Contacts of the helix formed by residues 139 - 165 (chain B) in PDB entry 4O46
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B VAL 4.1 6.3 + - - +
138B ALA* 1.3 79.7 - - - +
140B GLY* 1.3 68.6 + - - +
141B GLU 3.6 0.2 + - - -
142B LYS* 3.4 12.9 + - - +
143B ARG* 3.2 16.4 + - - +
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B THR* 1.3 74.5 - - - +
141B GLU* 1.3 62.5 + - - -
143B ARG* 3.3 6.8 + - - +
144B ALA* 3.3 18.5 + - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU 4.1 2.0 - - - +
33A LEU* 3.6 25.1 - - + +
34A ASN* 3.4 32.5 + - + +
140B GLY* 1.3 70.2 - - - -
142B LYS* 1.3 62.6 + - - +
144B ALA* 3.3 18.0 + - - +
145B THR* 2.9 29.3 + - - -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 5.4 0.8 - - - +
32A GLU* 3.2 55.2 + - + +
107A TYR* 3.5 20.6 + - - +
94B GLU* 3.0 39.0 + - - -
134B LEU* 6.0 2.7 - - - -
138B ALA* 4.2 17.9 - - + +
139B THR 3.4 10.3 + - - +
140B GLY 3.3 0.2 - - - -
141B GLU* 1.3 76.6 - - - +
143B ARG* 1.4 61.8 + - - +
145B THR* 3.5 5.2 + - - -
146B VAL* 3.3 26.8 + - + +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 3.7 18.2 + - - +
138B ALA* 3.4 29.5 + - + +
139B THR* 3.2 20.5 + - - +
140B GLY 3.4 10.5 - - - +
142B LYS* 1.4 72.8 - - - +
144B ALA* 1.3 65.3 + - - +
145B THR 3.2 0.2 + - - -
146B VAL* 3.3 3.7 - - - +
147B VAL* 3.0 51.6 + - + +
185B GLU 4.8 1.2 + - - -
186B ILE* 2.8 47.3 + - - +
187B GLN* 5.8 0.4 + - - -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 6.2 0.2 - - - +
140B GLY 3.3 10.1 + - - +
141B GLU* 3.3 26.7 + - - +
143B ARG* 1.3 78.5 - - - +
145B THR* 1.4 57.0 + - - +
147B VAL* 3.6 6.6 + - - +
148B GLU* 3.1 30.2 + - - +
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Residues in contact with THR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.8 16.6 + - - +
106A ASN* 4.0 22.0 - - + +
107A TYR* 3.7 32.4 - - + -
110A LYS* 5.0 7.9 - - + -
141B GLU 2.9 13.1 + - - -
142B LYS 3.5 9.0 - - - -
143B ARG 3.2 0.2 - - - -
144B ALA* 1.4 73.8 - - - +
146B VAL* 1.3 63.3 + - + +
148B GLU* 3.3 13.8 + - - +
149B SER* 3.1 33.9 + - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 5.2 4.3 - - + +
131B TYR* 3.6 35.4 - - + +
134B LEU* 3.9 20.2 - - + -
135B ALA* 3.7 27.4 - - - +
138B ALA* 4.2 3.6 - - + -
142B LYS* 3.4 17.0 - - + +
143B ARG* 3.3 16.4 - - - +
145B THR* 1.3 75.9 - - + +
147B VAL* 1.4 58.7 + - - +
149B SER* 3.4 7.1 + - - -
150B SER* 2.9 29.5 + - - -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 3.8 12.3 - - + -
143B ARG* 3.0 43.4 + - + +
144B ALA* 3.9 6.1 - - - +
146B VAL* 1.4 70.6 - - - +
148B GLU* 1.3 61.2 + - - +
150B SER* 3.4 5.8 + - - -
151B GLU* 3.0 28.8 + - - +
182B PHE* 3.5 9.1 - - + -
186B ILE* 3.6 23.1 - - + -
187B GLN* 3.2 33.9 - - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 5.3 8.8 - - - +
