Contacts of the helix formed by residues 120 - 145 (chain F) in PDB entry 3BVI
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 LEU 120 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 4.3 15.7 - - + -
57F LEU* 4.4 1.6 - - + -
101F ILE* 5.6 2.5 - - + -
104F ILE* 3.6 32.5 - - + -
105F VAL* 3.7 31.2 - - + +
108F ALA* 5.3 0.2 - - + -
116F THR* 3.0 31.5 + - + +
117F PHE* 3.8 5.8 - - - +
118F ASN 3.2 0.6 - - - -
119F PHE* 1.3 93.9 - - + +
121F GLN* 1.3 58.7 + - - +
122F TRP 3.4 0.7 - - - -
123F TYR* 2.9 47.9 + - + +
124F VAL* 3.0 15.5 + - + +
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Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F VAL* 4.4 8.9 - - - +
117F PHE* 3.0 56.6 + - + +
118F ASN* 3.6 17.7 - - - +
119F PHE 3.2 2.0 - - - -
120F LEU* 1.3 74.8 - - - +
122F TRP* 1.3 67.3 + - - +
124F VAL* 3.4 16.9 + - - +
125F ALA* 3.0 24.4 + - - +
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Residues in contact with TRP 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F HIS* 3.8 32.1 - + - -
56F LYS* 3.5 46.9 - - + -
57F LEU* 4.8 2.9 - - + -
118F ASN 4.8 0.6 + - - -
119F PHE* 2.8 58.4 + + - -
121F GLN* 1.3 76.6 - - - +
123F TYR* 1.3 86.9 + + + +
125F ALA* 3.4 5.2 + - - +
126F GLU* 2.9 57.9 + - + +
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Residues in contact with TYR 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLN* 3.0 32.1 + - + +
17F GLU* 2.4 41.8 + - + +
53F HIS* 4.0 16.4 - + + -
57F LEU* 4.2 15.0 - - + -
101F ILE* 3.7 31.8 - - + +
104F ILE* 5.6 0.9 - - + -
120F LEU* 2.9 32.8 + - + +
122F TRP* 1.3 110.8 - + + +
124F VAL* 1.3 64.2 + - - +
126F GLU* 4.6 1.1 - - + +
127F GLN* 2.9 30.1 + - + +
1006F FE 3.9 7.6 - - - -
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Residues in contact with VAL 124 (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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101F ILE* 3.8 25.7 - - + +
102F ASN* 5.0 11.2 - - - +
105F VAL* 3.9 18.6 - - + -
120F LEU 3.0 19.9 + - - +
121F GLN* 3.7 20.0 - - - +
123F TYR* 1.3 77.3 - - - +
125F ALA* 1.3 57.7 + - - +
127F GLN* 3.9 2.6 - - - +
128F HIS* 3.0 30.8 + - + +
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Residues in contact with ALA 125 (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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121F GLN 3.0 17.3 + - - +
122F TRP* 3.7 6.3 - - - +
124F VAL* 1.3 78.0 - - - +
126F GLU* 1.3 64.2 + - + +
128F HIS* 3.3 7.5 + - - +
129F GLU* 3.2 22.7 + - - +
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Residues in contact with GLU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLU* 4.0 8.1 - - - +
53F HIS* 3.5 27.9 + - + +
56F LYS* 4.6 10.0 + - - -
122F TRP* 2.9 44.8 + - + +
123F TYR* 4.2 1.8 - - - +
125F ALA* 1.3 77.0 - - + +
127F GLN* 1.3 57.7 + - - +
129F GLU* 3.4 16.2 + - - +
130F GLU* 3.0 35.0 + - - +
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Residues in contact with GLN 127 (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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53F HIS* 5.4 1.3 - - - -
94F GLU* 2.9 33.1 + - - +
97F ILE* 3.7 9.6 - - - +
98F SER* 2.9 32.7 + - - +
101F ILE* 3.4 25.4 - - + -
123F TYR* 2.9 20.0 + - + +
124F VAL* 4.0 3.4 - - - +
126F GLU* 1.3 75.5 - - - +
128F HIS* 1.3 59.2 + - - +
130F GLU* 3.2 4.3 + - - +
131F GLU* 2.9 26.9 + - - +
1006F FE 2.8 13.9 - - - -
1007F FE 2.5 26.0 - - - -
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Residues in contact with HIS 128 (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 SER* 5.1 0.4 - - - -
124F VAL* 3.0 20.9 + - + +
125F ALA* 3.3 6.7 + - - +
127F GLN* 1.3 76.7 - - - +
