Contacts of the helix formed by residues 158 - 180 (chain B) in PDB entry 2XWU
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 ASP 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B SER* 5.6 5.4 - - - -
157B VAL* 1.3 80.4 - - - +
159B GLY* 1.3 65.4 + - - +
160B GLN* 3.4 11.3 + - - +
161B GLY* 3.2 26.0 + - - -
162B ARG* 3.2 19.1 + - - +
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Residues in contact with GLY 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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158B ASP* 1.3 73.6 - - - +
160B GLN* 1.3 57.5 + - - +
162B ARG* 3.4 4.6 + - - +
163B CYS* 2.9 32.2 + - - +
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Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASP* 3.3 10.4 + - - +
159B GLY* 1.3 76.1 - - - +
161B GLY* 1.3 59.0 + - - +
163B CYS* 3.8 4.0 - - - +
164B LEU* 3.0 52.6 + - + +
215B PRO* 4.5 10.5 - - + +
217B CYS* 2.9 34.5 - - - +
218B VAL* 4.5 8.5 - - + -
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Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 3.7 24.9 - - - +
120B LEU* 5.6 0.3 - - - +
157B VAL* 5.1 1.8 - - - -
158B ASP* 3.2 19.8 + - - -
159B GLY 3.3 0.4 - - - -
160B GLN* 1.3 80.0 - - - +
162B ARG* 1.3 61.8 + - - +
164B LEU* 4.1 6.7 - - - +
165B ALA* 3.2 23.7 + - - +
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 4.9 2.5 - - - -
150B PHE* 3.6 35.4 - - + +
157B VAL* 4.6 13.8 - - + +
158B ASP 3.2 17.7 + - - +
159B GLY* 3.9 4.3 - - - +
161B GLY* 1.3 75.1 - - - +
163B CYS* 1.3 59.4 + - - +
165B ALA* 3.3 6.0 + - - +
166B LEU* 2.8 29.9 + - - +
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Residues in contact with CYS 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 GLY 2.9 19.3 + - - +
160B GLN* 3.8 5.6 - - - +
162B ARG* 1.3 75.3 - - - +
164B LEU* 1.3 65.4 + - - +
166B LEU* 3.2 9.9 + - - +
167B LEU* 3.0 32.2 + - - +
204B LEU* 6.1 0.7 - - - -
208B LEU* 3.9 38.8 - - - -
218B VAL* 4.2 18.8 - - + -
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Residues in contact with LEU 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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120B LEU* 5.4 2.7 - - + -
160B GLN* 3.0 45.3 + - + +
161B GLY* 4.2 6.7 - - - +
163B CYS* 1.3 75.3 - - - +
165B ALA* 1.3 57.3 + - - +
167B LEU* 3.4 5.9 + - + +
168B GLU* 2.9 28.2 + - - +
217B CYS* 3.9 8.5 - - + +
218B VAL* 3.6 31.2 - - + +
221B LYS* 3.7 42.6 + - + +
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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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109B ILE* 4.6 2.0 - - + -
113B ALA* 4.1 16.4 - - + -
120B LEU* 4.3 21.3 - - + +
124B CYS* 4.2 4.5 - - - -
150B PHE* 4.0 17.5 - - + -
161B GLY 3.2 19.2 + - - +
162B ARG* 3.5 5.4 - - - +
163B CYS 3.1 0.2 - - - -
164B LEU* 1.3 75.4 - - - +
166B LEU* 1.3 64.6 + - - +
168B GLU* 3.4 7.1 + - - +
169B LEU* 3.1 22.7 + - - +
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Residues in contact with LEU 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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146B MET* 3.8 20.2 - - + +
147B VAL* 3.7 20.9 - - + +
150B PHE* 3.6 40.8 - - + -
151B GLN* 5.6 2.5 - - + -
162B ARG 2.8 16.2 + - - +
163B CYS* 3.6 10.5 - - - +
165B ALA* 1.3 77.1 - - - +
167B LEU* 1.3 59.5 - - + +
169B LEU* 3.6 4.0 + - + +
170B LEU* 3.1 38.4 + - + +
204B LEU* 3.6 29.8 - - + -
