Contacts of the helix formed by residues 162 - 182 (chain X) in PDB entry 3G90
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 162 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X GLU 4.3 0.2 + - - -
161X LEU* 1.3 78.8 - - - +
163X HIS* 1.3 58.0 + - - +
164X GLU* 3.1 23.6 + - - +
165X ARG* 2.5 63.7 + - - +
166X MET* 3.0 24.5 + - - +
319X PRO* 4.5 7.2 - - - -
325X ASN* 6.0 1.1 - - - +
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Residues in contact with HIS 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161X LEU 5.6 0.2 + - - -
162X ASP* 1.3 71.8 - - - +
164X GLU* 1.3 62.6 + - - +
166X MET* 4.5 4.9 - - + +
167X SER* 2.7 40.8 + - - -
318X PHE* 4.1 16.4 - + - -
319X PRO* 3.2 38.3 + - + +
324X HIS* 5.0 0.2 - - + -
325X ASN* 3.5 33.0 + - - +
328X LYS* 3.3 32.7 - - + +
329X ALA* 3.5 21.7 + - - -
332X ALA* 4.6 0.7 - - + -
358X TYR* 2.7 28.9 + + + +
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Residues in contact with GLU 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162X ASP* 3.1 16.2 + - - +
163X HIS* 1.3 84.8 + - - +
165X ARG* 1.3 59.5 + - + +
167X SER* 3.3 6.0 + - - -
168X TYR* 3.1 29.3 + - - +
324X HIS* 2.9 38.5 + - - -
325X ASN* 5.0 2.1 - - - +
328X LYS* 4.9 3.8 - - - +
362X TRP* 3.3 22.3 - - + -
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Residues in contact with ARG 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161X LEU* 4.2 23.6 - - + -
162X ASP* 2.5 50.2 + - - +
164X GLU* 1.3 74.9 - - + +
166X MET* 1.3 66.9 + - - +
168X TYR* 3.2 1.7 + - - +
169X LEU* 3.0 31.0 + - - +
199X SER 5.6 3.4 + - - -
201X CYS* 3.8 29.6 - - - +
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Residues in contact with MET 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161X LEU* 4.2 31.2 - - + +
162X ASP 3.0 15.6 + - - +
163X HIS* 4.5 3.6 - - + +
165X ARG* 1.3 76.7 - - - +
167X SER* 1.3 61.8 + - - +
169X LEU* 3.7 4.1 - - - +
170X LEU* 3.2 37.1 + - + +
253X MET* 4.8 5.8 - - - +
256X MET* 3.5 45.0 - - + +
257X VAL* 4.0 28.3 - - + -
318X PHE* 5.8 3.1 - - + -
319X PRO* 6.0 3.6 - - + -
332X ALA* 5.7 1.8 - - - -
358X TYR* 3.9 18.2 - - - +
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Residues in contact with SER 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163X HIS 2.7 24.1 + - - -
164X GLU* 3.3 4.3 + - - -
166X MET* 1.3 77.5 - - - +
168X TYR* 1.3 56.0 + - - +
170X LEU* 3.6 3.5 + - - -
171X TYR* 2.8 29.1 + - - +
328X LYS* 6.3 0.2 - - - -
358X TYR* 3.3 46.9 + - - -
359X ILE* 3.6 5.8 - - - +
361X VAL* 5.0 1.2 - - - +
362X TRP* 2.9 19.6 + - - -
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Residues in contact with TYR 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X LYS* 5.9 2.8 - - - +
164X GLU 3.1 21.3 + - - +
165X ARG* 3.2 5.3 + - - +
167X SER* 1.3 73.6 + - - +
169X LEU* 1.3 65.1 + - - +
171X TYR* 3.3 21.8 + + - +
172X GLN* 3.0 63.2 + - + +
200X ASP 5.0 1.8 - - - -
201X CYS* 3.7 29.8 - - + -
202X THR* 4.6 10.6 - - + +
362X TRP* 3.6 42.6 - + + +
367X GLU* 5.4 4.4 + - - -
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Residues in contact with LEU 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LEU* 4.9 3.4 - - + -
156X VAL* 4.0 13.2 - - + -
