Contacts of the helix formed by residues 133 - 157 (chain F) in PDB entry 1O9R
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 ASP 133 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 3.4 30.5 - - + +
18F VAL* 3.6 18.9 - - + +
72F ARG* 3.0 23.4 + - - -
76F LEU* 3.7 2.1 - - - +
128F SER 3.0 18.3 + - - +
129F ASP 3.9 0.8 + - - -
131F ALA 4.9 0.7 - - - -
132F GLY* 1.4 81.8 - - - +
134F PRO* 1.3 63.1 - - - +
135F THR* 3.4 4.0 + - - -
136F THR* 2.5 35.2 + - - -
137F ALA* 3.0 18.2 + - - +
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Residues in contact with PRO 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F ASP* 3.7 23.3 - - - +
132F GLY* 3.3 10.5 - - - +
133F ASP* 1.3 89.8 - - - +
135F THR* 1.3 60.2 + - - +
137F ALA* 3.6 4.9 - - + +
138F ASP* 2.9 28.4 + - - +
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Residues in contact with THR 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ARG* 3.5 34.1 - - - +
133F ASP* 3.2 2.7 + - - -
134F PRO* 1.3 79.7 - - - +
136F THR* 1.3 62.2 + - - +
138F ASP* 3.2 15.0 + - - +
139F ILE* 3.3 18.9 + - + +
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Residues in contact with THR 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F VAL* 3.4 24.3 - - + +
22F LEU* 3.8 13.0 - - + -
72F ARG* 2.8 25.6 + - + +
76F LEU* 4.1 0.3 - - - +
128F SER* 3.6 4.3 - - - +
133F ASP* 2.5 35.6 + - - -
135F THR* 1.3 76.9 - - - +
137F ALA* 1.3 62.1 + - - +
139F ILE* 3.0 17.0 + - + +
140F PHE* 3.1 33.4 + - + -
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Residues in contact with ALA 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F ILE* 3.6 32.0 - - + +
128F SER* 3.8 10.2 - - - -
129F ASP* 4.0 11.7 - - + +
133F ASP 3.0 14.3 + - - +
134F PRO* 3.6 13.2 - - + +
136F THR* 1.3 76.8 - - - +
138F ASP* 1.3 58.6 + - - +
140F PHE* 3.3 5.1 + - - +
141F THR* 2.8 31.7 + - - +
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Residues in contact with ASP 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F PRO 2.9 14.0 + - - +
135F THR* 3.4 11.7 - - - +
136F THR 3.2 0.2 - - - -
137F ALA* 1.3 75.6 - - - +
139F ILE* 1.3 67.3 + - + +
141F THR* 3.6 11.2 - - - +
142F ALA* 2.9 26.3 + - - +
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Residues in contact with ILE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LEU* 5.1 3.6 - - + -
65F HIS* 4.7 2.9 + - - +
68F THR* 3.6 35.9 - - + +
69F ILE* 4.1 27.1 - - + +
72F ARG* 3.8 39.5 - - + +
75F GLN* 5.4 2.5 - - - +
135F THR* 3.3 16.5 + - + +
136F THR* 3.0 9.2 + - + +
138F ASP* 1.3 78.3 - - + +
140F PHE* 1.4 63.9 + - + +
142F ALA* 3.4 6.8 + - - +
143F ALA* 3.1 21.5 + - + +
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Residues in contact with PHE 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ILE* 3.8 14.4 - - + -
22F LEU* 3.5 24.0 - - + -
25F SER* 3.7 25.6 - - - -
69F ILE* 4.0 17.7 - - + -
121F ILE* 3.3 24.7 - - + +
124F ALA* 3.7 26.0 - - + -
125F ILE* 3.7 20.4 - - + +
128F SER* 3.4 27.1 - - - -
136F THR* 3.1 32.9 + - + -
137F ALA 3.7 3.4 - - - +
139F ILE* 1.4 77.3 - - + +
141F THR* 1.3 56.4 + - - +
143F ALA* 3.3 2.9 + - - -
144F SER* 2.8 25.6 + - - -
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Residues in contact with THR 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F ILE* 3.5 29.7 - - + +
137F ALA 2.8 21.8 + - - -
138F ASP* 3.1 13.3 + - - +
140F PHE* 1.3 72.4 - - - +
142F ALA* 1.3 67.9 + - - +
144F SER* 3.2 2.5 + - - -
145F ARG* 2.9 33.7 + - + +