129F GLU* 1.3 58.0 + - - +
131F GLU* 3.2 18.5 + - - +
132F VAL* 3.0 51.1 + - + +
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Residues in contact with GLU 129 (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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125F ALA 3.2 9.5 + - - +
126F GLU* 3.5 20.6 - - - +
128F HIS* 1.3 82.0 - - - +
130F GLU* 1.3 56.8 + - + +
132F VAL* 3.5 7.2 + - - +
133F LEU* 3.0 28.2 + - + +
165F ARG* 4.0 29.4 + - - +
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Residues in contact with GLU 130 (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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46F HIS* 3.4 19.5 - - + +
49F GLU* 3.7 12.3 - - - +
50F GLU* 2.9 13.7 - - - +
53F HIS* 2.9 25.8 + - - -
94F GLU* 4.1 4.0 - - - +
126F GLU* 3.0 19.4 + - - +
127F GLN* 3.5 8.3 - - - +
129F GLU* 1.3 73.5 - - + +
131F GLU* 1.3 65.2 + - - +
133F LEU* 3.3 9.3 + - + +
134F PHE* 3.1 31.3 + - - -
165F ARG* 5.1 12.0 + - - +
1006F FE 3.3 4.2 - - - -
1007F FE 2.3 36.2 - - - -
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Residues in contact with GLU 131 (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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91F TYR* 3.6 21.6 + - + -
94F GLU* 4.2 10.6 + - + -
95F GLN* 3.5 32.2 - - - +
98F SER* 2.5 37.0 + - - +
127F GLN* 2.9 20.8 + - - +
128F HIS* 3.6 18.2 + - - +
130F GLU* 1.3 73.2 - - - +
132F VAL* 1.3 62.7 + - + +
134F PHE* 3.4 0.7 + - - -
135F LYS* 3.1 22.1 + - - +
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Residues in contact with VAL 132 (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 HIS* 3.0 48.6 + - + +
129F GLU* 3.7 7.6 - - - +
131F GLU* 1.3 71.7 - - + +
133F LEU* 1.3 62.0 + - - +
135F LYS* 3.2 24.6 + - - +
136F ASP* 2.8 43.3 + - - +
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Residues in contact with LEU 133 (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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42F PHE* 3.8 27.1 - - + -
46F HIS* 6.2 1.1 - - - +
129F GLU* 3.0 17.7 + - + +
130F GLU* 3.3 9.8 + - + +
132F VAL* 1.3 77.8 - - - +
134F PHE* 1.3 59.7 + - + +
136F ASP* 3.2 12.7 + - + +
137F ILE* 2.9 40.2 + - + +
161F ILE* 3.9 25.8 - - + -
165F ARG* 3.6 42.6 - - - +
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Residues in contact with PHE 134 (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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24F TYR* 3.9 7.2 - + - -
42F PHE* 3.7 30.3 - + - -
43F LEU* 4.1 3.8 - - + -
46F HIS* 3.4 49.1 - + - -
87F PHE* 3.9 20.1 - + - +
90F ALA* 3.6 33.4 - - + -
91F TYR* 4.2 20.1 - - + +
94F GLU* 3.9 13.2 - - + -
130F GLU* 3.1 29.9 + - + +
131F GLU 3.9 4.0 - - - +
132F VAL 3.3 0.2 - - - -
133F LEU* 1.3 76.9 - - + +
135F LYS* 1.3 61.6 + - - +
137F ILE* 4.0 4.3 - - - +
138F LEU* 2.9 31.9 + - - +
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Residues in contact with LYS 135 (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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91F TYR* 3.6 36.0 - - + +
131F GLU 3.1 13.7 + - - +
132F VAL* 3.3 26.7 - - - +
134F PHE* 1.3 77.6 - - - +
136F ASP* 1.3 80.9 + - - +
138F LEU* 3.7 3.5 - - - +
139F ASP* 3.0 48.8 + - - +
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Residues in contact with ASP 136 (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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132F VAL* 2.8 27.6 + - - +
133F LEU* 3.4 16.1 - - + +
135F LYS* 1.3 104.1 + - - +
137F ILE* 1.3 61.8 + - + +
139F ASP* 3.5 8.1 + - - +
140F LYS* 3.1 29.8 + - - +
157F TYR* 5.0 6.8 + - - +
161F ILE* 6.3 0.9 - - + -
