Contacts of the helix formed by residues 139 - 160 (chain F) in PDB entry 3E8C
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 SER 139 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ARG* 4.2 8.4 + - - +
138F PHE* 1.3 76.1 - - - +
140F GLU* 1.3 60.0 + - - +
141F PRO* 4.0 10.6 - - - +
142F HIS* 3.1 24.8 + - - +
143F ALA* 2.8 26.5 + - - +
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F PHE 5.6 0.2 - - - +
139F SER* 1.3 73.5 - - - +
141F PRO* 1.3 62.0 - - + +
143F ALA* 3.7 5.3 - - - -
144F ARG* 2.8 43.7 + - - +
232F ALA* 4.7 6.1 - - + -
260F HIS* 3.9 6.3 + - - +
261F PHE* 3.5 6.9 - - + -
262F SER* 2.7 49.9 + - - -
265F LEU* 3.2 26.7 - - + +
296F TRP* 3.1 20.9 + - + +
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Residues in contact with PRO 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F SER* 3.6 13.0 - - - +
140F GLU* 1.3 96.0 - - + +
142F HIS* 1.3 55.5 + - - +
144F ARG* 3.5 24.4 - - - +
145F PHE* 3.1 27.2 + - - +
313F PRO* 5.3 1.1 - - - +
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Residues in contact with HIS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F ILE* 5.6 2.7 - - + -
138F PHE* 3.9 27.8 - + + +
139F SER* 3.1 27.7 + - - +
141F PRO* 1.3 75.5 - - - +
143F ALA* 1.3 65.2 + - - +
145F PHE* 3.3 15.2 + - - +
146F TYR* 3.1 44.2 + + - -
313F PRO* 3.3 34.3 + - + +
314F PHE* 3.4 26.6 - + + +
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Residues in contact with ALA 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F PHE* 4.1 3.5 - - + +
139F SER 2.8 20.1 + - - +
140F GLU* 3.8 7.6 - - - +
142F HIS* 1.3 73.1 - - - +
144F ARG* 1.3 56.7 + - - +
146F TYR* 3.4 1.3 + - - -
147F ALA* 2.9 25.6 + - - +
228F ILE 4.8 1.8 - - - +
231F MET* 3.2 46.2 - - + +
232F ALA* 4.4 13.7 - - + +
296F TRP* 4.1 9.6 - - + -
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Residues in contact with ARG 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F GLU* 2.8 30.5 + - - +
141F PRO* 3.5 36.0 - - - +
143F ALA* 1.3 71.0 - - - +
145F PHE* 1.3 60.7 + - - +
147F ALA* 3.7 0.7 - - - +
148F ALA* 2.9 29.8 + - - +
296F TRP* 2.6 69.0 + - + +
297F PHE* 3.9 12.3 - - + -
299F THR* 3.9 19.6 + - - -
300F THR* 3.5 25.1 - - - +
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Residues in contact with PHE 145 (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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141F PRO 3.1 14.1 + - - +
142F HIS 3.4 9.9 - - - +
144F ARG* 1.3 78.2 - - - +
146F TYR* 1.3 71.9 + + - +
148F ALA* 3.7 5.7 + - - +
149F GLN* 3.1 45.9 + - - +
178F GLY 3.5 20.6 - - - -
179F TYR* 3.6 31.4 - + - -
305F ILE* 5.0 10.3 - - + +
310F VAL* 3.8 30.5 - - + -
311F GLU 4.6 1.1 - - - -
312F ALA* 3.8 13.7 - - + -
313F PRO* 3.4 25.8 - - + -
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Residues in contact with TYR 146 (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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128F MET* 3.5 25.1 - - + -
138F PHE* 3.9 18.2 - + - -
142F HIS* 3.1 44.0 + + - -
143F ALA 3.4 1.5 + - - +
144F ARG 3.3 0.2 - - - -
145F PHE* 1.3 90.3 - + - +
147F ALA* 1.3 66.7 + - - +
149F GLN* 3.1 14.0 + - - +
150F ILE* 3.2 19.7 + - + +
174F ILE* 4.3 12.6 - - + +
178F GLY 3.6 23.1 + - - -
180F ILE* 3.4 27.9 - - + +
231F MET* 3.8 23.8 - - + -
313F PRO* 4.9 1.0 - - + +
314F PHE* 3.8 22.2 + - - +
