Contacts of the helix formed by residues 144 - 169 (chain B) in PDB entry 2O98
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 GLY 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B THR* 1.3 72.9 + - - +
145B ALA* 1.3 57.0 + - - -
147B ARG* 3.0 12.7 + - - +
148B LYS* 2.8 45.8 + - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B THR 3.3 2.4 + - - -
144B GLY* 1.3 69.8 - - - -
146B GLU* 1.3 63.0 + - + +
148B LYS* 3.2 26.0 + - - +
149B GLU* 3.2 13.2 + - - +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 2.8 50.1 + - + +
143B THR 3.9 6.7 + - - +
144B GLY 3.4 0.6 - - - -
145B ALA* 1.3 80.1 - - + +
147B ARG* 1.3 58.3 + - - +
149B GLU* 3.8 10.4 + - - +
150B ALA* 3.2 25.8 + - - +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ALA* 3.2 29.5 + - + +
140B GLU 5.2 1.8 + - - -
142B LYS* 3.5 31.1 + - - +
143B THR* 4.3 1.5 - - - +
144B GLY* 3.0 24.8 + - - +
146B GLU* 1.3 76.5 - - - +
148B LYS* 1.3 56.5 + - - +
150B ALA* 3.6 3.0 - - - +
151B ALA* 2.8 40.5 + - + +
189B GLU 5.2 1.6 + - - -
190B ILE* 2.7 46.2 + - - +
191B LEU* 5.5 0.8 - - - +
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY* 2.8 25.7 + - - +
145B ALA* 3.3 14.1 - - - +
147B ARG* 1.3 75.9 - - - +
149B GLU* 1.3 52.4 + - - +
151B ALA* 3.2 4.7 + - - +
152B GLU* 2.8 45.2 + - + +
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Residues in contact with GLU 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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135B HIS* 6.1 2.2 - - + +
145B ALA 3.2 9.0 + - - +
146B GLU* 3.8 13.4 - - - +
147B ARG 3.4 0.2 - - - -
148B LYS* 1.3 77.5 - - - +
150B ALA* 1.3 54.6 + - - +
152B GLU* 3.1 9.4 + - - +
153B SER* 2.7 46.1 + - - +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B HIS* 3.6 24.9 - - - +
138B LEU* 4.1 13.5 - - + -
139B ALA* 3.8 16.8 - - + +
142B LYS* 5.2 0.4 - - + -
146B GLU 3.2 15.9 + - - +
147B ARG* 3.6 5.2 - - - +
149B GLU* 1.3 80.6 - - - +
151B ALA* 1.3 57.9 + - - +
153B SER* 3.2 6.3 + - - -
154B THR* 2.8 34.5 + - - -
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Residues in contact with ALA 151 (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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139B ALA* 4.4 3.0 - - + +
147B ARG* 2.8 24.4 + - + +
148B LYS* 3.6 5.2 - - - +
150B ALA* 1.3 70.1 - - - +
152B GLU* 1.3 67.5 + - + +
154B THR* 3.3 3.7 + - - -
155B LEU* 3.0 21.5 + - - +
186B PHE* 3.5 26.0 - - + -
190B ILE* 4.4 8.7 - - + -
191B LEU* 4.3 15.0 - - + -
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Residues in contact with GLU 152 (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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148B LYS* 2.8 35.1 + - + +
149B GLU* 3.4 9.0 - - - +
151B ALA* 1.3 71.9 - - - +
153B SER* 1.3 64.2 + - - +
155B LEU* 3.0 21.8 + - - +
156B THR* 3.0 19.0 + - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 5.2 3.0 + - - +
135B HIS* 3.4 43.2 + - - -
149B GLU* 2.7 29.1 + - - +
150B ALA 3.5 0.7 - - - -
152B GLU* 1.3 73.1 - - - +
154B THR* 1.3 63.6 + - - +
156B THR* 3.4 7.3 + - - -
157B ALA* 3.1 24.6 + - - +
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Residues in contact with THR 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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132B GLY* 3.8 10.5 - - - +
135B HIS* 3.2 28.2 + - - +
136B ARG* 3.4 5.3 + - + -
139B ALA* 5.0 0.5 - - - +
150B ALA 2.8 17.2 + - - -
151B ALA* 3.4 9.3 - - - -
153B SER* 1.3 76.6 - - - +
155B LEU* 1.3 64.5 + - - +
157B ALA* 3.2 2.1 + - - +
158B TYR* 3.0 54.8 + - + +
186B PHE* 3.5 25.9 - - + -
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Residues in contact with LEU 155 (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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151B ALA 3.0 13.7 + - - +
152B GLU* 3.0 13.4 + - - +
154B THR* 1.3 75.3 - - - +
156B THR* 1.3 64.5 + - - +
158B TYR* 4.9 1.3 - - - -
159B LYS* 2.9 48.1 + - + +
183B PHE* 3.4 36.8 - - + -
186B PHE* 3.8 17.7 - - + -
187B TYR* 3.6 15.3 - - + +
191B LEU* 5.2 7.4 - - + -
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Residues in contact with THR 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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131B LYS* 6.6 0.2 - - - -
152B GLU* 3.0 15.1 + - - +
153B SER* 3.7 10.5 - - - -
155B LEU* 1.3 76.8 - - - +
157B ALA* 1.3 62.2 + - - +
159B LYS* 3.9 7.7 - - - +
160B ALA* 3.2 23.7 + - + +
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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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128B LEU* 3.8 17.9 - - + +
131B LYS* 3.9 23.6 - - + +
132B GLY 3.7 24.5 - - - +
153B SER 3.1 17.0 + - - +
154B THR 3.2 1.1 + - - +
156B THR* 1.3 74.9 - - - +
158B TYR* 1.3 65.9 + - - +
160B ALA* 3.5 6.7 + - - +
161B ALA* 3.1 23.2 + - - +
