Contacts of the helix formed by residues 154 - 176 (chain B) in PDB entry 1ADI
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 LYS 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B LEU* 3.5 17.5 - - - +
152B PHE 3.7 4.0 + - - +
153B ASP* 1.3 70.6 + - - +
155B GLU* 1.3 65.5 + - - +
157B PHE* 3.8 9.4 - - + +
158B ALA* 4.0 5.2 + - - +
191B MET* 3.4 47.8 + - + +
194B ALA* 5.0 10.1 - - + +
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Residues in contact with GLU 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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153B ASP* 3.3 9.0 + - - +
154B LYS* 1.3 77.6 - - - +
156B THR* 1.3 66.3 + - - +
157B PHE 3.3 0.3 + - - -
158B ALA* 3.7 5.6 + - - +
159B GLU* 3.7 15.0 + - - +
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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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150B ASP 5.7 0.2 - - - -
153B ASP* 2.5 35.0 + - - -
155B GLU* 1.3 79.5 - - - +
157B PHE* 1.3 69.1 + - - +
158B ALA 3.5 0.2 - - - -
159B GLU* 3.2 24.6 - - - +
160B LYS* 3.1 44.0 + - - +
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 5.1 5.6 - - + -
107B LEU* 5.1 4.0 - - + -
146B LEU* 3.8 31.2 - - + -
150B ASP* 3.7 18.3 + - + +
151B LEU* 3.8 22.4 - - + -
153B ASP 3.1 18.3 + - - +
154B LYS* 3.8 8.3 - - - +
155B GLU 3.3 0.4 - - - -
156B THR* 1.3 73.0 - - - +
158B ALA* 1.3 51.6 + - - +
160B LYS* 2.9 14.1 + - - +
161B LEU* 2.8 49.8 + - + +
187B LEU* 3.3 26.9 - - + -
190B THR* 3.5 35.9 - - + -
191B MET* 3.4 24.9 - - + -
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Residues in contact with ALA 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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154B LYS 4.0 5.8 + - - +
155B GLU 3.7 9.1 + - - +
156B THR 3.5 0.4 - - - -
157B PHE* 1.3 78.5 - - - +
159B GLU* 1.3 56.0 + - - +
161B LEU* 3.9 4.5 - - - -
162B LYS* 3.2 19.9 + - - +
183B TYR* 2.8 32.1 + - - +
187B LEU* 3.6 30.5 - - + -
191B MET* 5.1 0.7 - - + -
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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 GLU 3.7 7.2 + - - +
156B THR* 3.2 31.7 - - - +
158B ALA* 1.3 77.6 - - - +
160B LYS* 1.3 71.2 + - - +
162B LYS* 3.4 17.3 - - - +
163B GLU* 3.5 25.5 + - - +
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Residues in contact with LYS 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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235A TYR* 5.7 3.5 - - - -
236A PRO* 5.7 10.8 - - - -
144B ARG 5.9 1.8 - - - +
145B GLY 5.1 8.7 - - - +
146B LEU* 3.8 18.6 - - + -
150B ASP* 3.2 32.9 + - - +
156B THR* 3.3 35.1 + - + +
157B PHE* 2.9 5.5 + - - +
159B GLU* 1.3 79.7 - - - +
161B LEU* 1.3 69.6 + - - +
163B GLU* 3.0 19.4 + - - +
164B VAL* 3.1 15.4 + - - +
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Residues in contact with LEU 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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107B LEU* 4.6 4.9 - - + -
109B TYR* 4.3 13.7 - - + +
146B LEU* 4.3 10.0 - - + +
157B PHE* 2.8 30.3 + - + +
158B ALA 3.8 4.9 - - - +
160B LYS* 1.3 76.7 - - - +
162B LYS* 1.3 63.9 + - - +
164B VAL* 3.3 8.1 - - - +
165B MET* 3.0 44.0 + - + +
183B TYR* 3.7 15.5 - - + -
186B VAL* 4.1 13.5 - - + -
187B LEU* 3.5 52.3 - - + +
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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 ALA 3.2 14.0 + - - +