161X LEU* 3.8 19.5 - - + -
165X ARG 3.0 20.1 + - - +
166X MET 3.7 3.1 - - - +
168X TYR* 1.3 74.8 - - - +
170X LEU* 1.3 59.0 + - - +
172X GLN* 3.2 7.9 + - - +
173X MET* 3.0 38.6 + - + +
197X VAL* 3.9 19.7 - - + -
201X CYS* 3.7 29.4 - - - +
203X LEU* 3.6 25.5 - - + +
256X MET* 3.7 23.3 - - + -
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Residues in contact with LEU 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166X MET* 3.2 32.8 + - + +
167X SER 3.6 4.3 - - - +
169X LEU* 1.3 79.4 - - - +
171X TYR* 1.3 61.9 + - - +
173X MET* 3.6 28.8 - - + +
174X LEU* 3.1 31.8 + - + +
249X VAL* 4.5 11.1 - - + +
253X MET* 3.8 53.8 - - + +
256X MET* 4.2 11.7 - - + -
335X LEU* 5.3 2.2 - - + -
339X MET* 6.2 0.7 - - + -
358X TYR* 4.2 9.2 - - + -
359X ILE* 3.9 10.5 - - + -
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Residues in contact with TYR 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X ASN* 5.8 0.4 - - - -
167X SER 2.8 20.9 + - - +
168X TYR* 3.3 22.6 + + - +
170X LEU* 1.3 72.4 - - - +
172X GLN* 1.3 63.3 + - + +
174X LEU* 3.2 6.3 + - - +
175X CYS* 2.9 46.2 + - - -
354X LEU* 3.8 11.9 - - + -
359X ILE* 3.8 30.2 - - + +
362X TRP* 3.3 34.8 - - + -
363X TYR* 3.7 18.8 - - + -
364X ASP* 2.9 19.8 + - - +
367X GLU* 2.6 37.5 + - - +
368X VAL* 3.9 3.1 - - + +
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Residues in contact with GLN 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X LYS* 5.8 1.3 - - + +
122X ASN* 3.3 32.5 + - - +
168X TYR* 3.0 57.4 + - + +
169X LEU* 3.6 5.2 - - - +
171X TYR* 1.3 78.2 - - + +
173X MET* 1.3 55.8 + - - +
174X LEU 3.2 1.3 - - - -
175X CYS* 3.1 8.9 + - - +
176X GLY 2.8 30.8 + - - -
201X CYS 3.1 23.4 + - - -
202X THR* 3.5 9.4 - - - +
203X LEU* 2.9 36.5 + - + +
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Residues in contact with MET 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153X LEU* 3.7 25.4 - - + -
169X LEU* 3.0 21.4 + - + +
170X LEU* 3.6 34.3 - - + +
172X GLN* 1.3 73.9 - - - +
174X LEU* 1.3 60.6 + - - +
176X GLY* 4.0 0.5 - - - -
177X ILE* 3.1 40.5 + - + +
190X LEU* 5.2 0.7 - - + -
195X ILE* 4.3 20.0 - - + -
203X LEU* 3.7 35.7 - - + +
205X ILE* 4.1 7.4 - - + +
249X VAL* 4.6 14.8 - - + -
252X ILE* 4.3 14.8 - - + -
256X MET* 4.5 3.4 - - - -
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Residues in contact with LEU 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X LEU* 3.1 18.4 + - + +
171X TYR 3.4 7.0 - - - +
172X GLN 3.2 0.2 - - - -
173X MET* 1.3 79.5 - - - +
175X CYS* 1.3 57.5 + - - +
177X ILE* 3.8 4.6 - - + +
178X LYS* 3.0 30.3 + - - +
246X ILE* 3.7 30.7 - - + -
249X VAL* 4.9 12.1 - - + -
339X MET* 4.0 13.7 - - + -
350X VAL* 3.7 18.1 - - + +
353X ALA* 4.0 30.7 - - + +
354X LEU* 3.6 14.0 - - + +
359X ILE* 4.1 23.6 - - + -
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Residues in contact with CYS 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X HIS* 3.9 10.7 + - - +
122X ASN* 3.4 15.7 - - - +
171X TYR* 2.9 54.5 + - - +
172X GLN 3.1 8.7 + - - +
174X LEU* 1.3 73.7 - - - +
176X GLY* 1.3 64.3 + - - +
178X LYS* 3.3 5.5 + - - +
179X HIS* 3.1 24.9 + - - +
354X LEU* 4.5 1.3 - - - -
367X GLU* 4.0 14.8 - - - +
