Contacts of the helix formed by residues 134 - 157 (chain A) in PDB entry 4CEJ
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ARG* 4.6 1.6 - - - +
132A ILE 3.7 2.0 + - - -
133A ALA* 1.3 72.4 - - - +
135A GLN* 1.3 70.0 + - - +
136A THR* 3.3 29.8 + - - -
137A GLU* 3.0 24.1 + - + +
138A GLY* 2.8 21.5 + - - -
749A GLN* 6.0 0.9 - - - +
750A TYR* 4.0 29.7 + - + -
753A THR* 5.8 2.9 - - + -
755A PHE* 5.7 1.1 - - + -
764A PHE* 3.9 7.1 - - + -
768A MET* 4.9 0.3 - - - +
56X T 4.1 8.5 - - - +
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Residues in contact with GLN 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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133A ALA 3.6 2.5 + - - -
134A ASP* 1.3 78.0 + - - +
136A THR* 1.3 67.8 + - - +
138A GLY* 3.5 1.0 + - - -
139A GLU* 3.1 38.4 + - + +
773A ASP* 5.1 4.2 - - - +
55X T 4.6 18.4 - - - +
56X T 4.0 22.5 + - + +
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Residues in contact with THR 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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134A ASP* 3.3 11.0 + - - -
135A GLN* 1.3 77.2 - - - +
137A GLU* 1.3 60.0 + - - +
139A GLU* 3.3 3.1 + - - +
140A LEU* 2.8 39.1 + - + +
764A PHE* 4.2 5.2 - - + -
768A MET* 3.6 52.1 - - + +
771A ARG* 4.5 2.7 - - - -
773A ASP* 3.2 30.5 + - - +
774A ASP 5.6 1.0 + - - -
775A LEU* 5.6 1.9 - - - +
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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
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131A ARG* 2.3 40.2 + - - -
133A ALA* 3.9 10.3 - - + -
134A ASP* 3.0 38.4 + - + +
136A THR* 1.3 77.6 - - - +
138A GLY* 1.3 63.9 + - - +
140A LEU* 3.2 7.1 + - - +
141A ILE* 3.1 27.0 + - + +
363A LYS* 5.8 1.7 - - - +
365A ILE* 4.0 12.4 - - + +
753A THR* 4.0 3.5 - - - +
754A ALA* 3.8 6.2 - - - +
755A PHE* 4.0 24.4 - - + -
764A PHE* 4.1 9.9 - - + -
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Residues in contact with GLY 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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133A ALA* 4.0 13.9 - - - +
134A ASP 2.8 16.8 + - - -
135A GLN 4.0 1.3 - - - -
137A GLU* 1.3 74.9 - - - +
139A GLU* 1.3 56.6 + - - +
141A ILE* 3.3 12.0 + - - +
142A GLY 2.9 23.0 + - - -
356A PHE* 3.7 14.7 - - - -
360A LYS* 5.9 2.0 - - - -
365A ILE* 5.3 0.9 - - - -
367A ASP* 4.9 10.8 - - - -
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Residues in contact with GLU 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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135A GLN* 3.1 35.9 + - + +
136A THR* 3.6 7.0 - - - +
137A GLU 3.2 0.2 - - - -
138A GLY* 1.3 75.8 - - - +
140A LEU* 1.3 57.8 + - - +
142A GLY* 3.4 2.6 + - - +
143A ASP* 2.8 32.2 + - - -
182A LYS* 3.8 11.1 + - - +
356A PHE* 5.7 0.9 - - - -
771A ARG* 3.3 39.8 + - - +
773A ASP* 5.1 1.5 - - - +
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Residues in contact with LEU 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 THR* 2.8 24.6 + - + +
137A GLU* 3.4 5.8 - - - +
139A GLU* 1.3 74.1 - - - +
141A ILE* 1.3 60.5 + - + +
143A ASP* 3.1 8.7 + - + +
144A GLU* 2.9 34.0 + - - +
755A PHE* 5.6 2.0 - - + -
764A PHE* 4.1 26.2 - - + -
767A ARG* 3.7 67.0 + - + +
768A MET 4.7 0.4 - - - +
771A ARG* 3.6 29.6 - - + -
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Residues in contact with ILE 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 20.4 + - + +