159B GLU* 3.4 9.0 - - - +
161B LEU* 1.3 80.4 - - - +
163B GLU* 1.3 66.2 - - + +
165B MET* 3.3 8.1 + - - +
166B GLU* 3.3 18.3 + - + +
183B TYR* 3.3 48.5 + - + -
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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
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121A ARG* 4.8 32.5 + - - +
159B GLU* 3.6 27.6 - - - +
160B LYS* 3.0 9.1 + - - +
162B LYS* 1.3 81.6 - - + +
164B VAL* 1.3 65.0 + - - +
165B MET 3.0 1.6 + - - -
166B GLU* 3.0 22.1 + - - +
167B TYR* 3.3 10.4 + - - +
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Residues in contact with VAL 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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109B TYR* 3.8 21.1 - - + +
139B ASP* 3.9 13.7 - - - +
144B ARG* 3.5 49.4 - - + +
145B GLY* 5.1 1.3 - - - -
146B LEU* 3.9 17.7 - - + -
160B LYS 3.1 12.0 + - - +
161B LEU* 3.3 14.1 - - - +
163B GLU* 1.3 78.5 - - - +
165B MET* 1.3 56.3 + - - +
166B GLU 3.4 0.2 - - - -
167B TYR* 3.8 5.9 - - - +
168B HIS* 3.3 30.9 + - + +
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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
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109B TYR* 3.8 38.6 - - + -
161B LEU* 3.0 36.6 + - + +
162B LYS 3.8 4.7 - - - +
163B GLU 3.0 0.6 + - - -
164B VAL* 1.3 75.6 - - - +
166B GLU* 1.3 62.0 + - - +
167B TYR 3.3 0.2 - - - -
168B HIS* 3.9 4.6 - - - +
169B ASN* 3.0 41.5 + - - +
181B VAL* 3.4 38.6 - - + +
183B TYR* 3.8 34.8 - - + +
186B VAL* 4.3 7.2 - - - -
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Residues in contact with GLU 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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121A ARG* 2.9 37.5 + - - +
175A TYR* 3.0 16.6 + - - -
162B LYS* 3.3 14.7 + - + +
163B GLU* 3.0 19.2 + - - +
165B MET* 1.3 75.9 - - - +
167B TYR* 1.3 69.2 + - - +
169B ASN* 4.5 4.9 - - - +
170B PHE* 3.0 23.6 + - - +
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Residues in contact with TYR 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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117A ARG* 4.3 4.4 + - - -
138A GLU* 4.6 2.1 + - - -
167A TYR* 4.9 1.4 + - - -
171A GLN* 2.5 46.4 + - + -
175A TYR* 3.9 31.8 + + - +
176A TYR* 3.6 11.2 - - - -
144B ARG* 3.7 46.1 + - - -
163B GLU 3.3 10.7 + - - +
164B VAL* 3.8 10.3 - - - +
165B MET 3.3 0.2 - - - -
166B GLU* 1.3 82.1 - - - +
168B HIS* 1.3 83.9 + + - +
170B PHE* 3.4 13.7 - + - +
171B GLN* 3.4 30.4 + - + +
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Residues in contact with HIS 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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109B TYR* 2.9 44.1 - + + -
110B HIS* 4.5 1.0 + - - -
113B LEU* 3.8 36.9 - - + +
139B ASP* 2.7 38.0 + - - -
144B ARG* 4.1 1.6 - - - -
164B VAL* 3.3 18.6 + - + +
165B MET* 4.3 2.5 - - - +
166B GLU 3.2 0.2 - - - -
167B TYR* 1.3 98.7 - + - +
169B ASN* 1.3 60.5 + - - +
170B PHE 3.0 2.0 - - - -
171B GLN* 2.9 15.5 + - - +
172B LEU* 2.9 29.4 + - + +
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Residues in contact with ASN 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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109B TYR* 5.5 0.6 - - - +
165B MET* 3.0 35.3 + - - +
166B GLU* 4.4 4.4 - - - +
168B HIS* 1.3 76.3 - - - +
170B PHE* 1.3 61.7 + - - +
172B LEU* 4.1 8.8 - - - +
173B VAL* 3.0 31.7 + - + +