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Residues in contact with TYR 158 (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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129B LYS* 3.6 28.7 - - + -
132B GLY* 3.6 13.5 - - - -
133B ASP* 2.6 27.3 + - - -
136B ARG* 2.9 18.6 + - - -
154B THR* 3.0 37.7 + - + +
155B LEU 4.1 0.4 - - - +
157B ALA* 1.3 77.4 - - - +
159B LYS* 1.3 56.8 + - - +
161B ALA* 3.1 6.5 + - - +
162B GLN* 2.8 30.8 + - - +
179B LEU* 3.5 23.7 - - + +
182B ASN* 3.6 8.7 - - + +
183B PHE* 3.5 41.5 - + + -
186B PHE* 3.8 18.4 - + + -
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Residues in contact with LYS 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 LEU* 2.9 44.7 + - + +
156B THR* 3.9 6.3 - - - +
158B TYR* 1.3 75.6 - - - +
160B ALA* 1.3 60.6 + - - +
162B GLN* 3.7 8.0 + - - +
163B ASP* 3.3 21.3 + - - +
183B PHE* 3.7 19.3 - - + -
187B TYR* 6.0 0.2 - - - +
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Residues in contact with ALA 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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128B LEU* 3.6 18.6 - - + -
156B THR* 3.2 18.3 + - + +
157B ALA* 3.5 7.9 - - - +
159B LYS* 1.3 74.2 - - - +
161B ALA* 1.3 66.8 + - - +
163B ASP* 3.0 17.7 + - - +
164B ILE* 3.2 16.5 + - + +
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Residues in contact with ALA 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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125B VAL* 3.4 17.6 - - + +
128B LEU* 3.5 26.6 - - + +
129B LYS 4.2 7.0 - - - +
157B ALA 3.1 10.1 + - - +
158B TYR* 3.4 10.1 - - - +
160B ALA* 1.3 78.9 - - - +
162B GLN* 1.3 57.0 + - - +
164B ILE* 3.5 0.8 + - - -
165B ALA* 2.8 30.3 + - - +
179B LEU* 3.8 18.8 - - + -
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Residues in contact with GLN 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 TYR 2.8 16.2 + - - +
159B LYS* 3.9 9.9 - - - +
160B ALA 3.1 0.2 - - - -
161B ALA* 1.3 75.1 - - - +
163B ASP* 1.3 60.8 + - - +
165B ALA* 3.7 4.2 - - + +
166B THR* 2.8 41.2 + - - +
179B LEU* 3.5 18.6 - - + +
180B ALA* 5.7 2.9 - - - +
183B PHE* 3.9 17.1 - - + -
200B LEU* 4.0 34.2 - - - +
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Residues in contact with ASP 163 (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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159B LYS 3.3 11.2 + - - +
160B ALA* 3.0 10.0 + - - +
162B GLN* 1.3 78.3 + - - +
164B ILE* 1.3 66.3 + - + +
166B THR* 3.3 6.5 + - - +
167B THR* 3.1 35.0 + - - +
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Residues in contact with ILE 164 (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 GLY* 3.9 23.6 - - - +
124B LYS* 4.5 22.2 - - + -
125B VAL* 3.8 14.4 - - + -
128B LEU* 3.9 26.9 - - + -
160B ALA* 3.2 8.4 + - + +
161B ALA* 3.8 6.3 - - - +
163B ASP* 1.3 77.4 - - + +
165B ALA* 1.3 55.2 + - - +
167B THR* 3.3 7.7 + - - -
168B GLU* 2.8 43.6 + - - +
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Residues in contact with ALA 165 (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 VAL* 3.8 19.0 - - + +
161B ALA 2.8 19.6 + - - +
162B GLN* 3.7 8.5 - - + +
164B ILE* 1.3 76.2 - - - +
166B THR* 1.3 64.5 + - - +
169B LEU* 3.0 37.1 + - + +
176B ARG* 3.3 29.7 + - + -
179B LEU* 5.0 3.4 - - + -
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Residues in contact with THR 166 (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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162B GLN* 2.8 30.2 + - - +
163B ASP* 3.8 8.3 - - - +
165B ALA* 1.3 74.7 - - - +
167B THR* 1.3 65.6 + - + +
169B LEU 4.7 0.7 - - - +
176B ARG* 3.5 31.4 + - - +
207B GLU* 5.5 1.1 + - - +
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Residues in contact with THR 167 (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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163B ASP* 3.1 27.7 + - - +
164B ILE* 3.3 10.7 + - - -
166B THR* 1.3 86.4 - - + +
168B GLU* 1.3 71.7 + - - +
169B LEU 4.0 0.7 - - - -
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Residues in contact with GLU 168 (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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120B SER* 5.1 0.3 - - - -
121B GLY* 3.4 32.4 + - - -
164B ILE* 2.8 28.4 + - + +
167B THR* 1.3 86.4 + - - +
169B LEU* 1.3 66.1 + - + +
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Residues in contact with LEU 169 (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 GLY* 4.3 2.2 - - - -
122B ASP* 3.5 40.6 - - - +
125B VAL* 4.6 11.7 - - + -
165B ALA* 3.0 19.1 + - + +
166B THR 4.7 1.7 - - - +
167B THR 5.2 0.3 - - - -
168B GLU* 1.3 85.6 - - + +
170B ALA* 1.3 70.7 + - - +
171B PRO* 4.1 0.5 - - - +
173B HIS* 3.6 30.1 - - + +
175B ILE* 3.9 13.9 - - + -
176B ARG* 3.1 42.8 + - + +
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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