368X VAL* 3.8 17.4 - - - +
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Residues in contact with GLY 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X HIS* 4.3 4.3 - - - -
122X ASN* 3.9 16.5 - - - +
123X ILE* 3.6 27.1 - - - +
172X GLN 2.8 18.3 + - - -
173X MET 4.0 1.3 - - - -
175X CYS* 1.3 73.6 - - - +
177X ILE* 1.3 60.9 + - - +
179X HIS* 3.5 2.8 + - - +
180X LEU* 3.2 18.1 + - - +
205X ILE* 4.2 6.1 - - - -
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Residues in contact with ILE 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173X MET 3.1 21.1 + - - +
174X LEU* 3.8 6.7 - - + +
176X GLY* 1.3 73.7 - - - +
178X LYS* 1.3 60.3 + - - +
180X LEU* 3.3 11.7 + - + +
181X HIS* 3.0 58.6 + - + +
187X HIS* 5.7 0.4 - - + -
190X LEU* 3.3 44.0 - - + -
205X ILE* 4.3 7.6 - - + +
245X ASP* 4.1 10.5 - - + +
246X ILE* 6.1 0.7 - - + -
249X VAL* 3.6 20.2 - - + -
350X VAL* 4.0 12.8 - - + -
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Residues in contact with LYS 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174X LEU 3.0 20.5 + - - +
175X CYS* 3.3 6.0 + - - +
177X ILE* 1.3 72.9 - - - +
179X HIS* 1.3 66.0 + - - +
181X HIS* 3.2 17.7 + - + +
182X SER* 3.2 18.9 + - - -
350X VAL* 3.8 19.7 - - + -
351X ASP* 3.2 30.4 + - - +
354X LEU* 4.0 6.1 - - + -
368X VAL* 3.2 48.1 + - + +
369X GLU* 4.3 13.9 - - - +
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Residues in contact with HIS 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X VAL* 4.2 13.1 - - + +
119X ASN 4.6 8.7 + - - -
120X HIS* 3.5 42.5 + - + +
123X ILE* 5.5 0.2 - - + -
175X CYS 3.1 16.5 + - - +
176X GLY 3.6 4.9 - - - +
178X LYS* 1.3 77.7 - - - +
180X LEU* 1.3 63.0 + - + +
182X SER* 2.8 22.3 + - - -
183X ALA* 3.5 8.3 + - - +
368X VAL 5.4 2.4 + - - -
370X ALA* 3.6 26.4 + - + +
371X PRO 3.2 26.5 - - - -
373X PRO* 3.6 27.5 - - + +
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Residues in contact with LEU 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X VAL* 4.7 9.0 - - + -
123X ILE* 3.7 32.3 - - + -
176X GLY 3.2 10.7 + - - +
177X ILE* 3.4 15.7 - - + +
179X HIS* 1.3 83.5 - - + +
181X HIS* 1.3 60.1 + - + +
183X ALA* 3.1 9.9 + - + +
185X ILE* 2.8 61.4 + - + +
187X HIS* 4.3 29.2 - - + -
205X ILE* 5.5 2.7 - - + -
207X ASP 5.0 1.3 - - - +
208X PHE* 4.2 23.8 - - + -
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Residues in contact with HIS 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177X ILE* 3.0 41.6 + - + +
178X LYS* 3.2 10.8 + - + +
180X LEU* 1.3 75.7 - - + +
182X SER* 1.3 57.6 + - - +
183X ALA 3.1 0.4 - - - -
184X GLY* 3.0 19.1 + - - -
185X ILE 3.2 20.9 - - - +
186X ILE* 4.0 11.0 - - + +
187X HIS* 6.0 0.4 - - + -
242X GLU* 3.1 58.3 + - - +
245X ASP* 3.0 23.6 + - + -
350X VAL* 3.7 16.8 - - + +
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Residues in contact with SER 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178X LYS* 3.2 14.9 + - - -
179X HIS* 2.8 25.3 + - - -
181X HIS* 1.3 76.2 - - - +
183X ALA* 1.3 56.3 + - - +
184X GLY 3.3 1.6 - - - -
370X ALA 4.8 2.4 + - - -
372X PRO* 3.5 33.7 - - - +
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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