.1 - - + -
240B TYR* 5.3 4.3 - + - -
10G ALA* 4.9 4.7 - - + -
13G ALA* 3.4 35.4 - - + -
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Residues in contact with SER 178 (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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173B LEU 3.8 2.0 + - - -
174B LEU 2.9 24.5 - - - -
175B PHE 3.2 4.8 + - - -
177B PHE* 1.3 79.1 - - - +
179B PHE* 1.3 57.0 + - - +
181B TYR* 3.2 11.0 + - - +
182B LEU* 2.9 30.0 + - - +
202B ILE* 4.1 11.9 - - - +
205B PHE* 3.4 31.0 - - - -
232B LEU* 3.8 12.8 - - - +
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE 5.9 1.6 - - - -
241A SER* 6.0 0.9 - - - -
242A ILE* 3.9 36.6 - - + -
175B PHE 2.9 12.6 + - - +
176B PHE* 3.3 21.1 - + - +
178B SER* 1.3 77.1 - - - +
180B ILE* 1.3 75.5 + - + +
182B LEU* 3.2 4.7 + - - +
183B GLY* 2.9 25.6 + - - -
195B TYR* 5.5 8.5 - + - -
198B VAL* 4.3 17.7 - - + -
199B ALA* 6.4 0.7 - - - -
202B ILE* 3.7 24.8 - - + +
94D PHE* 3.7 33.3 - + - -
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Residues in contact with ILE 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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242A ILE* 4.7 11.7 - - + +
243A ASN* 4.6 13.0 - - - +
105B PHE* 4.3 15.9 - - + -
106B TYR* 4.3 9.4 - - + +
176B PHE* 2.9 50.7 + - + +
177B PHE* 3.3 13.7 - - + +
179B PHE* 1.3 90.7 - - + +
181B TYR* 1.3 61.1 + - - +
183B GLY* 3.2 3.0 + - - -
184B GLU* 2.9 47.7 + - - +
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Residues in contact with TYR 181 (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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95B VAL* 4.9 10.6 - - + +
99B THR* 3.0 34.4 + - + -
103B VAL* 4.8 0.9 - - + -
106B TYR* 3.4 30.5 - + - +
177B PHE 2.9 12.2 + - - +
178B SER* 3.2 14.1 + - - +
180B ILE* 1.3 76.9 - - - +
182B LEU* 1.3 61.9 + - + +
184B GLU* 3.2 5.3 + - - +
185B VAL* 2.9 51.9 + - + +
228B MET* 4.9 15.7 - - + -
232B LEU* 4.7 14.4 - - + -
235B LEU* 3.7 21.8 - - + -
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Residues in contact with LEU 182 (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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178B SER* 2.9 13.9 + - - +
179B PHE* 3.2 10.5 - - - +
181B TYR* 1.3 81.2 - - + +
183B GLY* 1.3 58.4 + - - +
185B VAL* 3.2 11.0 + - + +
186B PHE* 2.9 67.3 + - + -
198B VAL* 3.5 33.4 - - + +
201B LEU* 4.4 23.1 - - + -
202B ILE* 3.7 16.8 - - + -
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Residues in contact with GLY 183 (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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179B PHE 2.9 11.0 + - - -
180B ILE* 3.2 4.9 + - - -
182B LEU* 1.3 77.1 - - - +
184B GLU* 1.3 55.9 + - - +
186B PHE* 3.2 4.4 + - - +
187B LYS* 2.9 43.4 + - - +
94D PHE* 3.6 32.0 - - - -
95D THR* 4.2 0.9 + - - -
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Residues in contact with GLU 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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242A ILE 5.5 0.7 - - - +
243A ASN* 5.0 3.6 + - - +
103B VAL* 3.9 13.7 - - + -
105B PHE* 3.1 59.4 - - + +
106B TYR* 4.6 4.9 - - + -
180B ILE* 2.9 39.2 + - - +
181B TYR* 3.4 11.7 - - - +
183B GLY* 1.3 75.6 - - - +
185B VAL* 1.3 51.9 + - + +
187B LYS* 3.2 37.0 + - + +
188B THR* 2.7 37.3 + - - -
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Residues in contact with VAL 185 (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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99B THR* 5.1 0.2 - - - +
103B VAL* 4.7 10.3 - - + -
181B TYR* 2.9 52.8 + - + +
182B LEU* 3.3 12.8 - - + +
184B GLU* 1.3 75.5 - - - +
186B PHE* 1.3 74.0 + - + +
188B THR* 3.2 9.5 + - - -
189B TYR* 3.1 33.4 + - + +
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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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182B LEU* 2.9 56.3 + - + -
183B GLY 3.5 3.6 - - - +
185B VAL* 1.3 89.2 - - + +
187B LYS* 1.3 50.1 + - - +
189B TYR* 3.4 4.8 + - + +
190B ASN* 2.7 34.1 + - - -
191B VAL* 3.5 9.6 + - + +
193B VAL* 3.8 31.0 - - + -
198B VAL* 3.9 12.3 - - + -
201B LEU* 5.1 8.3 - - + -
94D PHE* 4.1 14.1 - + - -
95D THR* 3.2 25.5 - - + +
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Residues in contact with LYS 187 (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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241A SER* 4.5 5.7 + - - -
242A ILE 4.2 7.9 + - - -
243A ASN 3.6 24.3 + - - -
244A PRO 5.4 0.2 - - - -
245A GLU* 3.6 39.4 + - + +
183B GLY* 2.9 28.1 + - - +
184B GLU* 3.3 34.5 + - - +
186B PHE* 1.3 76.2 - - - +
188B THR* 1.3 64.3 + - - +
190B ASN* 3.2 18.8 + - - +
94D PHE* 5.5 5.1 - - - -
95D THR* 4.2 11.4 + - + +
98D LEU* 5.7 6.9 - - + +
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Residues in contact with THR 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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102B SER* 3.3 21.5 - - - +
103B VAL* 3.0 42.6 + - - +
104B SER* 4.5 1.1 + - - -
184B GLU 2.7 20.3 + - - -
185B VAL* 3.2 9.9 + - - -
187B LYS* 1.3 78.7 - - - +
189B TYR* 1.3 71.8 + - + +
190B ASN* 4.5 1.4 - - - +
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Residues in contact with TYR 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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66A ILE* 5.9 1.2 - - - +
102B SER* 5.6 9.6 - - - -
185B VAL* 3.1 23.5 + - + +
186B PHE* 4.1 4.9 - - + +
188B THR* 1.3 89.0 - - + +
190B ASN* 1.3 73.4 + - - +
191B VAL* 4.3 13.4 - - + +
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Residues in contact with ASN 190 (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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66A ILE* 4.6 24.0 - - + +
220A HIS* 4.7 7.7 + - - -
186B PHE 2.7 14.1 + - - -
187B LYS* 3.2 13.7 + - - +
188B THR 4.5 2.0 - - - +
189B TYR* 1.3 82.5 - - - +
191B VAL* 1.3 63.2 + - - +
95D THR* 5.2 2.8 - - - +
97D PRO* 3.6 10.8 - - - +
98D LEU* 3.2 47.5 + - + +
99D GLY 5.6 0.2 + - - -
100D THR* 4.5 11.7 + - - -
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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
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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