Contacts of the helix formed by residues 139 - 165 (chain A) in PDB entry 4E2E
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 THR 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL 4.5 6.5 + - - +
138A ALA* 1.3 78.4 - - - +
140A GLY* 1.3 65.4 + - - +
141A GLU 3.6 0.3 + - - -
142A LYS* 3.4 12.9 + - - +
143A ARG* 3.2 17.7 + - - +
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Residues in contact with GLY 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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139A THR* 1.3 73.7 - - - +
141A GLU* 1.4 61.8 + - - -
143A ARG* 3.5 6.7 + - - +
144A ALA* 3.4 18.5 + - - +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR 3.6 0.4 + - - -
140A GLY* 1.4 68.6 - - - -
142A LYS* 1.3 64.2 + - - +
143A ARG 3.2 0.2 - - - -
144A ALA* 3.3 8.9 + - - +
145A THR* 3.2 26.8 + - - -
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA* 4.2 11.2 - - + +
139A THR 3.5 10.5 - - - +
140A GLY 3.4 0.2 - - - -
141A GLU* 1.3 78.3 - - - +
143A ARG* 1.4 60.3 + - - +
145A THR* 3.6 7.0 + - - -
146A VAL* 3.4 25.5 + - - +
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Residues in contact with ARG 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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135A ALA 3.7 17.3 + - - +
138A ALA* 3.6 25.2 + - - +
139A THR* 3.2 19.6 + - - +
140A GLY 3.5 11.4 - - - +
141A GLU 3.2 0.4 - - - -
142A LYS* 1.4 75.6 - - - +
144A ALA* 1.3 60.1 + - - +
146A VAL* 3.2 4.3 - - - +
147A VAL* 3.0 55.7 + - + +
185A GLU 4.8 1.6 + - - -
186A ILE* 2.8 45.6 + - - +
187A GLN* 5.3 1.6 + - - -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY 3.4 9.1 + - - +
141A GLU* 3.3 12.7 + - - +
143A ARG* 1.3 79.1 - - - +
145A THR* 1.3 57.5 + - - +
147A VAL* 3.5 8.6 + - - +
148A GLU* 3.1 29.4 + - - +
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Residues in contact with THR 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 GLU 3.2 12.8 + - - -
142A LYS* 3.8 10.5 - - - -
143A ARG 3.3 0.6 - - - -
144A ALA* 1.3 77.5 - - - +
146A VAL* 1.4 63.1 + - + +
148A GLU* 3.4 12.4 + - - +
149A SER* 3.0 32.0 + - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 5.9 0.7 - - - +
131A TYR* 3.6 34.9 - - + +
134A LEU* 4.0 19.3 - - + -
135A ALA* 3.6 27.6 - - - +
138A ALA* 4.2 5.2 - - + -
142A LYS 3.4 13.0 + - - +
143A ARG* 3.2 16.8 - - - +
145A THR* 1.4 77.9 - - + +
147A VAL* 1.3 59.4 + - - +
149A SER* 4.1 5.8 - - - -
150A SER* 3.0 28.9 + - - -
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Residues in contact with VAL 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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135A ALA* 3.8 10.5 - - + -
143A ARG* 3.0 51.8 + - - +
144A ALA* 3.7 7.9 - - - +
146A VAL* 1.3 73.3 - - - +
148A GLU* 1.4 59.9 + - - +
150A SER* 3.2 5.2 + - - -
151A GLU* 2.9 25.6 + - + +
182A PHE* 3.3 12.2 - - + -
186A ILE* 3.6 15.0 - - + -
187A GLN* 3.2 36.1 - - - +
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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
----------------------------------------------------------
144A ALA 3.1 18.4 + - - +
145A THR* 3.6 10.4 - - - +
147A VAL* 1.4 72.1 - - - +
149A SER* 1.3 56.0 + - - +
151A GLU* 3.3 9.6 + - + +
152A LYS* 2.8 40.2 + - + +
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 5.3 1.4 - - - -
131A TYR* 3.6 45.7 + - - -
145A THR* 3.0 23.7 + - - +