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Residues in contact with LEU 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 CYS* 3.0 34.4 + - - +
164B LEU* 3.7 10.1 - - + +
166B LEU* 1.3 77.2 - - + +
168B GLU* 1.3 59.9 + - - +
169B LEU 3.2 0.2 - - - -
170B LEU* 3.2 9.5 + - + +
171B THR* 2.8 38.4 + - - +
204B LEU* 5.3 3.8 - - + -
205B LEU* 3.7 29.8 - - + -
208B LEU* 4.0 13.5 - - + -
218B VAL* 4.1 5.8 - - + +
221B LYS* 3.7 33.0 - - + +
222B VAL* 4.1 18.2 - - + -
225B CYS* 4.7 4.7 - - - -
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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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117B LYS 5.4 0.2 - - - +
120B LEU* 4.7 10.2 - - + +
121B THR* 3.4 43.4 + - + +
124B CYS* 4.0 16.8 - - + -
164B LEU 2.9 17.4 + - - +
165B ALA* 3.4 9.2 + - - +
167B LEU* 1.3 75.4 - - - +
169B LEU* 1.3 63.9 + - - +
171B THR* 3.6 7.5 - - - +
172B VAL* 3.0 35.5 + - - +
221B LYS* 4.1 22.8 + - - +
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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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109B ILE* 4.8 2.5 - - + -
124B CYS* 3.5 38.5 - - + +
127B LEU* 3.6 35.9 - - + -
128B ALA* 4.3 7.0 - - + +
146B MET* 4.1 34.5 - - + -
150B PHE* 4.1 22.7 - - + -
165B ALA 3.1 13.2 + - - +
166B LEU* 3.7 5.6 - - + +
168B GLU* 1.3 80.6 - - - +
170B LEU* 1.3 62.0 + - + +
172B VAL* 4.0 1.5 - - - +
173B LEU* 3.1 22.5 + - + +
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Residues in contact with LEU 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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143B VAL* 4.2 16.4 - - + -
146B MET* 4.7 15.5 - - - -
147B VAL* 4.8 4.5 - - + -
166B LEU* 3.1 34.5 + - + +
167B LEU* 3.2 10.3 + - + +
169B LEU* 1.3 75.8 - - + +
171B THR* 1.3 57.5 + - - +
173B LEU* 3.9 5.6 - - + +
174B PRO* 3.0 22.7 - - - +
201B VAL* 3.6 34.3 - - + -
204B LEU* 3.8 28.7 - - + -
205B LEU* 5.3 1.3 - - + -
225B CYS* 3.9 13.9 - - - -
229B TRP* 3.1 18.0 + - + +
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Residues in contact with THR 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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167B LEU* 2.8 23.1 + - - +
168B GLU* 3.6 10.3 - - - +
170B LEU* 1.3 77.9 - - - +
172B VAL* 1.3 64.6 + - + +
174B PRO* 3.4 2.0 - - - +
175B GLU* 3.2 17.2 - - - +
221B LYS* 4.4 4.3 + - - +
224B LYS* 4.3 14.5 - - + +
225B CYS* 3.2 25.9 + - - +
228B SER* 3.0 38.9 + - - -
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Residues in contact with VAL 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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121B THR* 4.1 10.8 - - + +
124B CYS* 4.6 2.5 - - + +
125B VAL* 3.0 51.6 - - + +
128B ALA* 4.6 1.6 - - + -
168B GLU* 3.0 32.8 + - + +
169B LEU* 3.4 4.5 + - - +
171B THR* 1.3 77.6 - - + +
173B LEU* 1.3 66.2 + - - +
174B PRO 3.4 0.2 - - - -
175B GLU* 3.2 16.3 + - + +
176B GLU* 2.9 23.5 + - + +
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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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128B ALA* 3.8 36.8 - - + +
131B ALA* 4.7 8.1 - - + -
132B LEU* 3.9 17.8 - - + +
135B MET* 5.9 0.9 - - - -
142B ALA* 5.6 4.9 - - + -
143B VAL* 4.8 13.2 - - + -
146B MET* 5.0 12.8 - - + -
169B LEU* 3.1 16.4 + - + +
170B LEU* 3.9 9.9 - - + +
172B VAL* 1.3 78.1 - - - +
