Contacts of the helix formed by residues 133 - 159 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLY 3.9 1.0 + - - -
132A GLN* 1.3 70.8 - - - +
134A THR* 1.3 63.3 + - - +
136A ILE* 3.4 10.6 + - - +
137A GLU* 3.0 24.3 + - - +
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Residues in contact with THR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLN* 3.2 4.6 - - - +
133A ALA* 1.3 77.3 - - - +
135A GLU* 1.3 61.0 + - - +
137A GLU* 3.4 16.1 + - - +
138A ILE* 3.1 32.1 + - + +
171B ARG* 3.7 41.5 + - + +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 5.4 0.4 - - - -
130A GLN 4.0 10.2 - - - +
131A GLY* 3.6 7.8 - - - -
132A GLN* 2.9 35.9 + - + +
134A THR* 1.3 75.9 - - - +
136A ILE* 1.3 66.5 + - - +
138A ILE* 3.2 10.2 + - + +
139A ALA* 3.1 22.0 + - - +
171B ARG* 3.7 33.4 + - + +
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 4.1 35.6 - - + +
130A GLN 4.5 3.4 - - - -
131A GLY 3.4 25.4 - - - +
132A GLN 2.9 12.3 + - - +
133A ALA* 3.8 10.5 - - - +
135A GLU* 1.3 74.8 - - - +
137A GLU* 1.3 52.1 + - - +
139A ALA* 3.2 2.8 + - - +
140A ALA* 2.8 38.1 + - + +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA 3.0 13.2 + - - +
134A THR* 3.5 18.0 + - - +
136A ILE* 1.3 76.6 - - - +
138A ILE* 1.3 59.4 + - + +
140A ALA* 3.3 6.7 + - + +
141A ASN* 3.0 51.0 + - - +
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A THR* 3.1 35.0 + - + +
135A GLU* 3.2 9.8 + - + +
137A GLU* 1.3 78.1 - - + +
139A ALA* 1.3 61.2 + - - +
141A ASN* 3.6 8.4 + - - +
142A HIS* 3.1 22.3 + - - +
171B ARG* 3.7 31.4 - - + -
172B ASP* 3.6 34.5 - - + +
174B PHE* 4.3 13.2 - - + -
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY 4.4 7.0 - - - +
129A ALA* 3.5 32.1 - - + -
135A GLU 3.1 11.2 + - - +
136A ILE 3.5 2.5 - - - +
138A ILE* 1.3 74.8 - - - +
140A ALA* 1.3 65.9 + - - +
142A HIS* 3.3 7.3 + - - +
143A ILE* 3.0 25.4 + - - +
174B PHE* 5.5 2.7 - - - -
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 2.8 24.8 + - + +
137A GLU* 3.6 8.1 - - + +
139A ALA* 1.3 72.0 - - - +
141A ASN* 1.3 60.4 + - - +
143A ILE* 3.3 11.7 + - - +
144A LEU* 3.0 40.0 + - + +
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Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU* 3.0 40.5 + - - +
138A ILE* 3.8 8.1 - - - +
140A ALA* 1.3 78.7 - - - +
142A HIS* 1.3 56.6 + - - +
144A LEU* 3.5 11.5 + - - +
145A LYS* 3.0 30.8 + - - +
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Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 6.0 1.3 - - + -
138A ILE 3.1 18.3 + - - +
139A ALA* 3.6 6.8 + - - +
141A ASN* 1.3 78.3 - - - +
143A ILE* 1.3 59.7 + - - +
145A LYS* 3.4 8.3 + - + +
146A THR* 2.9 42.5 + - - -
95B MET* 4.6 3.4 - - + -
119B GLU* 3.1 32.7 + - - -
174B PHE* 3.5 59.3 - + + -