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Residues in contact with ALA 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F HIS* 3.5 18.3 + - + -
138F ASP* 2.9 18.6 + - - +
139F ILE* 3.7 7.2 - - - +
141F THR* 1.3 78.7 - - - +
143F ALA* 1.4 60.0 + - - +
145F ARG* 3.3 18.6 + - - +
146F ASP* 3.4 11.1 + - - +
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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
----------------------------------------------------------
65F HIS* 3.4 36.3 + - + +
69F ILE* 5.0 10.8 - - + -
121F ILE* 4.1 11.0 - - + -
139F ILE* 3.1 13.4 + - + +
140F PHE* 3.7 9.4 - - - +
141F THR 3.2 0.2 - - - -
142F ALA* 1.4 77.9 - - - +
144F SER* 1.3 57.4 + - - +
146F ASP* 3.2 3.3 + - - +
147F LEU* 2.8 39.4 + - + +
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Residues in contact with SER 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ALA 5.1 1.5 + - - -
121F ILE* 3.6 15.8 - - - +
122F ARG* 4.2 13.6 + - - +
125F ILE* 3.9 18.8 - - - +
140F PHE 2.8 21.7 + - - -
141F THR* 3.4 6.3 - - - -
143F ALA* 1.3 68.5 - - - +
145F ARG* 1.4 68.8 + - - +
147F LEU* 4.4 4.3 - - - -
148F ASP* 2.8 39.5 + - - +
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Residues in contact with ARG 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 THR* 2.9 27.6 + - + +
142F ALA* 3.6 11.2 - - - +
143F ALA 3.2 0.2 - - - -
144F SER* 1.4 78.0 - - - +
146F ASP* 1.3 66.8 + - - +
148F ASP* 3.6 3.6 + - - +
149F LYS* 3.1 24.3 + - - +
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Residues in contact with ASP 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F GLN* 3.8 32.7 + - + +
65F HIS* 2.8 38.0 + - + +
142F ALA 3.4 4.1 + - - +
143F ALA 3.2 3.6 + - - +
145F ARG* 1.3 80.8 - - - +
147F LEU* 1.3 60.0 + - + +
149F LYS* 3.8 8.5 - - - +
150F SER* 2.9 35.0 + - - -
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Residues in contact with LEU 147 (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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29F VAL* 5.5 2.5 - - + -
32F LEU* 4.1 9.0 - - + -
62F LEU* 3.9 27.8 - - + -
65F HIS* 6.0 2.7 - - + -
114F TYR* 4.3 14.9 - - + +
117F VAL* 3.9 23.6 - - + +
118F ALA* 3.9 16.8 - - + +
121F ILE* 3.6 37.5 - - + -
143F ALA* 2.8 28.8 + - + +
144F SER* 4.0 3.1 - - - +
146F ASP* 1.3 71.9 - - + +
148F ASP* 1.4 59.2 + - - +
150F SER* 3.3 3.5 + - - -
151F LEU* 2.8 31.0 + - - +
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Residues in contact with ASP 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ALA* 3.6 11.4 - - - +
122F ARG* 2.9 44.1 + - - -
144F SER* 2.8 28.6 + - - +
145F ARG* 4.2 3.1 - - - +
147F LEU* 1.4 72.6 - - - +
149F LYS* 1.4 59.0 + - - +
151F LEU* 3.5 9.2 + - - +
152F TRP* 3.0 27.2 + - - +
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Residues in contact with LYS 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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52D HIS* 5.5 2.3 - - - -
145F ARG 3.1 18.8 + - - +
146F ASP* 3.9 9.2 - - - +
148F ASP* 1.4 76.2 - - - +
150F SER* 1.3 61.2 + - - +
152F TRP* 3.3 26.8 + - + +
153F PHE* 2.8 62.8 + - + -
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Residues in contact with SER 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F PHE* 3.5 37.5 - - - +
61F GLN* 3.5 11.4 + - - -
114F TYR* 3.9 21.4 - - - -
146F ASP 2.9 20.3 + - - -
147F LEU* 3.7 5.3 - - - -
149F LYS* 1.3 74.3 - - - +
151F LEU* 1.3 66.1 + - - +
153F PHE* 3.2 3.0 + - - +
