Contacts of the helix formed by residues 133 - 159 (chain G) in PDB entry 3V5I
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 ALA 133 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G GLY 3.8 1.0 + - - -
132G GLN* 1.3 70.4 - - - +
134G THR* 1.3 58.2 + - - +
136G ILE* 3.3 11.9 + - - +
137G GLU* 3.0 28.8 + - - +
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Residues in contact with THR 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ARG* 3.5 44.9 + - + +
132G GLN* 3.2 4.6 - - - +
133G ALA* 1.3 76.9 - - - +
135G GLU* 1.3 56.5 + - - +
137G GLU* 3.4 15.9 + - - +
138G ILE* 3.1 36.2 + - + +
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Residues in contact with GLU 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 3.6 31.2 + - - +
129G ALA* 5.4 0.4 - - - -
130G GLN 4.1 11.7 - - - +
131G GLY* 3.5 8.1 - - - -
132G GLN* 2.8 40.9 + - + +
134G THR* 1.3 73.7 - - - +
136G ILE* 1.3 64.9 + - - +
138G ILE* 3.3 10.4 + - + +
139G ALA* 3.2 21.7 + - - +
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Residues in contact with ILE 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G ALA* 4.1 32.9 - - + +
130G GLN 4.5 0.9 - - - -
131G GLY 3.4 30.5 - - - +
132G GLN 2.9 12.6 + - - +
133G ALA* 3.7 11.2 - - - +
135G GLU* 1.3 75.4 - - - +
137G GLU* 1.3 59.6 + - - +
139G ALA* 3.2 2.9 + - - +
140G ALA* 2.8 31.3 + - + +
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Residues in contact with GLU 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G ALA 3.0 13.6 + - - +
134G THR* 3.4 17.7 + - - +
136G ILE* 1.3 77.4 - - - +
138G ILE* 1.3 63.6 + - + +
140G ALA* 3.3 6.4 + - + +
141G ASN* 2.9 45.4 + - - +
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Residues in contact with ILE 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ARG* 3.6 35.9 - - + -
172A ASP* 3.5 35.9 - - + +
174A PHE* 4.3 13.2 - - + -
134G THR* 3.1 26.4 + - + +
135G GLU* 3.7 9.0 - - + +
136G ILE 3.3 0.4 - - - -
137G GLU* 1.3 76.7 - - + +
139G ALA* 1.3 58.5 + - - +
141G ASN* 3.4 8.8 + - - +
142G HIS* 3.0 26.7 + - - +
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Residues in contact with ALA 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 5.5 2.2 - - - -
128G GLY 4.4 7.4 - - - +
129G ALA* 3.6 30.5 - - + -
135G GLU 3.2 11.5 + - - +
136G ILE 3.7 2.0 - - - +
138G ILE* 1.3 76.4 - - - +
140G ALA* 1.3 64.7 + - - +
142G HIS* 3.3 7.5 + - - +
143G ILE* 3.0 25.7 + - - +
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Residues in contact with ALA 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G ALA* 5.4 0.6 - - - +
136G ILE* 2.8 22.3 + - + +
137G GLU* 3.3 7.6 + - - +
139G ALA* 1.3 75.0 - - - +
141G ASN* 1.3 64.2 + - - +
143G ILE* 3.3 10.3 - - - +
144G LEU* 3.0 37.4 + - + +
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Residues in contact with ASN 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G GLU* 2.9 38.2 + - - +
138G ILE* 3.6 8.7 - - - +
140G ALA* 1.3 76.7 - - - +
142G HIS* 1.3 56.6 + - - +
144G LEU* 3.3 12.0 + - - +
145G LYS* 2.9 31.8 + - - +
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Residues in contact with HIS 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET* 4.5 4.0 - - + -
119A GLU* 3.0 33.9 + - - -
174A PHE* 3.4 60.0 - + + -
72G THR* 6.0 1.8 - - + -
138G ILE 3.0 17.5 + - - +
139G ALA* 3.7 7.0 + - - +
140G ALA 3.3 0.2 - - - -
141G ASN* 1.3 77.5 - - - +
143G ILE* 1.3 58.8 + - - +
145G LYS* 3.4 7.2 + - + +
