Contacts of the helix formed by residues 135 - 161 (chain A) in PDB entry 3VLN
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 ASN 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A SER* 3.8 2.0 + - - -
134A GLN* 1.3 84.0 - - - +
136A LYS* 1.3 59.4 + - + +
137A GLU* 3.0 22.0 + - - +
138A ASP* 2.8 48.1 + - - +
139A TYR* 3.1 27.7 + - - +
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Residues in contact with LYS 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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135A ASN* 1.3 73.0 - - + +
137A GLU* 1.3 83.6 + - + +
139A TYR* 3.6 12.8 - - + +
140A ALA* 2.8 29.8 + - - +
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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
----------------------------------------------------------
135A ASN* 3.0 30.1 + - - +
136A LYS* 1.3 100.5 - - + +
138A ASP* 1.3 67.8 + - - +
140A ALA* 3.3 7.1 + - - +
141A GLY* 3.1 18.9 + - - -
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 3.8 13.5 + - - +
133A SER* 3.3 17.5 - - - +
134A GLN* 3.1 33.1 + - - +
135A ASN* 2.8 33.1 + - - +
137A GLU* 1.3 73.9 - - - +
139A TYR* 1.3 58.3 + - - +
141A GLY* 3.4 1.4 + - - -
142A LEU* 3.0 35.8 + - + +
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.4 33.4 - + - -
133A SER* 3.6 8.7 + - - +
135A ASN 3.1 18.0 + - - +
136A LYS* 3.6 12.1 - - + +
137A GLU 3.1 0.2 - - - -
138A ASP* 1.3 74.1 - - - +
140A ALA* 1.3 68.1 + - - +
142A LEU* 3.3 1.1 + - - +
143A LYS* 2.9 53.9 + - + +
188A LYS* 2.6 38.7 + - + +
189A LEU* 4.1 1.6 - - + -
191A GLU* 3.1 23.1 + - - -
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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 LYS 2.8 21.1 + - - +
137A GLU* 3.3 8.7 + - - +
139A TYR* 1.3 76.1 - - + +
141A GLY* 1.3 60.0 + - - +
143A LYS* 3.4 17.1 - - - +
144A GLU* 3.3 18.2 + - - +
147A ARG* 5.1 1.7 + - - -
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Residues in contact with GLY 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 3.1 13.6 + - - -
138A ASP* 3.4 3.6 + - - -
139A TYR 3.2 0.2 - - - -
140A ALA* 1.3 73.1 - - - +
142A LEU* 1.3 69.7 + - - +
144A GLU* 3.1 9.8 + - - +
145A GLU* 3.1 24.7 + - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 5.2 1.3 - - + +
129A SER* 4.0 7.4 - - - +
130A PHE* 3.5 53.8 - - + +
132A ARG* 3.7 22.4 - - - +
133A SER* 4.0 6.1 - - - +
138A ASP* 3.0 22.2 + - + +
139A TYR 3.3 2.0 + - - +
141A GLY* 1.3 77.0 - - - +
143A LYS* 1.3 62.5 + - - +
145A GLU* 3.2 25.4 + - - +
146A PHE* 2.9 37.9 + - + -
189A LEU* 5.1 0.2 - - - -
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Residues in contact with LYS 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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139A TYR* 2.9 60.5 + - + +
140A ALA* 3.4 15.5 - - - +
141A GLY 3.2 0.2 - - - -
142A LEU* 1.3 77.8 - - - +
144A GLU* 1.3 55.4 + - - +
147A ARG* 2.9 53.3 + - - +
189A LEU* 4.1 7.3 - - + +
191A GLU* 4.1 19.0 + - + +
192A CYS* 3.4 27.8 - - - -
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Residues in contact with GLU 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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140A ALA 3.3 8.0 + - - +
141A GLY* 3.1 12.2 + - - +
143A LYS* 1.3 74.7 - - - +
145A GLU* 1.3 66.2 + - + +
147A ARG* 3.1 36.3 + - - +
148A LYS* 3.1 47.7 + - + +
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Residues in contact with GLU 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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126A LEU* 3.2 35.3 - - + +
129A SER* 5.6 1.6 - - - -
