Contacts of the helix formed by residues 159 - 179 (chain D) in PDB entry 7A62
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 CYS 159 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D GLY* 3.2 6.8 - - - -
158D ASP* 1.3 79.5 + - - +
160D SER* 1.3 60.6 + - - +
161D LYS* 3.3 3.1 - - - +
162D GLY 3.3 4.2 + - - +
163D PHE* 2.9 28.2 + - - +
220D HIS 3.9 8.7 - - - +
221D VAL* 3.9 20.6 - - + -
222D ASN* 3.5 42.4 - - - -
225D ALA* 3.7 9.9 - - + -
226D PHE* 5.1 0.4 - - - +
230D LEU* 4.2 1.1 - - + +
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D VAL* 4.7 0.4 - - - -
153D SER* 2.7 29.0 + - - -
154D PHE* 5.4 0.2 - - - -
158D ASP* 2.5 34.7 + - - -
159D CYS* 1.3 74.9 - - - +
161D LYS* 1.3 66.2 + - - +
164D PHE* 2.9 53.3 + - - -
230D LEU* 4.0 18.2 - - - -
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Residues in contact with LYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D LYS* 4.1 16.6 - - - +
145D TYR* 3.5 34.7 + - - +
146D GLU* 6.0 0.4 - - - +
148D MET 3.8 14.5 + - - -
149D ASP* 4.0 18.1 + - - +
150D VAL* 3.9 19.1 - - + +
153D SER* 4.7 1.5 + - - +
159D CYS 3.3 0.8 - - - -
160D SER* 1.3 80.3 + - - +
162D GLY* 1.3 64.1 + - - +
165D LEU* 3.1 45.0 + - + +
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Residues in contact with GLY 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D TYR* 3.8 6.6 + - - -
159D CYS* 3.3 5.8 + - - +
160D SER 3.2 0.4 - - - -
161D LYS* 1.3 79.0 - - - +
163D PHE* 1.3 61.1 + - - +
166D VAL* 3.1 30.5 + - - +
220D HIS* 3.6 36.0 + - - -
221D VAL* 3.6 6.6 - - - +
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D TYR* 6.1 0.4 - + - -
129D CYS* 5.6 1.3 - - - -
130D VAL* 4.9 5.4 - - + -
159D CYS 2.9 17.4 + - - +
160D SER 4.2 0.2 - - - +
162D GLY* 1.3 74.8 - - - +
164D PHE* 1.3 92.1 + + - +
166D VAL* 4.5 0.2 - - - +
167D SER* 3.0 38.6 + - - -
217D ILE* 4.4 2.9 - - + +
221D VAL* 3.4 13.0 - - + +
226D PHE* 3.9 19.5 - + + -
230D LEU* 3.6 18.6 - - + -
234D LEU* 4.1 15.5 - - + -
263D SER* 5.6 0.9 - - - -
264D ALA* 3.8 27.1 - - + -
504D HEM 3.3 44.4 - + + -
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Residues in contact with PHE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D CYS* 3.1 50.5 - - + +
130D VAL* 3.7 16.2 - - + +
133D ASN* 3.3 22.4 - - - +
150D VAL* 3.7 14.6 - - + -
152D PHE 4.1 7.2 - - - -
153D SER* 5.5 0.2 - - - -
154D PHE* 4.8 8.1 - + - -
160D SER* 2.9 39.7 + - - +
163D PHE* 1.3 101.7 - + - +
165D LEU* 1.3 60.1 + - + +
167D SER* 3.3 2.6 + - - -
168D LEU* 2.8 29.5 + - - +
230D LEU* 4.5 10.5 - - + -
234D LEU* 4.6 10.1 - - + -
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ASN 5.0 0.2 - - - +
134D TRP* 4.1 4.0 - - + -
145D TYR* 4.0 19.5 - - + +
148D MET* 3.8 41.1 - - + +
149D ASP* 3.8 22.2 - - - +
150D VAL* 3.8 12.6 - - + -
161D LYS* 3.1 35.9 + - + +
164D PHE* 1.3 79.9 - - + +
166D VAL* 1.3 53.6 + - - +
168D LEU* 3.4 24.5 - - + +
169D LEU* 2.6 42.6 + - + +