146A VAL* 3.6 1.8 - - - -
148A GLU* 1.3 75.7 - - - +
150A SER* 1.4 59.5 + - - +
152A LYS* 3.6 8.8 + - - +
153A ALA* 3.2 23.0 + - - +
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Residues in contact with SER 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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128A GLY* 2.7 27.7 + - - -
131A TYR* 3.6 12.3 - - - +
132A ARG* 3.7 6.8 + - - +
146A VAL 3.0 17.3 + - - -
147A VAL* 3.2 6.3 + - - -
149A SER* 1.4 71.7 - - - +
151A GLU* 1.3 60.4 + - - +
153A ALA* 3.3 4.0 + - - +
154A TYR* 3.0 48.2 + - - -
182A PHE* 3.4 16.5 - - - -
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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 VAL* 2.9 16.4 + - + +
148A GLU* 3.5 10.8 - - + +
150A SER* 1.3 74.8 + - - +
152A LYS* 1.4 56.7 + - - +
154A TYR* 3.3 4.4 + - - +
155A SER* 2.9 42.1 + - - +
179A TYR* 3.1 22.0 + - - -
182A PHE* 3.2 28.9 - - + -
183A TYR* 3.4 21.0 + - - -
187A GLN* 3.8 11.4 + - - +
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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
----------------------------------------------------------
127A LYS* 5.6 6.1 - - - +
148A GLU* 2.8 24.5 + - + +
149A SER* 3.8 9.4 - - - +
151A GLU* 1.4 73.7 - - - +
153A ALA* 1.3 60.2 + - - +
155A SER* 3.7 5.3 + - - -
156A GLU* 3.3 35.0 + - + +
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Residues in contact with ALA 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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124A LEU* 3.5 23.0 - - + +
127A LYS* 3.9 22.2 - - + +
128A GLY* 3.5 26.5 - - - +
149A SER 3.2 17.4 + - - +
150A SER 3.3 2.7 + - - +
152A LYS* 1.3 75.1 - - - +
154A TYR* 1.4 62.6 + - - +
156A GLU* 3.7 1.3 + - - +
157A ALA* 3.2 23.7 + - - +
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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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125A LYS* 3.7 15.0 - - + -
128A GLY* 3.4 9.9 - - - -
129A ASP* 2.5 33.4 + - - -
132A ARG* 2.9 20.9 + - - -
150A SER* 3.0 42.2 + - - +
151A GLU 3.8 0.4 - - - +
153A ALA* 1.4 74.1 - - - +
155A SER* 1.4 58.7 + - - +
157A ALA* 3.5 5.5 + - - +
158A HIS* 2.9 28.9 + - - +
175A LEU* 3.8 22.1 - - + +
178A ASN* 3.8 9.2 - - + +
179A TYR* 3.4 46.3 - + + -
182A PHE* 3.6 23.3 - + + -
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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 GLU* 2.9 28.3 + - - +
152A LYS* 4.0 5.8 - - - -
153A ALA 3.4 0.2 - - - -
154A TYR* 1.4 73.7 - - - +
156A GLU* 1.3 60.3 + - - +
158A HIS* 3.3 7.3 + - - +
159A GLU* 3.0 38.3 + - - +
179A TYR* 2.7 24.3 + - - -
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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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120A LYS* 5.8 1.9 - - - +
124A LEU* 3.6 30.5 - - + +
152A LYS* 3.3 27.8 + - + +
153A ALA* 4.0 3.5 - - - +
155A SER* 1.3 75.0 - - - +
157A ALA* 1.4 63.1 + - - +
159A GLU* 3.2 8.1 + - + +
160A ILE* 3.2 39.4 + - + +
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Residues in contact with ALA 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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121A VAL* 3.7 20.2 - - + +
124A LEU* 3.7 23.6 - - + +
125A LYS 4.0 3.1 - - - +
153A ALA 3.2 16.0 + - - +
154A TYR 3.6 5.2 - - - +
155A SER 3.3 0.2 - - - -
156A GLU* 1.4 78.0 - - - +
