Contacts of the helix formed by residues 141 - 166 (chain F) in PDB entry 1UMN
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 141 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LEU* 3.9 22.4 - - + +
25F SER* 3.9 14.4 - - - +
79F ARG* 3.0 24.8 + - - -
83F LEU* 3.4 21.5 - - - +
136F SER* 2.9 13.9 + - - +
137F ASP* 5.7 0.2 - - - -
139F GLU 3.3 1.0 - - - -
140F GLY* 1.3 73.8 - - - +
142F SER* 1.3 57.8 + - - +
143F VAL 3.6 1.0 + - - -
144F THR* 2.6 31.3 + - - -
145F ASN* 3.0 26.4 + - - +
152K LYS* 5.1 0.9 + - - +
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Residues in contact with SER 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F GLY 3.1 9.2 + - - -
141F ASP* 1.3 71.4 + - - +
143F VAL* 1.3 65.3 + - - +
145F ASN* 3.4 10.2 - - - +
146F ASP* 3.0 18.5 + - - +
130K GLN* 4.9 7.8 + - - -
133K PHE* 3.2 40.6 - - - -
149K ASN* 2.6 34.4 + - - +
152K LYS* 5.1 2.9 + - - +
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Residues in contact with VAL 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ARG* 3.5 35.7 - - - +
141F ASP* 3.3 1.2 + - - -
142F SER* 1.3 76.0 + - - +
144F THR* 1.3 64.8 + - - +
146F ASP* 3.2 6.5 + - - +
147F ILE* 3.0 30.1 + - + +
149K ASN* 3.6 21.8 - - - +
152K LYS* 3.3 26.7 - - - +
153K ALA* 3.4 40.6 - - + +
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Residues in contact with THR 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F SER* 4.6 5.2 - - - -
29F LEU* 3.9 19.5 - - + +
79F ARG* 3.3 19.8 + - - +
136F SER* 3.7 11.4 - - - -
141F ASP* 2.6 33.6 + - - +
143F VAL* 1.3 77.5 - - - +
145F ASN* 1.3 64.5 + - - +
147F ILE* 3.2 12.4 + - - +
148F PHE* 3.1 48.6 + - + -
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Residues in contact with ASN 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F PHE* 2.9 65.5 + - - +
136F SER* 3.0 15.8 + - - +
137F ASP* 3.6 21.5 - - - +
141F ASP 3.0 13.2 + - - +
142F SER* 3.4 15.0 - - - +
144F THR* 1.3 78.0 - - - +
146F ASP* 1.3 59.4 + - - +
148F PHE* 3.3 4.3 + - - +
149F ASN* 3.0 24.9 + - - +
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Residues in contact with ASP 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ASP* 4.5 10.9 - - - +
142F SER 3.0 14.3 + - - +
143F VAL* 3.6 8.2 - - - +
145F ASN* 1.3 75.7 + - - +
147F ILE* 1.3 70.6 + - - +
149F ASN* 3.1 7.7 + - - +
150F VAL* 3.0 41.4 + - - +
146K ASP* 4.5 11.0 - - - +
149K ASN* 3.8 12.6 - - - +
150K VAL* 5.9 4.8 - - - +
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Residues in contact with ILE 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F LEU* 5.3 2.2 - - + -
75F GLU* 3.9 31.0 - - + +
76F MET* 3.7 32.3 - - + -
79F ARG* 3.7 38.6 - - + -
143F VAL* 3.0 24.8 + - + +
144F THR* 3.2 8.7 + - + +
146F ASP* 1.3 81.9 - - - +
148F PHE* 1.3 65.8 + - + +
150F VAL* 3.5 4.7 + - - +
151F ALA* 3.2 20.6 + - - +
157K LYS* 6.3 0.7 - - - +
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Residues in contact with PHE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 4.0 21.5 - - + -
29F LEU* 3.7 25.1 - - + -
32F ALA* 4.3 6.3 - - + -
76F MET* 3.7 30.1 - - + -
128F LEU* 4.8 0.7 - - + -
129F PHE* 3.5 44.6 - + - +
132F GLY* 3.5 30.5 - - - -
133F PHE* 3.8 6.1 - - - +
144F THR* 3.1 45.2 + - + -
145F ASN 3.7 5.6 - - - +
147F ILE* 1.3 78.8 - - + +
149F ASN* 1.3 57.4 + - - +
151F ALA* 3.9 0.2 - - - +
152F LYS* 2.9 31.9 + - - +
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Residues in contact with ASN 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D SER* 2.7 49.3 + - - +
143D VAL* 3.5 15.6 - - - +
146D ASP* 3.8 15.6 - - - +
133F PHE* 3.8 16.9 - - + -
145F ASN 3.0 13.8 + - - +
146F ASP* 3.1 12.9 + - - +
148F PHE* 1.3 76.6 - - - +
150F VAL* 1.3 59.3 + - + +
152F LYS* 3.4 7.5 + - - +
