Contacts of the helix formed by residues 152 - 178 (chain F) in PDB entry 4NFI
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 152 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ARG* 3.2 31.9 + - - +
147F CYS* 3.9 12.3 - - + -
150F GLN* 3.0 27.3 + - + -
151F PRO* 1.3 85.1 - - + +
153F TYR* 1.3 66.2 + - - +
154F LEU 3.4 2.2 - - - -
155F ASN* 3.2 14.2 + - + +
156F LEU* 3.0 48.3 + - + +
215F TYR* 3.5 27.1 - - + +
216F MET* 3.6 49.8 - - + +
218F GLY* 5.6 0.4 - - - -
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Residues in contact with TYR 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F TYR 4.9 1.2 + - - -
143F LEU* 3.5 28.0 - - + -
144F LYS* 3.5 26.2 + - - +
147F CYS* 3.4 32.3 - - + +
148F ARG* 3.6 37.8 + - + +
150F GLN 3.1 11.0 + - - +
151F PRO 3.4 1.0 - - - -
152F TYR* 1.3 83.9 - - - +
154F LEU* 1.3 66.8 + - + +
156F LEU* 3.2 4.7 + - + +
157F ILE* 3.0 50.9 + - + +
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F PRO 5.1 2.1 + - - +
152F TYR 3.4 0.2 - - - -
153F TYR* 1.3 78.8 - - + +
155F ASN* 1.3 68.9 + - - +
157F ILE* 3.3 18.0 + - + -
158F GLU* 2.9 52.3 + - + +
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Residues in contact with ASN 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F PRO 4.8 3.9 + - - -
152F TYR* 3.2 21.4 + - - +
154F LEU* 1.3 79.1 - - - +
156F LEU* 1.3 57.2 + - - +
158F GLU* 3.8 9.1 - - - +
159F LEU* 2.9 29.9 + - - +
215F TYR* 3.4 48.2 + - + +
220F ASP* 4.0 15.2 + - - +
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F VAL* 3.9 26.5 - - + -
143F LEU* 3.9 21.3 - - + -
147F CYS* 4.5 3.6 - - + -
152F TYR* 3.0 44.2 + - + +
153F TYR* 3.2 7.2 + - + +
155F ASN* 1.3 74.5 - - - +
157F ILE* 1.3 67.4 + - - +
159F LEU* 3.2 7.0 + - + +
160F PHE* 2.9 34.6 + - + -
212F ALA* 3.8 43.3 - - + +
215F TYR* 4.3 9.4 - - + -
216F MET* 4.3 2.0 - - + -
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Residues in contact with ILE 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F TYR* 4.0 13.6 - - + -
143F LEU* 4.2 16.8 - - + -
153F TYR* 3.0 63.0 + - + +
154F LEU* 3.7 19.7 - - + +
156F LEU* 1.3 75.9 - - - +
158F GLU* 1.3 65.0 + - + +
160F PHE* 3.3 2.3 + - - +
161F LEU* 3.0 45.0 + - + +
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Residues in contact with GLU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F LEU* 2.9 47.7 + - + +
155F ASN* 4.0 9.4 - - - +
157F ILE* 1.3 75.7 - - + +
159F LEU* 1.3 60.1 + - - +
161F LEU* 3.9 9.1 - - + +
162F GLN* 2.8 33.8 + - - +
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F ASN 2.9 18.7 + - - +
156F LEU* 3.2 8.5 + - + +
158F GLU* 1.3 77.9 - - - +
160F PHE* 1.3 54.1 + - + +
162F GLN* 4.0 4.6 - - + +
163F SER* 2.7 47.0 + - - +
207F TYR* 3.7 31.6 - - + +
208F LEU* 3.6 21.5 - - + +
211F ALA* 3.9 7.2 - - + -
212F ALA* 3.5 38.1 - - + +
215F TYR* 4.0 15.5 - - + -
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Residues in contact with PHE 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F VAL* 4.2 17.7 - - + -
91F CYS* 3.7 43.5 - - + -
92F VAL* 3.7 24.5 - - + -
95F LEU* 4.7 7.0 - - + +
139F ILE* 3.7 21.3 - - + -
140F TYR* 3.3 20.9 - - + +
143F LEU* 4.2 12.6 - - + -
156F LEU* 2.9 32.8 + - + +
157F ILE 3.8 2.7 - - - +
159F LEU* 1.3 77.4 - - + +
161F LEU* 1.3 61.1 + - - +
163F SER* 3.4 5.1 + - - -
164F SER* 2.8 29.8 + - - -
208F LEU* 4.2 24.0 - - + -
212F ALA* 4.8 6.3 - - + -
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Residues in contact with LEU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F GLU* 5.7 3.1 - - - +