138A GLY* 3.4 8.1 - - - +
140A LEU* 1.3 75.3 - - + +
142A GLY* 1.3 63.8 + - - +
144A GLU* 3.2 13.3 + - - +
145A VAL* 3.1 28.3 + - + +
356A PHE* 3.9 12.1 - - + -
359A ALA* 3.7 29.4 - - + +
360A LYS* 4.4 5.8 - - + -
363A LYS* 3.6 35.9 - - + +
365A ILE* 3.5 31.9 - - + -
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Residues in contact with GLY 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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138A GLY 2.9 12.0 + - - -
139A GLU* 3.6 4.0 - - - -
140A LEU 3.2 0.2 - - - -
141A ILE* 1.3 76.5 - - - +
143A ASP* 1.3 61.7 + - - +
145A VAL* 3.4 6.7 + - - +
146A LEU* 3.0 23.9 + - - +
182A LYS* 3.8 7.4 - - - -
352A TYR* 3.4 18.5 - - - -
356A PHE* 3.5 17.9 - - - -
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Residues in contact with ASP 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 GLU 2.8 16.4 + - - +
140A LEU* 3.4 14.2 - - + +
142A GLY* 1.3 70.9 - - - +
144A GLU* 1.3 62.5 - - + +
146A LEU* 3.3 5.0 + - - +
147A ASP* 3.1 30.0 + - - +
178A GLN* 4.0 13.5 + - - +
182A LYS* 2.9 22.0 + - - +
767A ARG* 5.7 1.8 - - - +
771A ARG* 2.6 42.5 + - - +
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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 LEU 2.9 14.3 + - - +
141A ILE* 3.2 15.5 + - - +
143A ASP* 1.3 76.5 - - - +
145A VAL* 1.3 60.1 + - + +
147A ASP* 3.0 13.0 + - - +
148A GLU* 2.9 31.6 + - + +
363A LYS* 4.3 16.1 + - - -
763A ARG* 5.9 0.7 + - - -
767A ARG* 3.5 34.3 + - - +
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Residues in contact with VAL 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 ILE* 3.1 18.0 + - + +
142A GLY* 3.4 11.0 - - - +
144A GLU* 1.3 73.8 - - + +
146A LEU* 1.3 64.1 + - - +
148A GLU* 3.7 14.8 - - - +
149A LEU* 2.8 32.2 + - - +
352A TYR* 3.4 24.0 - - + +
355A ARG* 4.4 13.1 + - + +
356A PHE* 4.1 20.4 - - + +
359A ALA* 3.7 29.2 - - + -
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Residues in contact with LEU 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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142A GLY 3.0 17.0 + - - +
143A ASP* 3.5 6.5 - - - +
145A VAL* 1.3 77.7 - - - +
147A ASP* 1.3 58.3 + - - +
149A LEU* 3.8 6.2 - - + +
150A PHE* 3.0 54.1 + - + +
178A GLN* 3.3 53.6 - - + +
181A VAL* 3.7 17.9 - - + -
182A LYS* 3.6 26.0 - - + -
352A TYR* 3.5 23.3 - - + -
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Residues in contact with ASP 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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143A ASP* 3.1 18.3 + - - +
144A GLU* 3.0 12.4 + - - +
146A LEU* 1.3 75.2 - - - +
148A GLU* 1.3 64.6 + - + +
150A PHE* 3.4 2.6 + - - +
151A GLU* 3.0 24.3 + - - +
178A GLN* 3.2 17.1 + - - -
881B ARG* 3.0 29.2 + - - +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLU* 2.9 15.4 + - + +
145A VAL* 3.7 16.4 - - - +
147A ASP* 1.3 76.3 - - + +
149A LEU* 1.3 63.1 + - - +
151A GLU* 3.2 8.1 + - - +
152A ASP* 3.0 27.2 + - - +
355A ARG* 3.9 15.3 + - - +
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Residues in contact with LEU 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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145A VAL 2.8 18.1 + - - +
146A LEU* 3.8 15.3 - - + +
148A GLU* 1.3 77.4 - - - +
150A PHE* 1.3 58.0 + - + +
152A ASP* 3.2 4.7 + - + +
153A GLU* 3.0 43.4 + - + +
348A LEU* 3.8 38.6 - - + +
