Contacts of the helix formed by residues 170 - 193 (chain T) in PDB entry 2P8Z
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 SER 170 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168T GLN 3.6 0.6 + - - -
169T VAL* 1.3 80.1 - - - +
171T LYS* 1.3 60.0 + - - +
172T GLU* 3.8 5.5 + - - +
173T ASP* 2.7 36.4 + - - -
174T LEU* 2.8 28.6 + - - +
282T PHE* 5.0 2.7 - - - -
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Residues in contact with LYS 171 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169T VAL 4.2 0.2 + - - -
170T SER* 1.3 73.9 - - - +
172T GLU* 1.3 58.3 + - - +
174T LEU* 3.2 4.0 + - - +
175T TYR* 2.8 29.3 + - - +
270T GLU* 2.8 28.2 + - - +
274T ASN* 4.0 19.2 + - + +
278T LEU* 4.5 19.2 - - + +
279T ASP* 3.9 18.8 + - - +
282T PHE* 3.3 49.7 - - + -
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Residues in contact with GLU 172 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170T SER* 3.4 5.2 + - - +
171T LYS* 1.3 78.9 - - - +
173T ASP* 1.3 60.7 + - - +
175T TYR* 3.5 8.6 + - - +
176T GLN* 3.0 61.8 + - + +
271T ARG* 3.8 26.0 + - - +
274T ASN* 3.8 17.4 + - - +
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Residues in contact with ASP 173 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169T VAL* 3.3 21.4 - - + +
170T SER* 2.7 27.9 + - - +
172T GLU* 1.3 76.5 - - - +
174T LEU* 1.3 64.7 + - - +
176T GLN* 3.4 8.1 + - - +
177T THR* 2.9 29.5 + - - +
180T ARG* 5.1 0.2 + - - -
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Residues in contact with LEU 174 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131T THR* 4.2 16.8 - - + -
160T VAL* 4.3 8.7 - - + -
163T ALA* 4.2 11.4 - - + -
164T LEU* 3.7 29.2 - - + -
169T VAL* 3.7 9.1 - - + +
170T SER 2.8 14.8 + - - +
171T LYS* 3.6 6.5 - - - +
173T ASP* 1.3 75.9 - - - +
175T TYR* 1.3 66.0 + - - +
177T THR* 3.1 8.1 + - - -
178T PHE* 2.9 67.2 + - + -
278T LEU* 5.4 8.5 - - + -
282T PHE* 4.5 12.6 - - + -
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Residues in contact with TYR 175 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171T LYS 2.8 17.8 + - - +
172T GLU* 3.5 17.5 - - - +
174T LEU* 1.3 75.8 - - - +
176T GLN* 1.3 90.8 + - - +
178T PHE* 2.9 14.8 + + + +
179T ALA* 2.9 34.5 + - + +
245T TRP* 3.6 43.1 - + - -
246T GLY* 4.4 12.6 - - - -
247T ASP* 5.5 0.9 + - - -
271T ARG* 4.3 34.5 + - - -
273T PHE* 4.6 10.1 - + - -
274T ASN* 4.7 6.3 - - - +
278T LEU* 5.6 4.6 - - + +
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Residues in contact with GLN 176 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172T GLU* 3.0 43.1 + - + +
173T ASP* 3.7 8.1 - - - +
175T TYR* 1.3 96.9 - - - +
177T THR* 1.3 62.9 + - - +
179T ALA* 3.3 7.6 + - - +
180T ARG* 2.9 50.6 + - - +
271T ARG* 5.2 1.2 - - - +
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Residues in contact with THR 177 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T THR* 3.2 35.4 - - + +
132T ILE* 5.3 2.5 - - - +
157T ILE* 6.4 0.2 - - + -
169T VAL* 5.4 2.6 - - - +
173T ASP* 2.9 19.3 + - - +
174T LEU* 3.1 13.7 + - - -
176T GLN* 1.3 75.5 - - - +
178T PHE* 1.3 65.5 + - + +
180T ARG* 3.3 25.9 + - - +
181T THR* 3.0 30.7 + - - +