141A GLY 3.1 16.3 + - - +
142A LEU* 3.2 28.0 + - - +
144A GLU* 1.3 77.0 - - + +
146A PHE* 1.3 62.6 + - - +
148A LYS* 3.3 8.3 + - - +
149A GLU* 3.3 26.9 + - - +
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Residues in contact with PHE 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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123A VAL* 4.5 9.4 - - + -
126A LEU* 3.7 49.6 - - + -
127A VAL* 3.7 21.8 - - + -
130A PHE* 4.0 15.5 - + + -
142A LEU* 2.9 35.1 + - + +
145A GLU* 1.3 77.2 - - + +
147A ARG* 1.3 58.0 + - - +
149A GLU* 3.2 2.9 + - - +
150A PHE* 2.8 56.1 + + + -
184A LEU* 4.7 3.4 - - + -
189A LEU* 3.4 35.9 - - + -
192A CYS* 3.7 19.5 - - + -
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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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140A ALA 5.1 1.8 + - - -
143A LYS* 2.9 48.9 + - - +
144A GLU* 3.1 46.2 + - - +
145A GLU 3.3 0.4 - - - -
146A PHE* 1.3 75.6 - - - +
148A LYS* 1.3 74.0 + - - +
150A PHE* 3.3 1.9 + - - +
151A THR* 2.8 33.8 + - + +
191A GLU 4.3 15.2 + - - -
192A CYS* 4.0 23.7 + - - +
195A HIS* 5.6 17.7 - - + +
196A THR* 5.1 1.0 - - + +
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Residues in contact with LYS 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 GLU* 3.1 42.9 + - + +
145A GLU* 3.6 10.8 - - - +
146A PHE 3.3 0.2 - - - -
147A ARG* 1.3 97.3 - - - +
149A GLU* 1.3 71.3 + - - +
151A THR* 3.4 21.2 + - - +
152A LYS* 3.4 17.1 + - + +
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Residues in contact with GLU 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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119A LEU 4.2 5.8 - - - +
122A LYS* 3.7 34.0 - - + +
123A VAL* 4.0 20.9 - - + -
126A LEU* 3.7 20.7 - - + +
145A GLU 3.4 14.4 - - - +
146A PHE* 3.2 6.8 + - - +
148A LYS* 1.3 81.2 - - - +
150A PHE* 1.3 67.1 + - + +
152A LYS* 3.0 50.4 + - - +
153A LEU* 3.5 11.2 + - - +
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Residues in contact with PHE 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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123A VAL* 4.5 14.6 - - + -
146A PHE* 2.8 42.9 + + + +
147A ARG 3.3 3.8 + - - +
149A GLU* 1.3 81.1 - - + +
151A THR* 1.3 57.0 + - - +
153A LEU* 3.1 9.7 + - + +
154A GLU* 2.9 27.2 + - - +
181A PHE* 3.7 26.2 - + - -
184A LEU* 3.5 26.7 - - + -
189A LEU 4.6 0.2 - - - -
192A CYS* 3.5 40.8 - - + +
193A VAL* 3.6 19.3 - - + -
196A THR* 4.0 10.3 - - + -
199A LEU* 3.6 16.7 - - + +
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Residues in contact with THR 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 30.2 + - + +
148A LYS* 4.0 20.1 + - - +
149A GLU 3.3 0.6 - - - -
150A PHE* 1.3 75.3 - - - +
152A LYS* 1.3 64.6 + - - +
154A GLU* 3.6 9.6 - - - +
155A GLU* 3.1 37.9 + - - +
195A HIS* 5.8 3.8 - - + +
196A THR* 4.0 11.2 - - + +
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Residues in contact with LYS 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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118A GLU 5.9 0.2 + - - -
119A LEU* 3.7 47.4 + - + +
122A LYS* 4.6 14.5 - - - +
148A LYS* 3.4 17.3 + - + +
149A GLU* 3.0 38.5 + - - +
151A THR* 1.3 81.2 + - - +
153A LEU* 1.3 62.2 + - + +
155A GLU* 3.5 19.6 + - - +
156A VAL* 3.6 16.1 + - - +
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Residues in contact with LEU 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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116A ILE* 4.2 21.8 - - + +
119A LEU* 4.3 18.8 - - + +
120A PHE* 4.3 22.7 - - + +
123A VAL* 5.2 2.5 - - + -