180B ALA* 3.2 14.4 - - + +
181B VAL* 2.6 50.8 + - - +
183B TYR* 5.3 2.2 - - - +
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Residues in contact with PHE 170 (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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170A PHE* 3.7 27.4 - + - -
171A GLN* 5.1 5.2 - - + -
174A ASN* 3.7 41.5 - - + -
175A TYR* 3.6 37.7 - + + -
177A LYS* 5.3 1.8 - - - -
166B GLU 3.0 19.3 + - - +
167B TYR* 3.4 8.3 - + - +
168B HIS 3.0 0.6 - - - -
169B ASN* 1.3 77.8 - - - +
171B GLN* 1.3 63.5 + - + +
173B VAL* 5.5 0.2 - - - -
174B ASN* 3.0 62.5 + - + +
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Residues in contact with GLN 171 (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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167A TYR* 3.2 35.7 + - - -
171A GLN* 4.1 14.2 + - + +
113B LEU* 4.8 11.0 - - + +
117B ARG* 5.4 2.6 - - - +
167B TYR* 3.4 41.3 + - + +
168B HIS* 2.9 17.5 + - - +
170B PHE* 1.3 83.6 - - + +
172B LEU* 1.3 69.5 + - + +
175B TYR* 3.2 13.4 + - + +
176B TYR* 3.1 37.0 + - + -
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Residues in contact with LEU 172 (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 TYR* 4.6 3.1 - - + -
112B ALA* 3.8 25.6 - - + +
113B LEU* 3.9 30.3 - - + -
116B ALA* 4.9 6.7 - - + -
168B HIS 2.9 17.0 + - - +
169B ASN* 3.9 15.3 - - - +
171B GLN* 1.3 78.1 - - + +
173B VAL* 1.3 57.9 + - + +
176B TYR* 3.6 9.0 - - + +
177B LYS 3.0 11.4 + - - -
178B ALA* 2.8 33.7 + - + +
179B GLU 3.6 19.5 - - - +
181B VAL* 3.7 30.3 - - + -
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Residues in contact with VAL 173 (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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169B ASN* 3.0 16.6 + - + +
172B LEU* 1.3 77.2 - - - +
174B ASN* 1.3 77.2 + - - +
177B LYS* 3.6 17.7 - - - +
178B ALA 3.3 11.2 - - - +
180B ALA* 3.4 40.4 - - + +
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Residues in contact with ASN 174 (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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170A PHE* 3.0 28.0 - - + -
170B PHE* 3.0 52.6 + - + +
173B VAL* 1.3 93.1 - - - +
175B TYR* 1.3 58.1 + - - +
177B LYS* 4.6 4.4 - - - +
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Residues in contact with TYR 175 (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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163A GLU 5.7 0.2 + - - -
166A GLU* 5.2 2.5 - - - +
167A TYR* 3.6 43.8 + + - +
170A PHE* 3.7 44.9 - + + -
121B ARG* 6.2 1.1 - - - -
171B GLN* 3.2 17.7 + - + +
174B ASN* 1.3 77.5 - - - +
176B TYR* 1.3 103.0 + + + +
177B LYS* 3.3 8.1 - - - +
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Residues in contact with TYR 176 (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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144A ARG* 5.4 0.9 + - - -
167A TYR* 4.1 17.2 - + - -
113B LEU* 5.5 6.3 - - + -
116B ALA* 3.7 33.9 - - + -
117B ARG* 3.8 43.5 + - + +
119B LYS* 5.5 5.2 - - - +
120B ALA* 4.7 7.6 - - + -
121B ARG* 4.6 13.2 + - - -
171B GLN* 3.1 33.4 + - + -
172B LEU* 3.6 17.3 - - + +
175B TYR* 1.3 110.2 - + + +
177B LYS* 1.3 75.8 + - - +
178B ALA* 4.4 3.8 - - + +
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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
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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