146G THR* 3.0 40.7 + - - -
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Residues in contact with ILE 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G PRO* 4.1 24.0 - - + +
126G LEU* 3.8 9.0 - - - +
127G GLY* 3.7 33.7 - - - +
128G GLY 5.2 0.2 - - - +
139G ALA 3.0 16.2 + - - +
140G ALA* 3.3 16.4 - - - +
142G HIS* 1.3 77.5 - - - +
144G LEU* 1.3 74.1 + - + +
146G THR* 3.4 8.1 + - - -
147G ARG* 3.0 22.0 + - - +
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Residues in contact with LEU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G GLN* 6.4 0.2 - - - +
140G ALA* 3.0 31.1 + - + +
141G ASN* 3.8 12.1 - - - +
143G ILE* 1.3 81.6 - - + +
145G LYS* 1.3 63.9 + - - +
147G ARG* 3.1 16.5 + - + +
148G GLU* 3.1 29.0 + - - +
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Residues in contact with LYS 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE 5.6 2.0 + - - -
176A THR* 3.8 22.8 - - + +
179A GLU* 3.7 22.8 + - - -
141G ASN 2.9 17.9 + - - +
142G HIS* 3.7 9.2 - - + +
144G LEU* 1.3 75.1 - - - +
146G THR* 1.3 63.6 + - - +
148G GLU* 3.2 21.0 + - - +
149G LYS* 3.0 21.4 + - - +
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Residues in contact with THR 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 3.5 21.6 + - - +
71G VAL* 3.7 33.2 - - + -
75G PHE* 5.2 3.4 - - + -
125G PRO* 5.0 5.4 - - + -
142G HIS* 3.0 29.8 + - - -
143G ILE* 3.7 10.5 - - + -
145G LYS* 1.3 75.6 - - - +
147G ARG* 1.3 57.2 + - - +
149G LYS* 3.3 8.5 + - - +
150G LEU* 2.9 35.0 + - + +
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Residues in contact with ARG 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G GLN* 3.4 38.4 + - - +
125G PRO* 3.7 22.0 - - + +
143G ILE 3.0 13.9 + - - +
144G LEU* 3.1 19.3 + - + +
146G THR* 1.3 77.1 - - - +
148G GLU* 1.3 57.0 + - - +
150G LEU* 3.3 4.0 + - + +
151G ASN* 2.9 40.3 + - - +
166G GLN* 3.1 52.8 + - - +
169G THR* 3.1 38.0 + - - -
170G ASP* 3.7 9.3 + - - +
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Residues in contact with GLU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LEU* 3.1 19.0 + - - +
145G LYS* 3.2 20.2 + - + +
147G ARG* 1.3 77.0 - - - +
149G LYS* 1.3 57.8 + - - +
151G ASN* 3.3 6.4 + - - +
152G ARG* 2.8 35.9 + - - +
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Residues in contact with LYS 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN* 2.8 45.2 + - - +
118A ALA 4.6 0.6 + - - -
119A GLU* 3.3 33.9 + - - +
176A THR* 6.2 3.6 - - + +
75G PHE* 3.5 35.2 - - + -
145G LYS 3.0 13.2 + - - +
146G THR* 3.5 13.2 - - - +
148G GLU* 1.3 75.7 - - - +
150G LEU* 1.3 64.1 + - - +
152G ARG* 3.7 27.5 - - - +
153G ILE* 3.1 25.8 + - + +
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Residues in contact with LEU 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G VAL* 4.3 4.9 - - + -
75G PHE* 3.6 28.3 - - + -
99G MET* 3.8 32.3 - - + -
102G PHE* 3.7 26.9 - - + -
125G PRO* 4.1 27.6 - - + -
146G THR* 2.9 30.1 + - + +
147G ARG* 3.7 4.5 - - + +
148G GLU 3.2 0.2 - - - -
149G LYS* 1.3 76.3 - - - +
151G ASN* 1.3 60.9 + - - +
153G ILE* 3.2 2.3 + - - -
154G LEU* 2.9 33.8 + - + +
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Residues in contact with ASN 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G ARG* 2.9 33.1 + - - +
148G GLU* 3.7 5.9 - - - +
150G LEU* 1.3 78.5 - - - +
152G ARG* 1.3 57.2 + - - +
154G LEU* 3.4 3.5 + - - +
155G SER* 2.9 30.0 + - - -
162G ILE* 4.3 16.6 + - + +