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Residues in contact with ALA 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F ALA 2.9 19.5 + - - +
144F ARG* 3.4 7.6 + - - +
146F TYR* 1.3 76.5 - - - +
148F ALA* 1.3 56.6 + - - +
150F ILE* 3.1 10.7 + - - +
151F VAL* 2.9 33.9 + - - +
224F LEU* 4.4 3.3 - - + +
227F LEU* 6.1 0.2 - - - -
228F ILE* 3.8 33.0 - - + -
231F MET* 4.1 4.2 - - + +
296F TRP* 4.1 1.6 - - + -
297F PHE* 4.0 11.7 - - + -
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Residues in contact with ALA 148 (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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144F ARG 2.9 17.7 + - - +
145F PHE 3.9 3.1 - - - +
146F TYR 3.2 0.2 - - - -
147F ALA* 1.3 76.6 - - - +
149F GLN* 1.3 61.5 + - - +
152F LEU* 3.2 23.5 + - - +
297F PHE* 4.0 3.7 - - + -
300F THR* 3.9 7.0 - - + -
302F TRP* 3.3 31.4 - - + -
305F ILE* 3.3 33.2 - - + -
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Residues in contact with GLN 149 (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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102F PHE* 3.6 27.4 - - + -
145F PHE* 3.1 55.8 + - - +
146F TYR 3.1 7.2 + - - +
148F ALA* 1.3 73.8 - - - +
150F ILE* 1.3 61.5 + - - +
152F LEU* 3.6 0.5 + - - +
153F THR* 2.9 32.4 + - - -
179F TYR* 3.4 16.8 - - - -
180F ILE* 2.6 45.7 + - + +
305F ILE* 3.8 17.7 - - + -
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Residues in contact with ILE 150 (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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102F PHE* 6.4 0.2 - - + -
146F TYR* 3.2 15.0 + - + +
147F ALA* 3.1 6.7 + - - +
149F GLN* 1.3 76.1 - - - +
151F VAL* 1.3 59.2 + - - +
153F THR* 3.2 3.3 + - - -
154F PHE* 2.8 46.2 + - + +
167F LEU* 3.7 19.7 - - + -
172F LEU* 3.6 34.8 - - + -
180F ILE* 4.2 10.5 - - + -
182F VAL* 4.1 14.4 - - + -
224F LEU* 3.5 23.3 - - + -
227F LEU* 4.1 15.7 - - + -
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Residues in contact with VAL 151 (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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147F ALA 2.9 23.9 + - - +
148F ALA 3.8 4.9 - - - +
150F ILE* 1.3 77.2 - - - +
152F LEU* 1.3 56.6 + - - +
154F PHE 3.6 0.2 + - - -
155F GLU* 3.0 27.5 + - - +
221F TRP* 3.8 12.6 - - + -
224F LEU* 3.5 25.4 - - + -
288F VAL* 3.7 25.1 - - + -
291F ILE* 3.9 22.2 - - + -
292F LYS* 4.3 4.9 - - + -
297F PHE* 4.4 10.1 - - + -
302F TRP* 4.0 17.0 - - + -
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Residues in contact with LEU 152 (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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100F PHE* 3.5 22.9 - - + -
102F PHE* 4.3 4.5 - - + -
148F ALA 3.2 17.5 + - - +
149F GLN 3.9 3.8 - - - +
151F VAL* 1.3 76.1 - - - +
153F THR* 1.3 59.6 + - - +
155F GLU* 3.5 23.1 + - - +
156F TYR* 3.1 21.5 + - - +
292F LYS* 3.6 22.4 - - - +
302F TRP* 3.6 36.8 - - + +
305F ILE* 3.9 17.7 - - + -
306F TYR* 4.0 17.9 - - + -
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Residues in contact with THR 153 (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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100F PHE* 3.6 13.7 - - + -
102F PHE* 3.5 22.3 + - - +
103F LEU* 3.5 32.8 - - + -
149F GLN 2.9 21.1 + - - -
150F ILE* 3.6 8.5 - - - -
152F LEU* 1.3 74.9 - - - +
154F PHE* 1.3 63.7 + - + +
156F TYR* 3.3 3.8 + - - +
157F LEU* 2.9 39.3 + - + +
182F VAL* 4.3 12.5 - - + +