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Residues in contact with ILE 137 (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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42F PHE* 3.3 46.2 - - + -
87F PHE* 3.6 18.6 - - + -
133F LEU* 2.9 29.0 + - + +
134F PHE* 4.0 3.8 - - - +
136F ASP* 1.3 73.1 - - + +
138F LEU* 1.3 58.2 + - - +
140F LYS* 3.2 5.8 + - - +
141F ILE* 2.8 49.6 + - + +
157F TYR* 4.8 3.6 - - + -
158F VAL* 3.8 18.8 - - + -
161F ILE* 3.9 24.0 - - + -
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Residues in contact with LEU 138 (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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84F THR* 4.3 10.1 - - + +
87F PHE* 3.9 19.2 - - + +
88F GLN* 3.7 37.9 - - + +
91F TYR* 4.0 25.8 - - + -
134F PHE 2.9 19.0 + - - +
135F LYS 3.7 4.7 - - - +
137F ILE* 1.3 76.2 - - - +
139F ASP* 1.3 64.6 + - - +
141F ILE* 3.3 8.7 + - + +
142F GLU* 3.0 52.2 + - + +
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Residues in contact with ASP 139 (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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135F LYS* 3.0 39.8 + - - +
136F ASP* 3.5 8.9 - - - +
138F LEU* 1.3 76.2 - - - +
140F LYS* 1.3 59.0 + - - +
142F GLU* 3.4 17.7 + - - +
143F LEU* 2.9 28.9 + - - +
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Residues in contact with LYS 140 (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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136F ASP 3.1 16.7 + - - +
137F ILE 3.2 4.2 + - - +
139F ASP* 1.3 75.0 - - - +
141F ILE* 1.3 60.9 + - - +
143F LEU* 3.3 27.7 + - + +
144F ILE* 2.9 48.0 + - + +
157F TYR* 3.5 55.0 - - + -
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Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F LEU* 4.1 27.8 - - + +
84F THR* 3.3 33.3 + - + +
87F PHE* 3.5 40.6 - - + -
137F ILE* 2.8 34.9 + - + +
138F LEU* 3.7 6.1 - - + +
140F LYS* 1.3 77.0 - - + +
142F GLU* 1.3 56.3 + - - +
144F ILE* 4.0 1.2 - - - +
145F GLY* 3.1 27.2 + - - +
151F LEU* 6.1 0.7 - - + -
154F ALA* 4.4 16.6 - - + +
157F TYR* 6.3 0.7 - - + -
158F VAL* 5.0 4.3 - - + -
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Residues in contact with GLU 142 (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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84F THR* 4.9 10.5 - - + -
88F GLN* 4.4 9.4 - - - +
138F LEU* 3.0 47.1 + - + +
139F ASP* 3.6 23.0 - - - +
141F ILE* 1.3 72.6 - - - +
143F LEU* 1.3 65.2 + - - +
145F GLY* 3.6 10.3 + - - -
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Residues in contact with LEU 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F ASP 2.9 18.3 + - - +
140F LYS* 3.3 34.7 + - + +
142F GLU* 1.3 77.7 - - - +
144F ILE* 1.3 64.0 + - + +
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Residues in contact with ILE 144 (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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140F LYS* 2.9 39.2 + - + +
141F ILE 4.0 2.5 - - - +
143F LEU* 1.3 80.8 - - + +
145F GLY* 1.3 64.6 + - - +
147F GLU* 4.6 8.8 - - - +
150F GLY* 3.2 33.6 - - - +
153F LEU* 4.1 19.1 - - + +
154F ALA* 3.6 30.1 - - + +
157F TYR* 4.8 6.1 - - + -
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Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F ILE 3.1 17.6 + - - +
142F GLU* 3.6 8.2 + - - -
143F LEU 3.5 2.0 - - - -
144F ILE* 1.3 85.3 - - - +
146F ASN* 1.3 61.5 + - - +
147F GLU* 3.6 9.2 - - - -
150F GLY* 3.3 17.2 - - - -
151F LEU* 4.9 0.2 - - - -
154F ALA* 5.4 1.0 - - - +
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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