Contacts of the helix formed by residues 158 - 178 (chain B) in PDB entry 2HKU
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 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B ALA* 1.3 77.4 - - - +
159B ILE* 1.3 67.4 + - - -
160B ASP* 3.1 13.9 - - - -
161B VAL* 2.9 19.2 + - - +
162B GLU* 2.9 10.9 + - - +
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Residues in contact with ILE 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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141B GLU* 3.6 33.4 - - + +
144B LEU* 3.3 38.4 - - + -
145B ILE* 3.7 25.6 - - + -
155B LEU* 3.2 30.9 - - + +
157B ALA 3.5 2.0 + - - -
158B GLY* 1.3 70.1 - - - -
160B ASP* 1.3 58.8 + - + +
162B GLU* 3.4 1.9 + - - -
163B SER 3.1 22.2 + - - -
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Residues in contact with ASP 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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137B HIS* 5.1 0.3 - - - -
141B GLU* 3.5 25.1 - - - +
158B GLY* 3.6 14.6 - - - -
159B ILE* 1.3 74.7 + - + +
161B VAL* 1.3 79.8 + - - +
163B SER* 3.5 3.3 + - - -
164B LYS* 3.2 41.5 + - - +
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Residues in contact with VAL 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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193A ALA* 4.4 9.4 - - + +
194A VAL* 4.2 21.0 - - + +
197A ALA* 3.6 31.2 - - + -
157B ALA* 4.2 9.0 - - + -
158B GLY* 2.9 13.5 + - - +
160B ASP* 1.3 91.3 - - - +
162B GLU* 1.3 59.1 + - - +
164B LYS* 3.2 17.8 + - - +
165B ALA* 3.0 26.4 + - + +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ALA* 5.5 5.5 - - - +
198A ASN* 5.4 0.2 + - - -
200A GLN* 5.7 0.2 + - - -
144B LEU* 3.9 16.9 - - + +
155B LEU* 3.8 26.0 - - + +
156B ARG* 3.5 13.5 + - - +
157B ALA* 3.3 35.8 + - + +
158B GLY 2.9 16.1 + - - +
159B ILE 3.7 7.4 - - - +
161B VAL* 1.3 75.1 - - - +
163B SER* 1.3 59.8 + - - +
165B ALA* 3.3 8.3 + - - +
166B PHE* 3.0 27.4 + - - +
198B ASN 4.1 9.0 - - - +
199B LEU* 3.7 30.9 - - + +
200B GLN* 4.9 0.9 - - - +
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B HIS* 2.7 42.7 + - - -
140B GLY* 3.7 8.4 - - - -
141B GLU* 3.6 18.2 + - - -
144B LEU* 3.8 7.1 - - - +
159B ILE 3.1 17.0 + - - -
160B ASP 3.9 3.8 - - - -
161B VAL 3.3 0.2 - - - -
162B GLU* 1.3 72.5 - - - +
164B LYS* 1.3 67.0 + - - +
166B PHE* 3.2 4.8 + - - +
167B TRP* 3.0 31.7 + - - -
214B PG4 5.4 0.4 - - - -
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Residues in contact with LYS 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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185A GLY* 3.0 38.4 + - - +
186A TYR* 3.1 27.3 + - + +
190A GLU* 3.4 26.3 + - - +
194A VAL* 3.6 22.2 - - + +
301A EDO 4.6 8.1 - - - -
137B HIS* 3.7 12.6 - - + -
160B ASP* 3.2 33.5 + - - +
161B VAL* 3.2 16.3 + - - +
163B SER* 1.3 75.7 - - - +
165B ALA* 1.3 58.1 + - - +
168B SER* 2.8 34.2 + - - -
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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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169A ALA* 5.9 1.1 - - - +
194A VAL* 3.9 14.1 - - + +
197A ALA* 6.0 0.7 - - + -
198A ASN* 3.2 31.5 - - - +
161B VAL* 3.0 18.2 + - + +
162B GLU* 3.7 15.7 - - - +
163B SER 3.2 0.4 - - - -
164B LYS* 1.3 73.4 - - - +
166B PHE* 1.3 65.7 + - - +
168B SER* 4.1 1.3 - - - -
169B ALA* 3.0 26.0 + - - +
198B ASN* 4.9 3.7 + - + -
199B LEU* 4.8 9.4 - - + +