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PRO* 3.9 25.0 - - + +
126A LEU 3.7 9.9 - - - +
127A GLY* 3.6 33.9 - - - +
128A GLY 5.3 0.2 - - - +
139A ALA 3.0 15.5 + - - +
140A ALA* 3.3 15.5 - - - +
142A HIS* 1.3 77.2 - - - +
144A LEU* 1.3 69.2 + - + +
146A THR* 3.3 8.4 + - - -
147A ARG* 2.9 26.9 + - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN* 6.4 0.4 - - - +
140A ALA* 3.0 30.4 + - + +
141A ASN* 3.8 11.9 - - - +
143A ILE* 1.3 80.8 - - + +
145A LYS* 1.3 59.7 + - - +
147A ARG* 3.2 17.9 + - + +
148A GLU* 3.2 27.7 + - - +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASN 3.0 19.0 + - - +
142A HIS* 3.6 10.1 - - + +
143A ILE 3.3 0.2 - - - -
144A LEU* 1.3 73.6 - - - +
146A THR* 1.3 65.4 + - - +
148A GLU* 3.1 19.2 + - + +
149A LYS* 2.9 23.7 + - + +
174B PHE 5.8 1.2 + - - -
176B THR* 4.0 21.4 - - + +
179B GLU* 3.9 21.6 + - - -
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.6 33.9 - - + -
75A PHE* 5.1 3.6 - - + -
125A PRO* 5.0 5.4 - - + -
142A HIS* 2.9 32.5 + - - -
143A ILE* 3.3 10.7 + - + -
145A LYS* 1.3 76.7 - - - +
147A ARG* 1.3 54.9 + - - +
149A LYS* 3.3 9.4 + - + +
150A LEU* 2.9 35.4 + - + +
119B GLU* 3.7 20.2 + - - +
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN* 3.5 35.3 + - - +
125A PRO* 3.7 24.0 - - + +
143A ILE 2.9 13.9 + - - +
144A LEU* 3.5 19.6 - - + +
145A LYS 3.2 0.4 - - - -
146A THR* 1.3 74.1 - - - +
148A GLU* 1.3 59.3 + - + +
150A LEU* 3.2 3.6 + - + -
151A ASN* 2.8 47.2 + - - +
166A GLN* 3.0 54.0 + - - +
169A THR* 3.0 38.2 + - - -
170A ASP* 3.6 8.7 + - - +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.2 17.0 + - - +
145A LYS* 3.1 20.7 + - - +
147A ARG* 1.3 75.7 - - - +
149A LYS* 1.3 64.0 + - - +
151A ASN* 3.7 5.4 - - - +
152A ARG* 2.9 30.4 + - - +
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Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.5 35.5 - - + -
145A LYS 2.9 11.9 + - - +
146A THR* 3.4 14.1 - - - +
148A GLU* 1.3 77.1 - - - +
150A LEU* 1.3 61.9 + - - +
152A ARG* 3.6 27.9 - - - +
153A ILE* 3.2 24.9 + - + +
117B ASN* 2.8 45.3 + - - +
118B ALA 4.7 0.6 + - - -
119B GLU* 3.4 31.5 + - - +
176B THR* 6.2 4.1 - - + +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 4.3 4.9 - - + -
75A PHE* 3.6 30.5 - - + -
99A MET* 3.7 32.1 - - + -
102A PHE* 3.7 26.2 - - + -
125A PRO* 4.1 28.7 - - + -
146A THR* 2.9 28.1 + - + +
147A ARG* 3.7 4.0 - - + +
149A LYS* 1.3 77.0 - - - +
151A ASN* 1.3 63.5 + - - +
153A ILE 3.4 0.2 + - - -
154A LEU* 2.9 31.3 + - + +
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Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ARG* 2.8 31.5 + - - +
148A GLU* 3.8 5.7 - - - +
150A LEU* 1.3 76.3 - - - +
152A ARG* 1.3 55.4 + - - +
154A LEU* 3.4 3.3 + - - +
155A SER* 2.8 35.6 + - - -
