Contacts of the helix formed by residues 149 - 174 (chain F) in PDB entry 3IFS
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 THR 149 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E HIS* 3.8 20.6 - - + +
82F ILE* 3.9 7.0 - - + -
144F SER* 4.0 8.9 + - - -
146F SER* 3.6 9.3 + - - -
147F GLY 3.7 0.8 - - - -
148F THR* 1.3 75.8 + - - +
150F THR* 1.3 68.5 + - - +
151F GLU* 3.8 14.8 - - - +
152F PRO* 3.4 19.3 - - + +
153F ALA* 3.0 23.2 + - - +
426F LYS* 5.5 7.8 + - - +
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Residues in contact with THR 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E LEU* 4.5 17.5 - - + +
354E LEU* 5.7 2.2 - - + -
362E VAL* 4.2 24.5 - - + -
121F ILE* 5.1 1.1 - - + -
148F THR 3.0 7.4 + - - -
149F THR* 1.3 73.6 - - - +
151F GLU* 1.3 75.8 + - + +
153F ALA* 3.8 2.4 - - - +
154F LEU* 3.0 29.6 + - + +
429F MSE 3.4 30.6 - - + +
430F PHE* 3.8 14.9 - - - -
433F LEU* 5.2 6.4 - - + +
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Residues in contact with GLU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E SER* 2.7 34.4 + - - +
312E HIS* 2.9 25.4 + - - -
82F ILE* 3.4 12.5 - - + +
118F GLY* 3.3 17.9 - - - +
120F ASN 3.9 12.2 - - - +
121F ILE* 3.4 24.4 - - + +
149F THR* 3.8 12.1 - - - +
150F THR* 1.3 81.7 + - - +
152F PRO* 1.3 64.2 - - + +
154F LEU* 3.8 5.3 - - - +
155F ALA* 3.1 23.2 + - - +
425F TYR* 4.4 5.3 + - - -
429F MSE 5.6 4.2 - - - +
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Residues in contact with PRO 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F VAL* 3.6 10.6 - - + +
81F GLY* 4.0 18.2 - - - -
82F ILE* 3.7 22.9 - - + +
118F GLY* 3.5 17.5 - - - +
142F VAL* 5.7 2.5 - - + -
143F ILE 4.9 4.3 - - - +
144F SER* 4.8 13.0 - - - +
149F THR* 3.4 24.7 - - + +
151F GLU* 1.3 96.2 - - + +
153F ALA* 1.3 57.1 + - - +
156F PHE* 2.8 33.3 + - - +
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349E ASP* 4.0 14.4 - - + +
351E LEU* 4.0 15.9 - - + -
144F SER* 6.2 0.2 - - - -
147F GLY* 3.5 25.8 - - - +
148F THR* 4.2 4.0 - - - +
149F THR 3.0 22.9 + - - +
150F THR 3.8 2.7 - - - +
152F PRO* 1.3 77.9 - - - +
154F LEU* 1.3 61.5 + - - +
156F PHE* 3.7 6.8 + - - +
157F ARG* 3.3 21.1 + - - +
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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
----------------------------------------------------------
341E ILE* 3.7 47.8 - - + -
351E LEU* 3.9 18.3 - - + +
354E LEU* 5.5 2.7 - - + -
359E VAL* 4.4 10.1 - - + -
362E VAL* 4.5 13.5 - - + -
121F ILE* 4.4 22.9 - - + -
126F MSE 5.8 2.7 - - + -
150F THR* 3.0 21.2 + - + +
151F GLU* 3.8 5.2 - - - +
153F ALA* 1.3 76.3 - - - +
155F ALA* 1.3 64.9 + - - +
157F ARG* 3.2 11.9 - - + +
158F ILE* 3.1 36.4 + - + +
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Residues in contact with ALA 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F VAL* 4.2 6.7 - - + -
117F VAL* 4.2 14.4 - - + -
118F GLY* 3.3 38.1 - - - +
120F ASN 5.8 0.2 - - - +
126F MSE 4.6 12.1 - - - -
151F GLU 3.1 7.6 + - - +
152F PRO 3.9 2.2 - - - +
154F LEU* 1.3 76.7 - - - +
156F PHE* 1.3 58.9 + - - +
158F ILE* 3.2 4.1 + - - -
159F PHE* 2.8 37.9 + - + +
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Residues in contact with PHE 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F VAL* 4.1 8.0 - - + +
140F ILE* 4.2 20.6 - - + -
142F VAL* 3.7 45.8 - - + -
152F PRO 2.8 18.4 + - - +
153F ALA* 3.9 7.2 - - - +
155F ALA* 1.3 78.1 - - - +
157F ARG* 1.3 58.0 + - - +
159F PHE* 4.6 0.7 - - - +
160F ARG* 2.8 69.4 + - + +
176F ILE* 4.2 15.7 - - + -
187F LEU* 4.3 8.7 - - + -