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Residues in contact with PHE 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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94B THR* 6.0 0.4 - - + -
97B LEU* 3.7 25.1 - - + -
98B VAL* 4.2 12.6 - - + -
101B LEU* 3.6 22.9 - - + -
144B LEU* 5.5 0.9 - - + -
162B GLU 3.0 16.4 + - - +
163B SER* 3.6 5.4 - - - +
164B LYS 3.2 0.2 - - - -
165B ALA* 1.3 79.0 - - - +
167B TRP* 1.3 88.5 + + - +
169B ALA* 3.2 5.1 + - - +
170B ILE* 2.9 56.6 + - + +
195B ILE* 4.1 23.8 - - + -
199B LEU* 4.9 10.7 - - + +
214B PG4 3.6 27.8 - - - +
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Residues in contact with TRP 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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176A GLN* 4.4 0.2 - - - +
73B VAL* 5.4 4.5 - - + -
77B GLY* 5.0 1.1 - - - -
101B LEU* 4.1 23.3 - - + -
109B VAL* 5.6 1.3 - - + -
136B LEU* 3.1 52.6 + - + -
137B HIS* 3.8 33.7 - + + +
140B GLY* 4.4 3.8 - - - -
163B SER* 3.0 38.1 + - - +
166B PHE* 1.3 97.6 - + - +
168B SER* 1.4 61.8 + - - +
170B ILE* 3.2 23.3 + - + +
171B PHE* 2.9 62.6 + + + -
214B PG4 3.9 24.0 - - - -
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Residues in contact with SER 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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168A SER 3.2 10.7 - - - +
169A ALA* 4.1 8.1 - - - -
172A GLY* 3.4 5.2 - - - -
173A LEU* 3.3 38.1 - - - +
176A GLN* 3.1 24.1 + - - +
186A TYR* 3.4 2.1 + - - -
194A VAL* 5.0 1.3 - - - -
164B LYS 2.8 23.0 + - - -
165B ALA* 4.1 4.3 - - - -
167B TRP* 1.4 70.7 - - - +
169B ALA* 1.3 67.3 + - - +
172B GLY 3.0 18.4 + - - -
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Residues in contact with ALA 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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168A SER* 4.0 10.7 - - - +
169A ALA* 4.6 2.7 - - - +
165B ALA 3.0 20.5 + - - +
166B PHE 3.5 3.6 - - - +
168B SER* 1.3 77.1 - - - +
170B ILE* 1.4 57.5 + - - +
172B GLY* 3.6 1.0 - - - -
173B LEU* 2.9 35.4 + - + +
194B VAL* 4.1 20.2 - - + -
195B ILE* 3.7 22.2 - - + -
198B ASN* 4.3 9.4 - - + +
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Residues in contact with ILE 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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98B VAL* 4.2 15.5 - - + -
101B LEU* 4.1 20.4 - - + -
102B LEU* 3.9 19.3 - - + -
109B VAL* 4.3 10.5 - - + -
166B PHE* 2.9 55.9 + - + +
167B TRP* 3.2 25.1 + - + +
169B ALA* 1.4 74.8 - - - +
171B PHE* 1.3 57.3 + - + +
173B LEU* 3.3 6.8 + - + +
174B VAL* 2.9 40.2 + - + +
195B ILE* 4.3 8.7 - - + -
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Residues in contact with PHE 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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172A GLY* 4.3 10.3 - - - -
175A ILE* 5.0 5.6 - - + -
176A GLN* 3.5 34.3 - - - -
73B VAL* 4.7 3.8 - - + -
109B VAL* 3.7 19.3 - - + -
112B PHE* 3.8 34.1 - + - -
113B THR* 3.5 23.6 - - + -
116B MSE 3.9 9.2 - - + -
133B LEU* 4.0 6.3 - - + -
136B LEU* 4.1 8.5 - - + -
167B TRP* 2.9 54.9 + + + +
168B SER 4.1 2.2 - - - +
170B ILE* 1.3 71.7 - - + +
172B GLY* 1.3 59.5 + - - +
174B VAL* 4.2 0.3 - - - +
175B ILE* 3.0 33.8 + - - +
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Residues in contact with GLY 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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168A SER* 3.3 28.9 - - - -