144B ALA 3.1 14.5 + - - +
145B THR* 3.4 15.3 - - - +
147B VAL* 1.3 76.1 - - - +
149B SER* 1.4 54.9 + - - +
151B GLU* 3.4 7.1 + - - +
152B LYS* 3.0 30.9 + - + +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASN* 5.2 4.9 + - - +
127B LYS* 5.5 1.6 - - - -
131B TYR* 3.6 40.3 + - - -
145B THR* 3.1 18.7 + - - +
146B VAL 3.5 8.1 - - - -
147B VAL 3.3 0.2 - - - -
148B GLU* 1.4 76.1 - - - +
150B SER* 1.4 55.3 + - - +
152B LYS* 3.4 9.3 + - - +
153B ALA* 3.1 28.6 + - - +
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLY* 2.8 27.7 + - - -
131B TYR* 3.7 13.2 - - - +
132B ARG* 3.8 6.3 + - - -
146B VAL 2.9 18.1 + - - -
147B VAL* 3.6 6.1 - - - -
149B SER* 1.4 71.0 - - - +
151B GLU* 1.4 60.1 + - - +
153B ALA* 3.3 2.8 + - - +
154B TYR* 3.0 48.5 + - - -
182B PHE* 3.4 17.9 - - - -
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Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL 3.0 17.3 + - - +
148B GLU* 3.6 6.7 - - - +
150B SER* 1.4 74.3 - - - +
152B LYS* 1.4 56.1 + - - +
154B TYR* 3.3 3.6 + - - +
155B SER* 2.8 45.2 + - - -
179B TYR* 2.7 25.7 + - - -
182B PHE* 3.7 18.9 - - + -
183B TYR* 3.9 14.3 + - - -
187B GLN* 3.2 23.5 + - - +
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU* 3.0 18.3 + - + +
149B SER* 3.6 9.0 - - - +
151B GLU* 1.4 77.2 - - - +
153B ALA* 1.3 61.1 + - - +
155B SER* 4.0 4.5 - - - -
156B GLU* 3.2 28.2 + - - +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.4 35.3 - - + +
127B LYS* 3.8 20.4 - - + -
128B GLY* 3.5 15.3 - - - +
149B SER 3.1 16.6 + - - +
150B SER 3.7 2.7 - - - +
151B GLU 3.3 0.2 - - - -
152B LYS* 1.3 73.5 - - - +
154B TYR* 1.3 63.8 + - - +
156B GLU* 3.5 2.5 + - - +
157B ALA* 3.1 23.6 + - - +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LYS* 3.6 21.8 - - + -
128B GLY* 3.3 11.0 - - - -
129B ASP* 2.6 28.3 + - - -
132B ARG* 2.9 20.3 + - - -
150B SER* 3.0 41.0 + - - +
151B GLU 3.9 0.9 - - - +
153B ALA* 1.3 74.5 - - - +
155B SER* 1.4 52.5 + - - +
157B ALA* 3.3 4.4 + - - +
158B HIS* 2.8 35.0 + - - +
175B LEU* 3.7 24.3 - - + +
178B ASN* 3.9 16.6 - - + +
179B TYR* 3.5 38.2 - + + -
182B PHE* 3.7 23.3 - + + -
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Residues in contact with SER 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLU* 2.8 31.1 + - - -
152B LYS* 4.0 5.4 - - - -
154B TYR* 1.4 71.5 - - - +
156B GLU* 1.4 61.1 + - - +
158B HIS* 3.4 3.5 + - - +
159B GLU* 3.1 30.6 + - - +
179B TYR* 3.8 19.6 + - - -
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ILE* 6.1 0.5 - - - +
120B LYS* 5.4 3.6 - - - +
124B LEU* 3.5 32.7 - - + +
152B LYS* 3.2 20.0 + - - +
153B ALA 3.8 3.6 - - - +
155B SER* 1.4 77.1 - - - +
157B ALA* 1.4 62.8 + - - +
159B GLU* 3.3 7.5 + - - +
160B ILE* 3.2 37.6 + - + +