153F ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ASP* 5.5 9.4 - - - +
72F TYR* 6.2 1.1 - - + -
146F ASP* 3.0 39.9 + - - +
147F ILE* 3.9 4.3 - - - +
149F ASN* 1.3 78.6 - - + +
151F ALA* 1.3 62.2 + - - +
153F ALA* 3.4 7.6 + - - +
154F SER* 3.3 21.4 + - - -
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Residues in contact with ALA 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 3.3 41.7 + - + -
76F MET* 3.8 10.5 - - + -
129F PHE* 3.5 22.0 - - + -
147F ILE 3.2 17.7 + - - +
148F PHE 3.9 1.1 - - - +
150F VAL* 1.3 74.1 - - - +
152F LYS* 1.3 66.6 + - - +
153F ALA 3.4 0.2 + - - -
154F SER 3.5 0.7 + - - -
155F ILE* 3.1 22.0 + - - +
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Residues in contact with LYS 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ARG* 4.0 6.9 - - - +
141D ASP* 5.1 1.4 + - - -
142D SER* 4.9 2.6 + - - +
143D VAL* 3.4 19.0 - - + +
126F ALA* 3.9 22.2 - - + +
129F PHE* 3.6 14.3 - - + -
130F GLN* 3.2 41.6 - - - +
133F PHE* 5.9 2.2 - - + -
148F PHE 2.9 19.0 + - - +
149F ASN* 3.7 10.3 - - - +
151F ALA* 1.3 78.2 - - - +
153F ALA* 1.3 56.4 + - - +
155F ILE* 3.4 3.2 + - - +
156F GLU* 2.9 74.9 + - + +
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ARG* 4.9 2.1 + - - -
143D VAL* 3.5 34.9 - - + +
147D ILE* 6.4 0.2 - - + -
149F ASN 3.0 16.1 + - - +
150F VAL* 3.6 8.7 - - - +
151F ALA 3.2 0.2 - - - -
152F LYS* 1.3 77.5 - - - +
154F SER* 1.3 63.2 + - - +
156F GLU* 3.4 4.6 + - - +
157F LYS* 3.1 23.6 + - - +
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Residues in contact with SER 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLU* 2.5 34.5 + - - -
72F TYR* 3.8 7.0 - - - -
150F VAL* 3.3 11.9 + - - -
153F ALA* 1.3 77.4 - - - +
155F ILE* 1.3 65.5 + - - +
157F LYS* 3.1 12.9 + - - +
158F HIS* 3.0 27.6 + - - -
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Residues in contact with ILE 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLU* 4.2 5.2 - - - +
69F ILE* 4.4 5.4 - - + -
72F TYR* 3.0 37.9 - - + +
122F PHE* 3.5 65.7 - - + +
125F LEU* 4.8 2.9 - - + -
126F ALA* 4.0 15.7 - - + +
129F PHE* 4.1 9.0 - - + -
151F ALA 3.1 15.5 + - - +
152F LYS* 3.8 4.3 - - - +
154F SER* 1.3 76.7 - - - +
156F GLU* 1.3 64.4 + - - +
158F HIS* 3.1 7.3 + - + +
159F ILE* 3.0 22.5 + - + +
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Residues in contact with GLU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ARG* 2.8 37.3 + - - +
82D THR* 3.6 10.6 - - + +
143D VAL* 3.9 2.6 - - - +
126F ALA* 4.2 17.3 - - + +
152F LYS* 2.9 59.3 + - - +
153F ALA 3.8 3.6 - - - +
155F ILE* 1.3 76.1 - - - +
157F LYS* 1.3 62.4 + - - +
159F ILE* 3.1 11.2 + - - +
160F TRP 3.1 18.0 + - - -
172F LEU* 4.0 31.0 - - + +
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Residues in contact with LYS 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D GLU* 4.6 16.5 + - - -
78D GLU* 2.7 47.7 + - - +
79D ARG* 4.7 3.0 - - - +
82D THR* 4.3 11.5 + - - +
147D ILE* 6.3 1.2 - - - +
153F ALA 3.1 14.6 + - - +
154F SER* 3.1 13.9 + - - +
156F GLU* 1.3 77.9 - - - +
158F HIS* 1.3 65.4 + - + +
160F TRP* 3.3 21.8 + - + +
161F MET* 3.2 28.1 + - + +
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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
----------------------------------------------------------
65F TYR* 3.6 35.7 + + - +
68F GLU* 2.8 38.0 + - - -
122F PHE* 3.7 23.1 - + + -
154F SER* 3.0 26.4 + - - -
155F ILE* 3.1 11.2 + - + +
157F LYS* 1.3 78.0 - - + +
159F ILE* 1.3 61.1 + - - +
161F MET* 3.3 13.1 + - - +
162F LEU* 2.9 34.9 + - - +
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Residues in contact with ILE 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F VAL* 4.5 8.1 - - + +
122F PHE* 3.7 24.2 - - + +
123F ARG* 3.8 47.3 - - + +