351A SER* 3.9 14.1 - - - -
352A TYR* 3.9 22.7 - - + +
355A ARG* 3.6 40.8 - - - +
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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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146A LEU* 3.0 47.1 + - + +
147A ASP 3.8 3.6 - - - +
149A LEU* 1.3 81.0 - - + +
151A GLU* 1.3 57.9 + - - +
153A GLU* 3.3 6.3 + - - +
154A TYR* 3.0 46.4 + + + -
161A PHE* 4.7 5.2 - + - -
174A ASP* 3.9 22.7 - - - -
177A LEU* 3.5 46.4 - - + -
178A GLN* 4.0 20.9 - - + -
181A VAL* 4.1 10.8 - - + -
348A LEU* 4.2 13.9 - - + -
881B ARG* 4.2 18.2 - - - +
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Residues in contact with GLU 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 ASP 3.0 14.0 + - - +
148A GLU* 3.5 10.3 - - - +
150A PHE* 1.3 76.0 - - - +
152A ASP* 1.3 64.0 + - - +
154A TYR* 3.8 3.0 - - - +
155A ALA* 2.9 28.3 + - + +
879B SER* 3.6 15.9 + - - -
880B ASN* 2.8 39.1 + - - +
881B ARG* 3.4 26.5 + - + +
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Residues in contact with ASP 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* 3.0 15.8 + - - +
149A LEU* 3.2 8.3 + - - +
151A GLU* 1.3 83.1 - - - +
153A GLU* 1.3 62.4 + - - +
155A ALA* 3.4 6.6 + - - +
156A LYS* 2.9 36.2 + - - +
355A ARG* 2.6 31.8 + - - +
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Residues in contact with GLU 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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149A LEU* 3.0 30.3 + - + +
150A PHE* 3.3 1.5 + - - +
152A ASP* 1.3 76.4 - - - +
154A TYR* 1.3 59.1 + - - +
156A LYS* 3.1 37.0 + - - +
157A GLY* 2.8 25.8 + - - -
158A GLU* 4.3 9.7 + - - +
161A PHE* 3.4 53.6 - - + +
348A LEU* 4.0 18.4 - - + -
351A SER* 5.6 1.4 + - - -
355A ARG* 5.7 0.5 + - - -
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Residues in contact with TYR 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* 3.0 33.2 + + - +
151A GLU 3.8 2.0 - - - +
153A GLU* 1.3 75.5 - - - +
155A ALA* 1.3 64.1 + - - +
157A GLY* 3.1 14.8 + - - +
161A PHE* 3.7 27.5 - + - -
162A PHE* 3.9 22.1 - + - -
165A VAL* 3.6 15.0 - - + +
174A ASP* 2.6 40.6 + - - +
880B ASN* 3.7 24.3 - - + +
881B ARG* 3.6 29.4 - - + +
884B TYR* 3.5 37.4 - + + -
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Residues in contact with ALA 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 GLU* 2.9 20.1 + - + +
152A ASP* 3.5 10.1 - - - +
154A TYR* 1.3 79.0 - - - +
156A LYS* 1.3 63.0 + - + +
157A GLY* 4.2 0.7 - - - -
880B ASN* 3.6 26.9 - - - +
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Residues in contact with LYS 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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152A ASP* 2.9 20.3 + - + +
153A GLU* 3.1 41.1 + - - +
155A ALA* 1.3 77.0 - - + +
157A GLY* 1.3 64.1 + - - +
158A GLU* 3.3 34.3 + - + +
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Residues in contact with GLY 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 GLU 2.8 10.8 + - - -
154A TYR 3.1 12.3 + - - -
155A ALA 4.2 1.1 - - - -
156A LYS* 1.3 77.7 - - - +
158A GLU* 1.3 65.6 + - - +
159A LYS 3.6 1.7 + - - -
162A PHE* 3.2 28.1 - - - -
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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) + - + + + + + -
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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