165G ILE* 3.4 29.9 - - + +
166G GLN* 2.9 43.2 + - - +
169G THR* 4.2 7.1 + - - +
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Residues in contact with ARG 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN* 3.8 24.2 - - - +
148G GLU* 2.8 20.3 + - - +
149G LYS* 3.7 36.5 - - - +
151G ASN* 1.3 76.1 - - - +
153G ILE* 1.3 69.6 + - - +
155G SER* 3.2 5.4 + - - -
156G GLU* 3.2 40.8 + - + +
162G ILE* 4.2 23.3 - - + +
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Residues in contact with ILE 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN* 3.4 39.5 - - - +
75G PHE* 3.7 18.6 - - + -
78G TYR* 3.2 33.7 - - + +
102G PHE* 3.7 13.2 - - + -
149G LYS* 3.1 19.5 + - + +
150G LEU 4.0 2.2 - - - +
152G ARG* 1.3 87.1 - - - +
154G LEU* 1.3 62.4 + - - +
156G GLU* 3.3 18.9 + - - +
157G ARG* 3.1 25.7 + - - +
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Residues in contact with LEU 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G SER* 6.1 0.2 - - - +
102G PHE* 3.9 27.7 - - + -
105G ALA* 4.2 14.8 - - + -
122G ILE* 5.1 13.9 - - + -
150G LEU* 2.9 19.6 + - + +
151G ASN* 3.6 6.5 - - - +
153G ILE* 1.3 75.9 - - - +
155G SER* 1.3 65.2 + - - +
157G ARG* 3.0 5.1 + - + +
158G THR* 2.9 35.5 + - + +
165G ILE* 4.0 29.6 - - + -
169G THR* 5.3 6.1 - - + -
183G TYR* 5.8 0.9 - - + -
185G LEU* 4.1 24.2 - - + -
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Residues in contact with SER 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G ASN 2.9 14.1 + - - -
152G ARG 3.3 10.8 - - - -
154G LEU* 1.3 75.3 - - - +
156G GLU* 1.3 55.7 + - - +
158G THR* 3.9 2.5 - - - -
159G GLY* 2.8 34.1 + - - -
160G GLN 2.5 26.1 + - - -
161G SER* 3.8 1.4 - - - -
162G ILE* 3.4 27.5 + - - +
165G ILE* 4.5 4.0 - - - +
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Residues in contact with GLU 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G TYR* 5.2 1.4 + - - -
109G LYS* 3.7 11.1 + - - -
152G ARG* 3.2 34.7 + - + +
153G ILE* 3.4 24.9 - - - +
154G LEU 3.1 0.2 - - - -
155G SER* 1.3 79.1 - - - +
157G ARG* 1.3 62.0 + - + +
158G THR 3.5 0.4 + - - -
159G GLY* 4.2 3.8 + - - -
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Residues in contact with ARG 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G TYR* 3.2 28.9 + - - -
82G GLN* 3.5 32.8 - - - +
102G PHE* 5.8 1.3 - - - -
105G ALA* 3.6 36.8 + - + +
106G ALA* 4.1 8.7 + - - +
107G GLY 3.8 14.6 + - - -
108G ALA* 5.7 0.4 - - - +
109G LYS* 3.7 36.6 + - - +
112G ARG* 3.1 24.1 + - - +
153G ILE* 3.1 19.5 - - + +
154G LEU* 3.0 6.3 + - + +
156G GLU* 1.3 84.3 + - + +
158G THR* 1.3 61.9 + - + +
159G GLY 3.6 0.2 - - - -
184G GLY 3.4 2.9 - - - +
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Residues in contact with THR 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ALA* 5.0 2.2 - - + -
154G LEU* 2.9 32.1 + - + +
155G SER* 3.6 0.5 + - - -
157G ARG* 1.3 78.4 - - - +
159G GLY* 1.3 63.3 + - - +
160G GLN* 3.2 21.6 + - - +
165G ILE* 4.0 2.3 - - - +
183G TYR* 3.6 27.2 - - + +
184G GLY* 3.4 30.1 - - - +
185G LEU* 3.9 24.5 - - + +
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Residues in contact with GLY 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G SER 2.8 12.9 + - - -
156G GLU 4.2 3.6 + - - -
157G ARG 3.6 1.4 - - - -
158G THR* 1.3 77.6 - - - +
160G GLN* 1.3 62.9 + - - +
161G SER 4.1 0.2 + - - -
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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