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Residues in contact with PHE 154 (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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150F ILE* 2.8 34.2 + - + +
153F THR* 1.3 75.4 - - + +
155F GLU* 1.3 61.2 + - - +
157F LEU* 4.2 15.9 - - + -
158F HIS* 2.8 43.8 + - - +
164F TYR* 3.9 28.0 - + + -
167F LEU* 3.7 34.8 - - + -
182F VAL* 6.1 2.7 - - + -
220F ASP* 3.2 47.6 - - + -
221F TRP* 3.5 34.5 - + + -
224F LEU* 4.5 1.8 - - + -
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Residues in contact with GLU 155 (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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15F VAL* 4.6 11.7 - - - +
19F LEU* 4.3 20.2 - - + +
151F VAL 3.0 17.4 + - - +
152F LEU* 3.5 17.0 - - - +
153F THR 3.3 0.2 - - - -
154F PHE* 1.3 75.6 - - - +
156F TYR* 1.3 62.7 + - - +
158F HIS* 4.4 3.0 - - - +
159F SER* 3.3 23.6 + - - -
221F TRP* 4.2 5.7 - - - -
288F VAL* 3.4 29.7 - - + +
289F ASN* 5.3 0.9 - - - +
292F LYS* 3.0 38.4 + - - -
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Residues in contact with TYR 156 (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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18F PHE* 4.8 7.4 - + - -
19F LEU* 4.3 7.6 - - + -
22F ALA* 3.9 31.4 + - + -
26F PHE* 5.0 0.7 - - - +
97F ALA 4.6 1.4 + - - -
98F VAL* 3.5 21.8 - - + -
99F ASN* 2.8 40.6 + - - +
100F PHE* 3.5 40.6 - + + -
103F LEU* 4.2 4.5 - - + -
152F LEU 3.1 14.5 + - - +
153F THR 3.5 7.9 - - - +
154F PHE 3.2 0.2 - - - -
155F GLU* 1.3 76.2 - - - +
157F LEU* 1.3 74.8 + - + +
159F SER* 2.7 22.1 + - - -
160F LEU* 3.1 38.3 - - + +
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Residues in contact with LEU 157 (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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98F VAL* 4.5 1.3 - - + -
103F LEU* 4.5 6.5 - - + -
153F THR* 2.9 34.9 + - + +
154F PHE* 4.0 17.5 - - + +
156F TYR* 1.3 91.5 - - + +
158F HIS* 1.3 64.5 + - + +
160F LEU* 3.1 9.6 + - - +
162F LEU* 2.9 60.0 + - + +
164F TYR* 4.2 23.3 - - + +
182F VAL* 6.2 1.1 - - + -
185F PHE* 4.2 26.7 - - + -
220F ASP* 5.5 0.2 - - - +
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Residues in contact with HIS 158 (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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154F PHE* 2.8 29.8 + - + +
155F GLU* 4.4 3.1 - - - +
157F LEU* 1.3 78.1 - - + +
159F SER* 1.3 57.9 + - - +
161F ASP* 2.9 23.2 + - - +
162F LEU 3.3 19.5 - - - -
217F LYS* 3.4 48.5 + - + +
220F ASP* 2.8 32.4 + - + +
221F TRP* 3.5 34.3 + + + -
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Residues in contact with SER 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 3.6 32.1 + - - +
23F LYS* 4.1 17.0 - - - +
155F GLU 3.3 14.4 + - - -
156F TYR 2.7 20.4 + - - -
158F HIS* 1.3 76.9 - - - +
160F LEU* 1.3 69.2 + - - +
161F ASP* 3.2 6.2 + - - +
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Residues in contact with LEU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU 5.1 0.7 - - - +
22F ALA* 4.7 2.2 - - + +
23F LYS* 4.5 24.2 - - + +
26F PHE* 3.5 46.8 - - + -
98F VAL* 4.5 0.4 - - + -
156F TYR* 3.1 45.8 - - + +
157F LEU 3.1 9.7 + - - +
159F SER* 1.3 94.4 - - - +
161F ASP* 1.3 70.9 + - - +
162F LEU* 3.2 17.2 + - + +
190F ARG* 3.1 22.6 + - - +
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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