171A PHE* 3.9 16.1 - - - -
172A GLY* 4.0 1.9 - - - -
168B SER 3.0 9.9 + - - -
169B ALA 3.6 0.9 - - - -
171B PHE* 1.3 77.9 - - - +
173B LEU* 1.3 56.9 + - - +
175B ILE* 3.3 8.6 - - - +
176B GLN* 2.9 28.4 + - - +
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Residues in contact with LEU 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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164A LYS* 5.3 4.0 - - + +
168A SER* 4.0 15.7 - - - +
102B LEU* 4.7 8.1 - - + -
169B ALA* 2.9 25.5 + - + +
170B ILE* 3.8 8.7 - - + +
172B GLY* 1.3 75.4 - - - +
174B VAL* 1.3 58.4 + - - +
175B ILE 3.2 1.1 - - - -
176B GLN* 3.2 7.3 + - - +
177B LYS* 2.7 63.8 + - - +
190B GLU* 5.6 1.3 - - + -
191B ALA* 4.0 35.2 - - + +
194B VAL* 4.3 24.2 - - + -
195B ILE* 4.9 3.8 - - + -
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Residues in contact with VAL 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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101B LEU 4.3 7.2 - - - +
102B LEU* 3.8 28.0 - - + -
106B ALA* 3.9 16.2 - - + +
109B VAL* 3.7 32.5 - - + -
110B GLU* 3.9 23.1 - - + +
170B ILE* 2.9 24.1 + - + +
171B PHE 4.2 1.3 - - - +
173B LEU* 1.3 76.8 - - - +
175B ILE* 1.3 63.5 + - + +
177B LYS* 3.4 9.2 + - + +
178B THR* 2.9 25.7 + - - +
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Residues in contact with ILE 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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113A THR* 3.6 25.6 - - + -
116A MSE 3.2 47.2 - - + +
117A LEU* 4.1 15.9 - - + -
171A PHE* 3.8 10.3 - - + -
175A ILE* 3.8 13.7 - - + -
113B THR* 3.7 30.1 - - + +
171B PHE 3.0 16.0 + - - +
172B GLY 3.3 13.0 - - - +
174B VAL* 1.3 79.9 - - + +
176B GLN* 1.3 61.5 + - - +
178B THR* 3.1 25.0 - - - -
179B ALA 4.1 0.5 + - - -
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Residues in contact with GLN 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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116A MSE 4.1 15.9 - - - -
133A LEU* 3.8 22.8 - - + +
137A HIS* 3.4 28.2 + - - -
164A LYS* 4.9 2.0 + - - +
168A SER* 3.6 21.4 - - - +
171A PHE* 3.9 18.2 - - + -
172B GLY 2.9 22.4 + - - +
173B LEU* 3.2 14.0 + - - +
175B ILE* 1.3 73.6 - - + +
177B LYS* 1.3 66.9 + - - +
178B THR 2.9 2.9 - - - -
179B ALA* 2.6 36.9 + - - +
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Residues in contact with LYS 177 (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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126A ARG* 5.3 1.2 + - - -
102B LEU* 4.3 26.7 - - + +
173B LEU* 2.7 62.8 + - - +
174B VAL* 3.4 10.0 + - - +
176B GLN* 1.3 93.0 + - - +
178B THR* 1.3 59.7 + - - +
179B ALA 3.3 9.2 + - - +
187B SER 4.2 27.7 - - - +
188B LEU* 6.5 0.9 - - + -
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Residues in contact with THR 178 (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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116A MSE 3.4 19.1 - - - +
117A LEU* 4.4 9.9 - - + +
119A THR 3.8 4.8 - - - +
120A GLY* 3.8 18.3 - - - +
110B GLU* 3.1 44.5 + - + +
174B VAL 2.9 17.0 + - - -
175B ILE* 3.1 18.8 + - - -
177B LYS* 1.3 76.9 - - - +
179B ALA* 1.3 56.6 + - - +
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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
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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