190F LEU* 3.5 30.1 - - + -
196F TYR* 4.3 3.4 - + - -
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Residues in contact with ARG 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E ILE* 4.6 4.9 - - - +
342E GLU 2.7 34.6 + - - +
343E SER* 3.7 0.6 - - - +
344E GLU* 3.3 35.3 + - + +
347E ASP* 3.4 7.5 + - - -
349E ASP* 2.9 38.8 + - - +
351E LEU* 3.8 21.9 + - - +
352E ASN* 2.7 36.3 + - - +
355E ALA* 5.5 0.2 - - - +
153F ALA 3.3 9.7 + - - +
154F LEU* 3.2 18.8 - - + +
156F PHE* 1.3 83.5 - - - +
158F ILE* 1.3 64.1 + - + +
160F ARG* 4.2 7.1 + - - +
161F LYS* 3.4 20.6 + - - +
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Residues in contact with ILE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E LEU* 4.4 9.6 - - + -
340E THR 5.9 4.0 - - - +
341E ILE* 5.7 4.9 - - + -
359E VAL* 3.9 27.6 - - + -
126F MSE 4.0 18.2 - - - -
130F MSE 3.6 30.5 - - + -
154F LEU* 3.1 22.9 + - + +
155F ALA 3.2 5.6 + - - +
157F ARG* 1.3 83.5 - - + +
159F PHE* 1.3 70.2 + - + +
161F LYS* 3.6 5.9 + - - +
162F LEU* 3.4 20.4 + - + +
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Residues in contact with PHE 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F LEU* 3.7 27.1 - - + -
80F VAL* 5.4 1.8 - - + -
117F VAL* 3.6 26.9 - - + -
126F MSE 3.7 33.9 - - + -
129F LEU* 4.0 17.9 - - + -
130F MSE 3.9 20.2 - - + -
133F LEU* 3.8 20.6 - - + -
138F PHE* 4.6 2.6 - + + -
140F ILE* 3.7 10.8 - - + +
155F ALA 2.8 31.8 + - - +
156F PHE* 4.7 1.6 - - - +
158F ILE* 1.3 79.6 - - + +
160F ARG* 1.3 66.0 + - - +
161F LYS 3.1 2.0 - - - -
162F LEU* 3.2 17.0 + - + +
163F LEU* 3.0 23.0 + - - +
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Residues in contact with ARG 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E GLU* 3.0 31.5 + - - +
140F ILE* 4.0 10.4 - - - +
156F PHE* 2.8 57.6 + - + +
157F ARG* 4.2 6.6 + - - +
159F PHE* 1.3 73.1 - - - +
161F LYS* 1.3 57.6 + - - +
163F LEU* 3.3 3.9 + - - +
164F GLU* 3.0 57.8 + - - +
169F LYS* 4.2 9.1 - - - +
176F ILE* 3.9 11.7 - - + -
190F LEU* 4.4 19.9 - - - +
194F GLU* 5.1 1.8 + - - -
196F TYR* 3.3 25.7 + - - -
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Residues in contact with LYS 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E GLU* 3.6 39.4 + - + +
157F ARG 3.4 17.1 + - - +
158F ILE* 3.7 7.0 - - - +
159F PHE 3.1 0.4 - - - -
160F ARG* 1.3 81.4 - - - +
162F LEU* 1.3 57.0 + - + +
164F GLU* 3.4 14.1 + - - +
165F GLU* 2.9 68.0 + - + +
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Residues in contact with LEU 162 (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 MSE 3.7 43.1 - - + -
133F LEU* 4.7 5.8 - - + -
138F PHE* 4.4 10.4 - - + -
158F ILE* 3.4 11.1 + - + +
159F PHE* 3.2 28.3 + - + +
161F LYS* 1.3 77.0 - - + +
163F LEU* 1.3 64.4 + - - +
165F GLU* 3.4 19.8 + - - +
166F LYS* 3.0 24.8 + - - +
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Residues in contact with LEU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F PHE* 3.6 41.6 - - + +
140F ILE* 4.1 10.5 - - + -
159F PHE 3.0 13.2 + - - +
160F ARG 3.3 8.3 + - - +
162F LEU* 1.3 77.2 - - - +
164F GLU* 1.3 56.4 + - - +
166F LYS* 3.3 1.7 + - - +
167F TYR* 3.0 59.5 + - + +
172F ALA* 3.8 19.2 - - + +
175F ARG* 4.1 11.4 - - + +
176F ILE* 3.4 35.9 - - + -
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Residues in contact with GLU 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F ARG* 3.0 56.3 + - + +
161F LYS* 3.8 13.8 - - - +
163F LEU* 1.3 73.2 - - + +
165F GLU* 1.3 62.6 + - + +
168F GLY* 2.8 31.3 + - - -
169F LYS* 3.1 40.3 + - + +
172F ALA* 3.9 23.1 - - + -
176F ILE* 5.5 0.4 - - + +