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Residues in contact with PHE 178 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131T THR* 4.1 9.0 - - + -
157T ILE* 3.6 36.5 - - + +
160T VAL* 3.9 18.4 - - + -
174T LEU* 2.9 53.7 + - + -
175T TYR* 2.9 12.9 + + - +
177T THR* 1.3 79.9 - - + +
179T ALA* 1.3 56.6 + - - +
181T THR* 3.3 3.4 + - - -
182T VAL* 3.0 34.3 + - - +
211T PHE* 3.5 41.7 - + + -
245T TRP* 5.3 7.0 - + + -
273T PHE* 5.3 14.4 - + - -
278T LEU* 5.5 5.6 - - + -
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Residues in contact with ALA 179 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175T TYR* 2.9 36.7 + - + +
176T GLN* 3.7 13.2 - - - +
178T PHE* 1.3 76.2 - - - +
180T ARG* 1.3 59.5 + - + +
182T VAL* 3.5 8.5 + - - +
183T GLU* 3.1 27.7 + - - +
245T TRP* 5.6 6.7 - - + -
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Residues in contact with ARG 180 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T ASP 5.1 0.2 + - - -
176T GLN* 2.9 51.0 + - - +
177T THR* 3.5 29.7 + - + +
179T ALA* 1.3 74.8 - - + +
181T THR* 1.3 61.7 + - - +
183T GLU* 3.2 6.8 + - - +
184T SER* 2.9 33.2 + - - +
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Residues in contact with THR 181 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129T VAL* 3.2 39.0 - - + -
130T ASP 4.5 1.9 + - - +
131T THR 4.5 2.4 + - - -
134T GLY* 4.2 13.6 - - - -
135T VAL* 4.2 5.2 - - + -
155T VAL* 5.6 1.1 - - + -
157T ILE* 4.2 19.3 - - + +
177T THR* 3.0 24.8 + - - +
178T PHE* 3.6 5.3 - - - -
180T ARG* 1.3 76.4 - - - +
182T VAL* 1.3 64.2 + - - +
184T SER* 3.4 7.6 + - - -
185T VAL* 3.1 24.4 + - + +
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Residues in contact with VAL 182 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155T VAL* 5.8 3.6 - - + -
157T ILE* 4.1 15.3 - - + -
178T PHE 3.0 24.2 + - - +
179T ALA* 3.7 7.9 - - - +
180T ARG 3.2 0.2 - - - -
181T THR* 1.3 77.3 - - - +
183T GLU* 1.3 57.5 + - - +
185T VAL* 3.5 6.6 + - + +
186T ASN* 3.1 42.4 + - - +
202T VAL* 3.8 13.2 - - + +
204T PRO* 4.2 29.4 - - + -
209T VAL* 4.4 11.9 - - + -
211T PHE* 5.3 1.1 - - + -
245T TRP* 5.9 0.9 - - + -
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Residues in contact with GLU 183 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179T ALA 3.1 17.3 + - - +
180T ARG* 3.6 8.1 - - - +
181T THR 3.2 0.2 - - - -
182T VAL* 1.3 76.2 - - - +
184T SER* 1.3 65.0 + - - +
186T ASN* 3.2 13.6 + - - +
187T VAL* 3.1 32.5 + - - +
201T GLN* 5.1 1.2 - - - +
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Residues in contact with SER 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135T VAL* 3.9 21.1 - - - -
180T ARG* 2.9 18.5 + - - +
181T THR* 3.4 7.6 + - - -
183T GLU* 1.3 77.8 - - - +
185T VAL* 1.3 62.3 + - - +
187T VAL* 3.4 19.3 + - - +
188T ILE* 3.5 13.6 + - - +
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Residues in contact with VAL 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127T VAL* 5.8 1.3 - - + -
129T VAL* 4.3 15.9 - - + -
135T VAL* 3.5 22.0 - - + -
139T THR* 6.3 0.2 - - + -
143T LEU* 4.3 13.2 - - + -
153T PRO* 6.1 1.8 - - + -
155T VAL* 4.0 26.0 - - + -
181T THR* 3.1 19.7 + - + +
182T VAL* 3.7 7.4 - - - +
183T GLU 3.1 0.6 - - - -
184T SER* 1.3 74.2 - - - +
186T ASN* 1.3 64.8 + - - +
187T VAL 3.0 5.8 + - - -