140F TYR* 3.3 27.4 - - + +
157F ILE* 3.0 40.3 + - + +
158F GLU* 3.9 8.5 - - + +
160F PHE* 1.3 74.2 - - - +
162F GLN* 1.3 64.1 + - - +
164F SER* 3.3 6.7 + - - -
165F TYR* 3.0 22.7 + - - +
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Residues in contact with GLN 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F GLU 2.8 18.7 + - - +
159F LEU* 4.1 5.2 - - + +
161F LEU* 1.3 78.6 - - - +
163F SER* 1.3 56.8 + - - +
165F TYR* 3.3 24.0 + - - +
166F GLN* 3.0 58.7 + - - +
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Residues in contact with SER 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F LEU* 5.1 0.9 - - - -
99F PHE* 5.3 0.7 - - - -
159F LEU* 2.7 36.9 + - - +
160F PHE 3.8 3.6 - - - -
162F GLN* 1.3 77.2 - - - +
164F SER* 1.3 53.5 + - - +
166F GLN* 3.4 14.7 + - - +
167F THR* 2.6 38.7 + - - -
203F PHE* 4.8 2.6 + - - +
204F TYR* 4.6 9.4 - - - +
207F TYR* 5.1 2.4 - - - -
208F LEU* 3.8 31.3 + - - +
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Residues in contact with SER 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F LEU* 3.5 23.3 - - - +
99F PHE* 4.3 12.3 - - - -
136F GLU* 4.5 11.5 + - - -
140F TYR* 4.3 4.7 + - - -
160F PHE 2.8 18.4 + - - -
161F LEU* 3.5 7.9 - - - -
163F SER* 1.3 73.7 - - - +
165F TYR* 1.3 66.5 + - - +
167F THR* 3.4 1.7 + - - -
168F GLU* 2.9 43.7 + - - +
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Residues in contact with TYR 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F LEU 3.0 13.3 + - - +
162F GLN* 3.6 31.9 - - - +
164F SER* 1.3 77.9 - - - +
166F GLN* 1.3 62.9 + - + +
168F GLU* 3.3 11.0 + - + +
169F ILE* 2.8 61.9 + - + +
199F TYR* 6.4 1.3 - + - -
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Residues in contact with GLN 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F GLN* 3.0 50.8 + - - +
163F SER* 3.4 16.4 + - - +
165F TYR* 1.3 82.4 - - + +
167F THR* 1.3 58.1 + - - +
169F ILE* 3.2 5.0 + - - +
170F GLY 2.9 23.9 + - - -
199F TYR* 3.2 24.3 - - + +
203F PHE* 3.3 61.1 - - + +
207F TYR* 5.7 1.2 - - - -
229F LYS* 5.2 4.9 - - - +
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Residues in contact with THR 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE* 3.6 20.2 - - + -
163F SER 2.6 21.2 + - - -
164F SER 3.7 4.3 - - - -
166F GLN* 1.3 79.3 - - - +
168F GLU* 1.3 55.8 + - - +
170F GLY* 3.3 2.4 + - - -
171F GLN* 2.9 26.9 + - - +
199F TYR 3.2 9.8 + - - -
200F LYS* 3.4 22.7 - - - +
204F TYR* 3.4 23.7 + - + +
401F JD5 3.6 25.4 - - + -
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Residues in contact with GLU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F PHE* 3.9 27.7 - - - -
99F PHE* 4.5 2.3 - - + -
136F GLU* 4.6 3.3 - - - +
164F SER* 2.9 32.2 + - - +
165F TYR* 3.7 9.7 - - + +
167F THR* 1.3 72.1 - - - +
169F ILE* 1.3 66.2 + - - +
171F GLN* 3.4 7.8 + - - +
172F THR* 3.0 25.9 + - - -
401F JD5 4.1 23.9 - - + -
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Residues in contact with ILE 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F TYR* 2.8 57.2 + - + +
166F GLN* 3.5 8.3 - - - +
168F GLU* 1.3 75.7 - - + +
170F GLY* 1.3 64.1 + - - +
172F THR* 3.1 12.6 + - + +
173F LEU* 3.1 29.5 + - + +
199F TYR* 4.1 22.7 - - + -
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Residues in contact with GLY 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F GLN 2.9 10.5 + - - -
167F THR 3.6 4.3 - - - -