162A ILE* 4.3 16.1 + - + +
165A ILE* 3.5 28.6 - - + +
166A GLN* 2.9 43.9 + - - +
169A THR* 4.3 5.7 + - - +
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Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 2.9 19.5 + - - +
149A LYS* 3.6 36.3 - - - +
151A ASN* 1.3 76.0 - - - +
153A ILE* 1.3 70.7 + - - +
155A SER* 3.2 6.4 + - - -
156A GLU* 3.1 39.2 + - + +
162A ILE* 4.3 23.1 - - + +
117B ASN* 3.9 22.4 - - - +
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.8 19.1 - - + -
78A TYR* 3.2 34.3 - - + +
102A PHE* 3.8 13.9 - - + -
149A LYS* 3.2 18.1 + - + +
150A LEU 4.0 2.7 - - - +
152A ARG* 1.3 85.1 - - - +
154A LEU* 1.3 63.5 + - - +
156A GLU* 3.3 22.7 + - - +
157A ARG* 3.2 22.3 - - - +
117B ASN* 3.6 37.9 - - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 4.0 27.5 - - + +
105A ALA* 4.3 14.8 - - + -
122A ILE* 5.1 14.4 - - + -
150A LEU* 2.9 18.7 + - + +
151A ASN* 3.7 6.3 - - - +
153A ILE* 1.3 75.3 - - - +
155A SER* 1.3 57.8 + - - +
157A ARG* 3.2 4.1 + - + -
158A THR* 2.7 45.3 + - + +
165A ILE* 4.1 26.9 - - + -
169A THR* 5.3 6.3 - - + -
183A TYR* 5.7 0.4 - - + -
185A LEU* 4.2 24.7 - - + -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASN 2.8 17.6 + - - -
152A ARG 3.2 11.0 - - - -
154A LEU* 1.3 72.2 - - - +
156A GLU* 1.3 57.3 + - - +
158A THR* 3.9 2.2 - - - -
159A GLY* 2.9 32.1 + - - -
160A GLN 2.5 25.9 + - - +
161A SER* 3.8 1.8 - - - -
162A ILE* 3.5 28.5 + - - +
165A ILE* 4.5 4.4 - - - +
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 5.2 1.7 + - - -
109A LYS* 3.7 11.5 + - - -
152A ARG* 3.1 32.0 + - + +
153A ILE* 3.3 25.3 + - - +
155A SER* 1.3 80.2 - - - +
157A ARG* 1.3 62.3 + - + +
159A GLY* 4.4 3.3 + - - -
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 3.2 28.7 + - - -
82A GLN* 3.6 31.7 - - - +
102A PHE* 5.8 0.9 - - - -
105A ALA* 3.6 35.2 + - + +
106A ALA* 4.1 10.0 + - - +
107A GLY 3.8 14.3 + - - -
109A LYS* 3.7 37.7 + - - +
112A ARG* 3.1 26.7 + - - +
153A ILE* 3.2 19.3 - - + +
154A LEU* 3.2 7.4 + - - +
155A SER 3.2 0.4 - - - -
156A GLU* 1.3 83.2 + - + +
158A THR* 1.3 62.8 + - - +
184A GLY 3.3 2.8 - - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA* 5.0 1.6 - - + -
154A LEU* 2.7 31.8 + - + +
155A SER* 3.6 0.5 + - - -
157A ARG* 1.3 80.9 - - - +
159A GLY* 1.3 60.7 + - - +
160A GLN* 3.2 22.1 + - - +
165A ILE* 4.1 2.1 - - - +
183A TYR* 3.5 27.2 - - + +
184A GLY* 3.3 28.2 - - - +
185A LEU* 3.9 24.7 - - + +
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER 2.9 11.9 + - - -
156A GLU 4.3 2.4 + - - -
157A ARG 3.6 1.8 - - - +
158A THR* 1.3 77.9 - - - +
160A GLN* 1.3 64.5 + - - +
161A SER 4.1 0.3 + - - -
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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