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 3.7 22.5 - - + +
124B LEU* 3.7 23.2 - - + +
125B LYS 4.2 2.2 - - - +
153B ALA 3.1 13.5 + - - +
154B TYR 3.5 7.6 - - - +
156B GLU* 1.4 74.5 - - - +
158B HIS* 1.4 57.0 + - - +
160B ILE* 3.5 0.4 + - - -
161B SER* 3.0 31.7 + - - -
175B LEU* 3.5 23.5 - - + +
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Residues in contact with HIS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR 2.8 17.4 + - - +
155B SER* 3.6 5.6 - - - +
157B ALA* 1.4 73.7 - - - +
159B GLU* 1.3 64.5 + - - +
161B SER* 3.1 7.8 + - - -
162B LYS* 3.1 59.4 + - + +
172B ARG* 6.0 2.8 + - + -
175B LEU* 3.5 14.3 - - + +
176B ALA* 5.4 6.6 - - + +
179B TYR* 4.0 22.3 - + + -
196B LEU* 3.4 31.8 - - + +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B SER* 3.1 19.7 + - - +
156B GLU* 3.3 10.5 + - - +
158B HIS* 1.3 83.5 + - - +
160B ILE* 1.4 61.3 + - + +
162B LYS* 3.9 18.3 - - - +
163B GLU* 3.3 26.6 + - - +
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TYR* 4.0 22.9 - - + +
120B LYS* 4.0 22.2 - - + -
121B VAL* 3.7 19.1 - - + -
124B LEU* 3.8 25.4 - - + -
156B GLU* 3.2 26.5 + - + +
157B ALA* 4.7 0.9 - - - -
159B GLU* 1.4 74.0 - - + +
161B SER* 1.4 54.6 + - - +
163B GLU* 3.2 3.1 + - - -
164B HIS* 2.9 53.7 + - + +
165B MET* 6.0 0.2 - - - -
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 3.8 10.0 - - - +
157B ALA 3.0 15.5 + - - -
158B HIS* 3.1 14.6 + - - -
160B ILE* 1.4 75.1 - - - +
162B LYS* 1.3 58.9 + - - +
165B MET* 2.9 58.1 + - - +
172B ARG* 3.6 27.4 + - - +
175B LEU* 3.6 11.4 - - - +
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B HIS* 3.1 48.7 + - + +
159B GLU* 3.9 15.9 - - - +
160B ILE 3.3 0.2 - - - -
161B SER* 1.3 82.9 + - - +
163B GLU* 1.3 60.1 + - - +
165B MET 4.2 2.1 - - - +
172B ARG* 4.0 32.5 + - - +
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLU 3.3 16.4 + - - +
160B ILE* 3.2 4.9 + - - +
162B LYS* 1.3 80.6 - - - +
164B HIS* 1.3 90.7 + - + +
165B MET 3.8 0.2 - - - -
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Residues in contact with HIS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 3.3 72.5 + + + +
160B ILE* 2.9 28.3 + - + +
163B GLU* 1.3 110.4 + - + +
165B MET* 1.3 63.8 + - + +
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Residues in contact with MET 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 4.8 5.4 - - + +
118B GLU* 3.8 22.9 - - + -
121B VAL* 3.8 29.8 - - - -
160B ILE 5.0 0.2 - - - +
161B SER* 2.9 26.0 + - - +
162B LYS 4.2 3.6 - - - +
163B GLU 5.2 0.2 - - - -
164B HIS* 1.3 87.4 - - + +
166B GLN* 1.3 61.7 + - - +
167B PRO* 4.3 0.2 - - - +
169B HIS* 3.4 45.1 - - + +
171B ILE* 3.7 18.4 - - + -
172B ARG* 2.8 33.4 + - - +
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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