188T ILE* 3.1 10.1 + - - +
189T VAL* 3.0 34.2 + - + +
202T VAL* 5.0 4.7 - - + -
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Residues in contact with ASN 186 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182T VAL* 3.1 24.2 + - - +
183T GLU* 3.2 13.0 + - - +
185T VAL* 1.3 76.2 - - - +
187T VAL* 1.3 52.8 + - - +
189T VAL* 3.8 8.2 - - - +
190T SER* 2.8 35.5 + - - -
201T GLN* 3.1 30.0 + - - +
202T VAL* 2.8 54.4 + - - +
203T TYR* 5.0 5.9 - - - -
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Residues in contact with VAL 187 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183T GLU* 3.1 30.3 + - - +
184T SER* 3.4 13.0 - - - +
185T VAL 3.0 0.4 - - - -
186T ASN* 1.3 76.6 - - - +
188T ILE* 1.3 71.1 + - + +
190T SER* 3.2 6.0 + - - -
191T THR* 2.9 36.6 + - - +
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Residues in contact with ILE 188 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135T VAL* 4.0 20.0 - - + -
140T GLU* 3.4 56.1 - - + +
143T LEU* 3.8 29.4 - - + -
144T ARG 4.6 1.8 - - - +
147T LEU* 3.7 5.0 - - + +
184T SER* 3.5 13.7 + - - +
185T VAL* 3.1 7.5 + - - +
187T VAL* 1.3 83.4 - - + +
189T VAL* 1.3 61.4 - - - +
191T THR* 3.4 1.2 + - - -
192T TYR* 3.1 42.3 + - + -
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Residues in contact with VAL 189 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143T LEU* 4.5 6.5 - - + -
147T LEU* 3.6 15.0 - - + -
153T PRO* 4.2 19.5 - - + -
185T VAL* 3.0 28.3 + - + +
186T ASN* 4.1 10.5 - - - +
188T ILE* 1.3 75.9 - - - +
190T SER* 1.3 64.8 + - - +
191T THR 3.0 0.3 + - - -
193T ALA* 2.9 30.7 + - + +
200T VAL* 3.1 48.7 - - + +
201T GLN* 3.9 7.9 - - + +
202T VAL* 5.5 0.7 - - + -
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Residues in contact with SER 190 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186T ASN 2.8 24.0 + - - -
187T VAL* 3.2 11.8 + - - -
189T VAL* 1.3 79.0 - - - +
191T THR* 1.3 60.0 + - - +
193T ALA* 4.7 6.7 + - - +
200T VAL* 6.1 0.2 - - - -
201T GLN* 4.3 15.2 - - - +
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Residues in contact with THR 191 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187T VAL* 2.9 26.5 + - - +
188T ILE* 3.7 4.7 - - - -
189T VAL 3.0 0.8 - - - -
190T SER* 1.3 80.9 + - - +
192T TYR* 1.3 91.9 + - + +
193T ALA 3.8 1.1 - - - +
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Residues in contact with TYR 192 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140T GLU* 4.8 3.9 + - - -
144T ARG* 2.9 63.5 + - + +
147T LEU* 4.0 25.3 - - + +
148T GLY* 5.1 1.8 + - - +
188T ILE* 3.1 41.4 + - + +
191T THR* 1.3 100.5 - - + +
193T ALA* 1.3 63.6 + - - +
194T ASP* 3.6 8.5 + - - +
482T LYS* 3.3 17.1 - - + +
764T PRO* 6.6 0.2 - - + -
765T LEU* 4.8 4.7 - - - +
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Residues in contact with ALA 193 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147T LEU* 4.4 15.6 - - + +
189T VAL* 2.9 17.6 + - + +
190T SER* 4.8 6.1 - - - +
191T THR 3.8 1.6 - - - +
192T TYR* 1.3 77.4 - - - +
194T ASP* 1.3 67.0 + - - +
195T GLU* 3.3 8.3 + - - +
197T LEU* 5.4 3.8 - - + -
200T VAL* 3.2 35.9 - - + -
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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