154F LEU* 3.0 29.6 + - - +
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Residues in contact with LEU 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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111F ILE* 3.9 15.9 - - + +
114F TYR* 4.2 10.9 - - + -
115F GLY* 3.8 34.1 - - - +
118F ALA* 4.4 11.9 - - + -
119F ASN* 5.7 2.5 - - - +
122F ARG* 5.4 3.4 - - - +
147F LEU 2.8 18.5 + - - +
148F ASP* 3.7 9.9 - - - +
150F SER* 1.3 76.3 - - - +
152F TRP* 1.3 58.4 + - - +
154F LEU* 3.2 8.6 + - - +
155F GLU* 2.8 63.8 + - + +
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Residues in contact with TRP 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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41D TRP* 3.6 33.0 + + - -
43D LEU 5.3 0.2 + - - -
44D LYS* 4.7 10.6 - - - +
48D PHE* 3.9 18.3 - + - -
52D HIS* 3.9 14.1 - + - -
148F ASP 3.0 14.9 + - - +
149F LYS* 3.5 25.6 - - + +
151F LEU* 1.3 77.6 - - - +
153F PHE* 1.3 91.0 + + - +
155F GLU* 3.2 9.1 + - + -
156F ALA* 2.8 39.0 + - + +
159F GLN* 5.0 6.3 - - - -
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Residues in contact with PHE 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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48D PHE* 3.5 21.4 - + + -
49D ILE* 3.6 22.9 - - + -
52D HIS* 3.7 27.8 - + - -
53D GLU* 5.5 1.3 - - - -
54F LEU* 3.9 20.4 - - + -
58F PHE* 3.9 17.5 - + + -
149F LYS* 2.8 46.1 + - + +
150F SER* 3.2 8.0 + - - +
152F TRP* 1.3 105.6 - + - +
154F LEU* 1.3 61.4 + - - +
156F ALA 3.6 3.6 + - - -
157F HIS* 2.8 26.8 + - - -
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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
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51F VAL* 5.9 0.9 - - + -
54F LEU* 5.3 4.7 - - + -
55F LEU* 4.4 6.1 - - + -
58F PHE* 3.8 20.4 - - + -
107F LEU* 3.7 25.7 - - + +
110F LEU* 4.1 27.1 - - + +
111F ILE* 3.6 21.3 - - + +
114F TYR* 3.6 42.8 - - + -
150F SER 3.0 18.7 + - - +
151F LEU* 3.6 6.1 - - - +
153F PHE* 1.3 74.1 - - - +
155F GLU* 1.3 67.0 + - - +
157F HIS* 3.2 22.5 + - - +
158F VAL* 3.9 2.1 + - - +
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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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111F ILE* 3.8 33.0 - - + +
151F LEU* 2.8 52.1 + - + +
152F TRP* 3.9 6.6 - - - +
154F LEU* 1.3 71.8 - - - +
156F ALA* 1.3 58.6 + - - +
158F VAL* 2.9 21.4 + - + +
159F GLN* 3.0 40.2 + - + +
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Residues in contact with ALA 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU 4.3 5.8 - - - +
44D LYS* 3.4 7.1 - - + +
45D GLY 2.7 32.2 + - - +
48D PHE* 3.7 29.6 - - + +
152F TRP* 2.8 38.7 + - + +
153F PHE 4.0 2.0 - - - +
154F LEU 3.2 0.2 - - - -
155F GLU* 1.3 72.3 - - - +
157F HIS* 1.3 51.9 + - - +
158F VAL 3.5 0.2 + - - -
159F GLN* 3.3 15.4 + - - +
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Residues in contact with HIS 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLY 3.3 21.9 - - - -
46D PRO* 3.3 33.1 + - + +
47D GLN 4.7 0.2 - - - -
48D PHE* 3.8 12.9 + + + +
49D ILE* 3.3 41.8 + - + +
50F ALA* 5.8 0.2 - - - +
51F VAL* 4.1 19.4 - - + +
54F LEU* 4.0 14.8 - - + -
107F LEU* 3.8 24.4 - - + +
153F PHE 2.8 26.5 + - - -
154F LEU* 3.2 12.6 + - + +
155F GLU 3.1 1.0 + - - -
156F ALA* 1.3 77.2 - - - +
158F VAL* 1.3 60.9 + - - +
160F GLU 3.7 3.8 - - - +
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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