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Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D TYR* 4.2 9.6 - - + -
162D GLY 3.1 21.0 + - - +
165D LEU* 1.3 73.9 - - - +
167D SER* 1.3 65.7 + - - +
169D LEU* 3.2 6.1 + - + +
170D VAL* 3.0 27.3 + - + +
213D VAL* 4.2 16.6 - - + +
214D PHE* 4.5 4.5 - - + +
216D GLN* 4.0 26.7 - - + +
217D ILE* 3.8 35.4 - - + +
220D HIS* 4.2 13.2 - - + +
504D HEM 5.8 0.9 - - + -
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D TYR* 3.7 22.9 + - - -
130D VAL* 4.0 9.6 - - - -
163D PHE* 3.0 35.6 + - - -
164D PHE 3.5 3.1 - - - -
166D VAL* 1.3 77.5 - - - +
168D LEU* 1.3 63.4 + - - +
170D VAL* 3.2 4.5 + - - +
171D GLU* 3.1 24.6 + - - +
217D ILE* 5.5 0.2 - - - +
504D HEM 3.4 29.2 - - - +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA* 3.5 32.1 - - + -
130D VAL* 3.7 18.8 - - + +
131D LEU* 4.6 2.9 - - + -
134D TRP* 3.3 45.5 - - + +
148D MET* 3.5 23.1 - - + -
164D PHE 2.8 20.6 + - - +
165D LEU* 3.4 11.0 - - + +
167D SER* 1.3 74.0 - - - +
169D LEU* 1.3 60.6 + - - +
171D GLU* 3.1 7.3 + - + +
172D ILE* 3.0 32.1 + - + +
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU 3.8 17.0 - - - +
144D THR* 4.5 0.2 - - - -
145D TYR* 3.8 42.8 - - + +
148D MET* 3.8 27.6 - - + -
165D LEU* 2.6 23.5 + - + +
166D VAL* 3.2 8.5 + - - +
168D LEU* 1.3 73.8 - - - +
170D VAL* 1.3 56.3 + - - +
172D ILE* 3.5 15.1 + - + +
173D ALA* 3.0 26.3 + - - +
213D VAL* 3.7 18.2 - - + +
216D GLN* 4.1 13.9 - - - +
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D VAL* 3.0 18.2 + - + +
167D SER 3.5 7.9 - - - +
168D LEU 3.2 0.2 - - - -
169D LEU* 1.3 76.2 - - - +
171D GLU* 1.3 61.6 + - - +
173D ALA* 3.1 5.5 + - - +
174D ALA* 2.8 29.0 + - + +
210D ALA* 4.1 16.5 - - + +
213D VAL* 3.9 7.2 - - + -
214D PHE* 3.9 44.4 - - + +
269D VAL* 5.8 4.5 - - + -
270D PHE* 6.0 2.7 - - + -
342D LEU* 5.6 2.9 - - + -
504D HEM 3.6 30.5 - - + -
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Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL 4.1 5.2 - - - +
22D GLY* 4.8 1.9 - - - -
23D PHE* 3.7 21.0 + - - +
24D ALA* 4.8 8.1 - - + +
126D TYR* 2.7 33.8 + - - +
131D LEU* 3.9 18.2 - - + -
167D SER 3.1 9.0 + - - +
168D LEU* 3.3 8.5 - - - +
170D VAL* 1.3 76.5 - - - +
172D ILE* 1.3 62.5 + - - +
174D ALA* 3.1 8.9 + - - +
175D ALA* 3.0 19.6 + - - +
178D ILE* 5.0 1.0 - - - +
267D SER* 2.5 29.2 + - - -
268D SER 5.2 0.4 + - - -
269D VAL* 3.2 19.9 - - - +
504D HEM 3.8 3.9 - - + +
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Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU* 3.7 16.4 - - + +
21D VAL* 4.1 26.7 - - + +
134D TRP* 5.6 2.2 - - + -
143D LEU* 4.1 32.8 - - + +
148D MET* 4.3 15.0 - - + -
168D LEU* 3.0 38.7 + - + +
169D LEU* 3.7 17.7 - - + +
170D VAL 3.2 0.2 - - - -
171D GLU* 1.3 71.3 - - - +
173D ALA* 1.3 67.4 + - - +
175D ALA* 3.2 15.9 + - - +
176D SER* 4.0 5.2 + - - -
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LEU 3.0 14.4 + - - +
170D VAL* 3.4 8.1 - - - +
172D ILE* 1.3 78.5 - - - +
174D ALA* 1.3 62.4 + - - +