169F ILE* 1.3 78.6 - - - +
171F GLN* 1.3 55.6 + - - +
173F LEU* 3.1 9.8 + - - +
174F ASP* 2.9 26.9 + - - +
196F ILE* 4.1 4.7 - - - +
199F TYR* 3.4 23.3 - - - -
200F LYS* 3.6 15.3 - - - +
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Residues in contact with GLN 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ASP* 3.7 17.5 + - - +
106F MET* 3.9 13.0 - - + +
107F ASP* 4.8 0.4 + - - -
167F THR 2.9 17.4 + - - +
168F GLU* 3.7 9.2 - - - +
170F GLY* 1.3 74.9 - - - +
172F THR* 1.3 60.8 + - - +
174F ASP* 3.3 12.3 + - - +
175F LEU* 3.0 62.6 + - + +
200F LYS* 3.8 5.5 - - + +
401F JD5 3.3 51.0 - - + +
402F MG 4.1 6.5 - - - -
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Residues in contact with THR 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F GLU 3.0 16.1 + - - -
169F ILE* 3.1 16.2 + - + +
171F GLN* 1.3 74.4 - - - +
173F LEU* 1.3 60.0 + - + +
175F LEU* 3.3 7.2 + - - +
176F LEU* 2.9 53.2 + - + +
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Residues in contact with LEU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F ILE* 3.1 28.4 + - + +
170F GLY* 3.1 8.9 + - - +
172F THR* 1.3 78.9 - - + +
174F ASP* 1.3 61.5 + - - +
176F LEU* 3.8 10.9 - - + +
177F THR* 2.7 32.2 + - - -
192F ARG* 3.9 28.9 - - - +
195F SER* 4.1 33.9 - - - +
196F ILE* 3.8 16.2 - - + +
199F TYR* 4.9 6.1 - - + -
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Residues in contact with ASP 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F GLY 2.9 13.0 + - - +
171F GLN* 3.4 21.5 + - - +
173F LEU* 1.3 78.0 - - - +
175F LEU* 1.3 69.7 + - - +
177F THR* 3.5 2.3 + - - -
178F ALA* 3.3 23.7 + - - +
196F ILE* 4.1 19.2 - - + +
200F LYS* 2.9 30.3 + - + -
266F LYS* 3.3 34.7 + - - +
267F CYS* 5.6 1.1 + - - +
401F JD5 4.3 1.0 + - - -
402F MG 4.1 6.2 - - - -
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Residues in contact with LEU 175 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F MET* 3.8 33.7 - - + +
107F ASP* 4.6 6.5 - - - +
171F GLN* 3.0 47.0 + - + +
172F THR* 3.9 6.1 - - - +
174F ASP* 1.3 86.8 - - - +
176F LEU* 1.3 64.4 + - + +
178F ALA* 3.3 22.7 + - + +
179F PRO* 3.6 3.8 - - - +
266F LYS* 4.8 5.4 - - - -
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Residues in contact with LEU 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F THR* 2.9 45.7 + - + +
173F LEU* 3.8 11.7 - - + +
175F LEU* 1.3 75.2 - - + +
177F THR* 1.3 58.6 + - - +
178F ALA 3.1 6.0 + - - -
179F PRO* 3.5 14.2 - - - +
187F ARG* 4.8 4.2 - - - -
192F ARG* 4.5 12.8 - - - +
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Residues in contact with THR 177 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F LEU 2.7 21.3 + - - -
174F ASP 4.2 2.5 - - - -
175F LEU 3.3 0.2 - - - -
176F LEU* 1.3 75.3 - - - +
178F ALA* 1.3 58.8 + - - +
179F PRO* 3.4 7.7 - - - +
187F ARG* 4.0 20.8 + - + +
188F PHE* 3.3 27.0 - - + -
192F ARG* 2.9 44.5 + - + +
196F ILE* 3.8 7.9 - - - +
267F CYS* 3.7 24.0 - - + -
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Residues in contact with ALA 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F ASP 3.3 17.7 + - - +
175F LEU* 3.4 9.0 - - - +
176F LEU 3.1 0.2 - - - -
177F THR* 1.3 78.7 - - - +
179F PRO* 1.3 68.2 - - - +
180F GLN 3.2 3.1 + - - -
264F ASP 3.6 9.3 - - - +
265F ASN* 3.2 24.7 - - - +
266F LYS* 3.6 29.5 - - + -
267F CYS 4.8 0.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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