194F GLU* 5.0 0.2 - - - +
196F TYR* 4.7 2.1 + - - -
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Residues in contact with GLU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F LYS* 2.9 55.5 + - + +
162F LEU* 3.7 26.0 - - - +
164F GLU* 1.3 79.1 - - + +
166F LYS* 1.3 63.0 + - - +
168F GLY 4.6 0.9 + - - -
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Residues in contact with LYS 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F LEU 5.3 0.9 + - - +
135F GLY* 4.8 8.1 - - - +
136F LYS 3.1 37.2 + - - +
137F ASP* 4.3 4.0 - - - -
138F PHE* 3.9 15.7 - - + -
162F LEU 3.0 16.7 + - - +
163F LEU 3.6 4.5 - - - +
164F GLU 3.2 0.2 - - - -
165F GLU* 1.3 80.4 - - - +
167F TYR* 1.3 93.6 + - + +
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Residues in contact with TYR 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ASP* 2.6 50.2 + - - +
138F PHE 3.0 7.7 + - - -
163F LEU* 3.0 49.6 + - + +
166F LYS* 1.3 99.7 - - + +
168F GLY* 1.3 64.3 + - - +
171F GLU* 3.6 38.4 + - + +
172F ALA* 4.2 2.2 - - - +
175F ARG* 3.5 27.1 + - - -
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Residues in contact with GLY 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F GLU* 2.8 24.6 + - - -
165F GLU 4.5 1.2 + - - -
166F LYS 3.7 0.6 - - - -
167F TYR* 1.3 77.3 - - - +
169F LYS* 1.3 65.9 + - - -
170F GLU 3.4 2.6 + - - -
172F ALA* 3.0 21.7 + - - +
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Residues in contact with LYS 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F ARG* 4.2 5.9 - - - +
164F GLU* 3.1 42.1 + - + +
168F GLY* 1.3 71.4 - - - -
170F GLU* 1.3 63.4 + - - +
172F ALA* 3.8 6.7 - - - +
173F ARG* 3.2 28.8 + - + +
194F GLU* 3.6 29.1 + - - -
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Residues in contact with GLU 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F GLY 3.4 1.0 - - - -
169F LYS* 1.3 79.5 - - - +
171F GLU* 1.3 61.7 + - - +
172F ALA 3.5 0.2 + - - -
173F ARG* 3.3 49.9 + - - +
174F LYS* 3.6 7.1 - - + +
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Residues in contact with GLU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LYS* 5.1 3.8 + - - -
73F ASP* 5.2 0.3 - - - +
167F TYR* 3.6 43.0 + - + +
168F GLY 3.6 2.2 + - - -
170F GLU* 1.3 77.3 - - - +
172F ALA* 1.3 65.2 + - - +
174F LYS* 3.1 35.0 + - - +
175F ARG* 2.7 38.6 + - - +
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Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F LEU* 4.1 22.2 - - + +
164F GLU* 3.9 29.8 - - + -
167F TYR* 4.2 3.1 - - - +
168F GLY 3.0 19.5 + - - +
169F LYS 3.8 4.3 - - - +
170F GLU 3.3 0.6 - - - -
171F GLU* 1.3 78.1 - - - +
173F ARG* 1.3 58.4 + - - +
175F ARG* 2.8 20.4 + - - +
176F ILE* 3.2 22.4 + - + +
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Residues in contact with ARG 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LYS* 3.2 13.6 + - + +
170F GLU* 3.3 41.1 + - - +
172F ALA* 1.3 78.6 - - - +
174F LYS* 1.3 79.6 + - - +
175F ARG 3.3 0.9 + - - -
176F ILE 3.5 16.8 + - - +
194F GLU* 3.2 38.2 + - - +
195F GLY* 4.2 14.9 + - - +
196F TYR* 3.7 26.4 - - + -
197F GLU 4.8 1.0 + - - -
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Residues in contact with LYS 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LYS* 3.1 36.2 + - - +
170F GLU* 3.6 17.7 - - + +
171F GLU* 3.1 28.8 + - - +
172F ALA 3.1 0.8 - - - -
173F ARG* 1.3 95.8 - - - +
175F ARG* 1.3 58.3 + - - +
176F ILE 3.5 0.7 - - - -
177F TYR* 3.4 11.2 + - - -
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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