174B PRO* 1.3 72.2 - - + +
176B GLU* 3.2 3.1 + - - +
177B PHE* 3.2 17.8 + - - +
194B LEU* 4.4 14.4 - - + -
197B GLU* 5.7 0.2 - - + -
229B TRP* 4.0 23.3 - - + -
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Residues in contact with PRO 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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170B LEU 3.0 15.7 - - - +
171B THR 3.4 7.0 - - - +
173B LEU* 1.3 94.5 - - + +
175B GLU* 1.3 60.2 + - - +
177B PHE* 3.2 9.3 + - + +
178B GLN* 3.1 28.4 + - + +
194B LEU* 5.2 1.3 - - + -
228B SER* 3.3 23.3 - - - +
229B TRP* 3.3 37.9 - - + +
232B LEU* 3.8 22.2 - - + +
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Residues in contact with GLU 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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171B THR* 3.2 29.0 - - - +
172B VAL* 3.2 20.9 + - + +
174B PRO* 1.3 75.9 - - - +
176B GLU* 1.3 61.1 + - - +
178B GLN* 3.6 10.5 + - - +
179B THR* 3.4 26.3 + - - +
228B SER* 3.5 16.7 + - - +
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Residues in contact with GLU 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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83B HIS* 3.5 31.3 + - - -
87B SER* 4.7 2.1 - - - -
125B VAL* 3.6 28.7 - - + +
128B ALA* 4.6 6.7 - - + -
129B SER* 3.5 19.2 + - - -
132B LEU* 4.0 11.8 - - + +
172B VAL* 2.9 20.1 + - + +
173B LEU 3.6 4.9 - - - +
174B PRO 3.2 0.2 - - - -
175B GLU* 1.3 75.0 - - - +
177B PHE* 1.3 55.2 + - - +
179B THR* 3.0 20.2 + - - -
180B SER* 2.8 36.0 + - - -
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Residues in contact with PHE 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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132B LEU* 3.6 14.5 - - + +
173B LEU 3.2 4.6 + - - +
174B PRO 3.2 8.4 + - - +
176B GLU* 1.3 78.9 - - - +
178B GLN* 1.3 83.7 + - - +
180B SER* 2.9 26.7 + - - +
182B LEU* 5.4 3.4 - - + -
187B LYS* 4.1 15.7 - - + -
190B VAL* 3.3 36.3 - - + -
191B ARG* 3.3 39.5 - - + -
194B LEU* 3.7 20.2 - - + -
232B LEU* 3.7 13.2 - - + -
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Residues in contact with GLN 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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104A ARG* 3.1 56.8 - - - +
174B PRO 3.1 19.5 + - - +
175B GLU* 3.6 12.3 - - - +
176B GLU 3.3 0.2 - - - -
177B PHE* 1.3 99.7 - - - +
179B THR* 1.3 59.0 + - - +
180B SER 4.6 2.3 - - - +
228B SER 6.1 0.4 - - - +
231B GLN* 4.2 26.1 + - + +
232B LEU* 3.5 15.4 - - + +
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Residues in contact with THR 179 (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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101A LYS 5.4 2.1 - - - +
102A ASP* 3.5 35.9 - - + +
104A ARG* 4.7 13.9 - - - +
175B GLU 3.4 13.4 + - - +
176B GLU* 3.0 32.2 + - - -
177B PHE 3.1 0.4 - - - -
178B GLN* 1.3 78.2 - - - +
180B SER* 1.3 64.5 + - - +
181B ARG* 3.0 19.0 + - - +
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Residues in contact with SER 180 (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 LEU* 4.8 8.1 - - - -
176B GLU* 2.8 15.9 + - - -
177B PHE* 2.9 23.9 + - - +
178B GLN 4.6 2.3 - - - +
179B THR* 1.3 74.5 - - - +
181B ARG* 1.3 62.3 + - - +
182B LEU* 3.2 30.3 + - - +
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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