149A GLU 3.5 11.6 + - - +
150A PHE* 3.1 14.4 + - + +
152A LYS* 1.3 75.1 - - + +
154A GLU* 1.3 66.0 + - - +
156A VAL* 3.2 15.8 + - - +
157A LEU* 3.3 10.2 + - - +
165A PHE* 3.5 32.1 - - + -
177A ILE* 4.8 4.3 - - + -
181A PHE* 3.9 32.5 - - + -
199A LEU* 4.4 7.4 - - + -
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Residues in contact with GLU 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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150A PHE 2.9 13.8 + - - +
151A THR* 3.4 11.0 + - - +
153A LEU* 1.3 74.8 - - - +
155A GLU* 1.3 60.2 + - + +
157A LEU* 3.3 6.6 + - - +
158A THR* 2.9 38.5 + - - +
195A HIS 5.0 2.0 - - - +
196A THR* 3.2 27.1 - - + -
197A PRO* 3.2 14.3 - - + +
198A LYS* 2.9 35.3 + - - +
199A LEU* 2.8 32.7 + - - +
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Residues in contact with GLU 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 THR* 3.1 27.7 + - - +
152A LYS* 3.7 13.6 - - - +
153A LEU 3.2 0.4 - - - -
154A GLU* 1.3 79.6 - - + +
156A VAL* 1.3 60.7 + - - +
158A THR* 3.3 9.6 + - - +
159A ASN* 3.3 22.7 + - - +
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Residues in contact with VAL 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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116A ILE* 3.7 31.2 - - + -
119A LEU* 3.5 32.3 - - + -
152A LYS 3.7 8.3 - - - +
153A LEU* 3.2 10.3 + - - +
155A GLU* 1.3 77.9 - - + +
157A LEU* 1.3 64.4 + - + +
159A ASN* 3.5 3.0 + - - +
160A LYS* 3.2 37.4 + - + +
165A PHE* 3.9 14.1 - - + -
906A GOL 4.0 15.5 - - - +
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Residues in contact with LEU 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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153A LEU 3.3 4.2 + - - +
154A GLU* 3.3 7.9 + - - +
156A VAL* 1.3 81.4 - - + +
158A THR* 1.3 55.9 + - - +
160A LYS* 4.6 3.8 - - + -
161A LYS* 2.9 30.1 + - - -
162A THR* 4.2 14.4 + - - +
163A THR 4.6 3.4 - - - +
164A PHE* 3.9 23.6 - - - +
165A PHE* 3.6 47.8 - - + -
198A LYS* 3.7 46.2 - - + +
199A LEU* 3.9 9.9 - - + +
202A TRP* 4.1 9.2 - - + -
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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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154A GLU* 2.9 28.8 + - - +
155A GLU* 3.5 10.2 - - - +
156A VAL 3.3 0.2 - - - -
157A LEU* 1.3 76.5 - - - +
159A ASN* 1.3 60.8 + - - +
161A LYS* 3.0 35.4 + - - +
198A LYS* 3.8 28.5 + - - +
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Residues in contact with ASN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU 3.3 12.1 + - - +
156A VAL* 4.1 3.6 - - - +
158A THR* 1.3 81.7 - - - +
160A LYS* 1.3 71.5 + - + +
161A LYS* 3.4 9.8 + - - +
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Residues in contact with LYS 160 (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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116A ILE* 5.2 1.6 - - + -
156A VAL* 3.2 31.0 + - + +
157A LEU* 4.1 3.1 - - - +
159A ASN* 1.3 84.6 - - - +
161A LYS* 1.3 68.7 + - - +
162A THR* 3.2 38.4 + - + +
164A PHE 4.8 0.7 - - - +
165A PHE* 3.5 26.9 + - - +
166A GLY* 4.1 11.3 + - - -
167A GLY* 3.8 10.2 - - - +
906A GOL 5.2 4.9 - - - +
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Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU 2.9 14.1 + - - +
158A THR* 3.0 26.3 + - - +
159A ASN* 3.9 8.7 + - - +
160A LYS* 1.3 79.7 - - - +
162A THR* 1.3 60.8 + - - +
163A THR 4.3 0.2 + - - -
168A ASN* 4.6 1.6 - - - +
198A LYS* 5.5 14.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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