158A HIS* 1.4 56.8 + - - +
160A ILE* 3.5 1.2 + - - -
161A SER* 3.0 30.8 + - - -
175A LEU* 3.5 23.0 - - + +
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Residues in contact with HIS 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 TYR 2.9 19.0 + - - +
155A SER* 3.4 7.6 - - - +
157A ALA* 1.4 76.8 - - - +
159A GLU* 1.3 65.4 + - - +
161A SER* 3.1 5.8 + - - -
162A LYS* 3.1 55.5 + - + +
172A ARG* 5.9 3.0 + - + -
175A LEU* 3.5 18.1 - - + +
176A ALA* 5.5 6.8 - - + +
179A TYR* 4.1 23.8 - + + -
196A LEU* 3.8 24.6 - - + +
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Residues in contact with GLU 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* 3.0 24.8 + - - +
156A GLU* 3.2 9.4 + - + +
158A HIS* 1.3 89.6 + - - +
160A ILE* 1.3 63.4 + - + +
162A LYS* 3.7 13.7 - - - +
163A GLU* 3.3 23.4 + - - +
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Residues in contact with ILE 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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117A TYR* 3.8 35.4 - - + +
120A LYS* 4.3 20.9 - - + -
121A VAL* 3.5 20.4 - - + -
124A LEU* 3.9 24.5 - - + -
156A GLU* 3.2 28.8 + - + +
157A ALA* 4.8 0.9 - - - -
159A GLU* 1.3 76.6 - - + +
161A SER* 1.4 53.9 + - - +
163A GLU* 3.3 1.0 + - - -
164A HIS* 2.8 47.0 + - + +
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Residues in contact with SER 161 (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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121A VAL* 3.6 20.1 - - - +
157A ALA 3.0 14.9 + - - -
158A HIS* 3.1 13.5 + - - -
160A ILE* 1.4 75.0 - - - +
162A LYS* 1.4 61.5 + - - +
165A MSE 2.9 52.1 + - - +
172A ARG* 3.7 23.9 + - - +
175A LEU* 3.6 12.5 - - - +
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Residues in contact with LYS 162 (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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158A HIS* 3.1 43.5 + - + +
159A GLU* 3.7 17.5 - - - +
161A SER* 1.4 81.0 + - - +
163A GLU* 1.3 60.7 + - + +
165A MSE 4.3 1.9 - - - +
172A ARG* 3.6 33.2 + - - +
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Residues in contact with GLU 163 (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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159A GLU 3.3 14.3 + - - +
160A ILE* 3.3 1.0 + - - -
161A SER 3.2 0.2 - - - -
162A LYS* 1.3 80.5 - - - +
164A HIS* 1.4 87.6 + - + +
165A MSE 3.8 0.4 - - - -
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Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 3.3 73.3 + + + +
160A ILE* 2.8 30.1 + - + +
163A GLU* 1.4 98.1 - - + +
165A MSE 1.3 63.2 + - + +
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Residues in contact with MSE 165 (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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117A TYR* 5.5 2.0 - - + +
118A GLU* 3.6 25.4 - - + +
121A VAL* 4.1 21.1 - - + -
160A ILE 4.7 0.2 - - - +
161A SER* 2.9 34.9 + - - +
162A LYS 4.3 2.9 - - - +
163A GLU 3.8 0.6 - - - -
164A HIS* 1.3 87.2 - - + +
166A GLN* 1.4 70.9 + - - +
167A PRO* 4.4 0.5 - - - +
169A HIS* 3.4 52.0 - - + +
171A ILE* 3.8 14.6 - - + -
172A ARG* 3.1 26.6 + - + -
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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
------------------------------------------------------------
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