175D ALA 3.2 0.7 + - - -
176D SER* 3.3 20.2 + - - -
177D ALA 4.3 1.4 + - - -
206D CYS* 4.5 8.9 - - - +
209D LYS* 4.8 3.5 - - + +
210D ALA* 3.7 30.1 - - - +
213D VAL* 4.1 14.6 - - + -
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Residues in contact with ALA 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL* 2.8 13.8 + - + +
171D GLU 3.1 8.9 + - - +
173D ALA* 1.3 74.6 - - - +
175D ALA* 1.3 65.9 + - - +
177D ALA* 2.9 16.1 + - - +
178D ILE* 3.0 18.8 + - + +
206D CYS 5.7 0.2 - - - -
207D LEU* 5.0 9.6 - - + -
210D ALA* 4.4 7.5 - - + +
269D VAL* 3.7 37.5 - - + -
273D PHE* 4.6 3.3 - - + -
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Residues in contact with ALA 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASP 4.3 0.9 - - - +
19D GLU 3.9 7.1 - - - +
20D GLU 3.5 16.4 - - - +
21D VAL 3.6 2.7 - - - -
22D GLY* 3.3 32.8 - - - +
171D GLU 3.0 6.4 + - - +
172D ILE 3.3 12.8 - - - +
173D ALA 3.1 1.0 - - - -
174D ALA* 1.3 77.9 - - - +
176D SER* 1.3 61.1 + - - +
178D ILE* 3.7 12.3 - - - +
179D LYS* 3.1 27.2 + - - +
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Residues in contact with SER 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLU 5.2 0.4 - - - -
20D GLU 5.7 0.2 + - - -
172D ILE 4.2 5.2 + - - -
173D ALA* 3.3 11.6 + - - -
174D ALA 3.0 1.0 + - - -
175D ALA* 1.3 77.9 - - - +
177D ALA* 1.3 59.3 + - - +
179D LYS* 3.5 34.9 + - - +
180D VAL* 3.6 11.6 - - - +
202D GLU* 4.8 0.9 - - - +
206D CYS* 3.5 26.5 - - - -
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Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ALA 2.9 6.6 + - - +
176D SER* 1.3 78.1 - - - +
178D ILE* 1.3 64.6 + - - +
179D LYS 3.2 0.4 - - - -
180D VAL* 3.1 16.9 + - - +
181D ILE* 3.7 5.5 + - - +
203D ILE* 3.6 28.5 - - - +
206D CYS* 3.7 21.3 - - + +
207D LEU* 4.2 7.2 - - + -
273D PHE* 3.6 26.5 - - + -
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Residues in contact with ILE 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER* 5.7 1.7 + - - +
17D ILE* 3.8 33.9 - - + -
18D ASP 5.8 0.2 - - - +
22D GLY* 4.6 6.5 - - - -
23D PHE* 3.5 33.0 - - + -
171D GLU 5.0 0.7 - - - +
174D ALA* 3.0 34.3 + - + +
175D ALA* 3.8 10.5 - - - +
177D ALA* 1.3 76.6 - - - +
179D LYS* 1.3 59.3 + - - +
180D VAL 3.0 0.2 - - - -
181D ILE* 2.9 38.1 + - + +
182D PRO* 3.7 2.9 - - - +
269D VAL* 4.5 1.8 - - + -
272D CYS* 4.4 7.0 - - - -
273D PHE* 4.0 15.7 - - + -
306D PHE* 4.6 7.4 - - + -
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Residues in contact with LYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLY 3.8 25.2 + - - +
17D ILE* 6.4 0.2 - - - -
18D ASP 5.7 0.7 - - - +
19D GLU* 3.9 38.6 + - + +
175D ALA 3.1 9.4 + - - +
176D SER* 3.5 33.9 + - - +
178D ILE* 1.3 78.3 - - - +
180D VAL* 1.3 66.4 + - + +
181D ILE 3.3 0.2 - - - -
182D PRO* 3.4 13.8 - - - +
183D THR* 4.6 4.2 + - - -
202D GLU* 6.0 2.0 - - - -
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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