126F ALA* 4.6 4.5 - - + -
155F ILE* 3.0 22.6 + - + +
156F GLU* 3.1 9.8 + - - +
158F HIS* 1.3 73.3 - - - +
160F TRP* 1.3 68.7 + - - +
162F LEU* 4.0 5.8 - - - +
163F GLN* 2.8 31.5 + - + +
170F PRO* 3.9 8.5 - - + +
172F LEU* 3.8 30.1 - - + -
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Residues in contact with TRP 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 4.7 5.3 + + - -
50B MET 5.4 0.6 + - - -
51B ARG* 6.4 0.2 - - - -
55B PHE* 3.9 14.1 - + - -
59B HIS* 3.5 36.6 - + - -
107B TYR* 6.0 0.4 - - - -
78D GLU* 3.8 33.7 - - + -
81D ILE* 3.3 40.9 - - + +
82D THR* 3.5 27.4 - - + +
156F GLU 3.1 9.0 + - - +
157F LYS* 3.4 25.1 - - + +
158F HIS 3.2 0.2 - - - -
159F ILE* 1.3 76.7 - - - +
161F MET* 1.3 77.5 + - + +
163F GLN* 3.3 2.3 + - - +
164F ALA* 2.8 36.9 + - + +
168F GLN 5.0 0.8 - - - +
170F PRO* 3.9 28.1 - - + +
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Residues in contact with MET 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.7 24.1 - - + -
56B MET* 4.0 28.0 - - + +
59B HIS* 3.6 26.0 - - + +
78D GLU* 5.3 3.6 - - - +
58F TRP* 4.9 0.9 - - - -
65F TYR* 5.2 2.0 - - - +
157F LYS* 3.2 23.3 + - + +
158F HIS* 3.8 16.2 - - - +
160F TRP* 1.3 101.3 - - + +
162F LEU* 1.3 62.2 + - - +
164F ALA* 3.3 2.6 + - - +
165F GLU* 3.0 27.2 + - - +
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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
----------------------------------------------------------
58F TRP* 3.5 28.3 - - + -
62F MET* 4.9 0.2 - - + -
65F TYR* 3.7 19.5 - - + +
115F LEU* 3.9 30.7 - - + +
118F VAL* 3.9 24.2 - - + -
119F VAL* 3.5 21.5 - - + -
122F PHE* 3.9 18.4 - - + -
158F HIS 2.9 22.2 + - - +
159F ILE* 4.0 1.6 - - - +
161F MET* 1.3 75.6 - - - +
163F GLN* 1.3 63.9 + - - +
165F GLU* 3.3 7.2 + - - +
166F LEU* 3.0 29.4 + - + +
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Residues in contact with GLN 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F VAL* 3.6 26.1 - - + +
120F GLU* 4.9 3.0 + - - -
123F ARG* 3.3 24.9 + - - +
159F ILE* 2.8 25.1 + - + +
160F TRP 3.7 2.9 - - - +
162F LEU* 1.3 77.2 - - - +
164F ALA* 1.3 56.4 + - - +
166F LEU* 3.0 17.7 + - - +
167F GLY 3.0 5.4 + - - -
168F GLN* 2.8 58.3 + - - +
169F ALA 3.0 29.7 - - - +
170F PRO* 3.9 8.7 - - + +
171F LYS* 3.5 2.6 - - - -
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Residues in contact with ALA 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET 3.8 8.3 - - - +
51B ARG* 3.4 9.3 - - + +
52B GLY 2.7 30.2 + - - -
55B PHE* 3.6 33.0 - - + -
160F TRP* 2.8 24.5 + - + +
161F MET 3.6 5.8 - - - +
162F LEU 3.2 0.2 - - - -
163F GLN* 1.3 73.4 - - - +
165F GLU* 1.3 60.7 + - - +
167F GLY* 2.9 6.6 + - - -
168F GLN 3.6 8.2 + - - -
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Residues in contact with GLU 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY* 3.2 24.4 - - - -
53B ARG* 2.9 35.0 + - - +
54B GLY* 2.9 25.3 + - - -
55B PHE* 3.3 6.6 + - + +
56B MET* 3.0 29.6 + - - +
58F TRP* 3.4 40.2 + - + +
115F LEU* 3.9 13.2 - - + -
161F MET 3.0 13.6 + - - +
162F LEU 3.5 9.6 - - - +
164F ALA* 1.3 75.1 - - - +
166F LEU* 1.3 57.5 + - - +
167F GLY 3.2 2.1 + - - -
1174J EPE 4.6 3.3 + - - -
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Residues in contact with LEU 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 5.2 7.0 - - - +
112F GLU* 4.0 36.6 - - + +
115F LEU* 4.0 23.3 - - + -
116F ALA* 4.1 27.4 - - + +
119F VAL* 4.3 3.6 - - + -
162F LEU 3.0 18.2 + - - +
163F GLN* 3.0 28.2 + - - +
165F GLU* 1.3 77.0 - - + +
167F GLY* 1.3 60.7 + - - +
168F GLN* 3.4 21.4 + - - +
----------------------------------------------------------
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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