Contacts of the helix formed by residues 159 - 179 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLY* 3.3 7.3 - - - -
158B ASP* 1.3 80.2 + - - +
160B SER* 1.3 60.2 + - - +
161B LYS* 3.3 3.4 - - - +
162B GLY 3.4 3.5 + - - +
163B PHE* 3.0 28.4 + - - +
220B HIS 4.0 15.7 - - - +
221B VAL* 4.3 12.6 - - + -
222B ASN* 3.7 27.6 - - - +
225B ALA* 4.1 17.0 - - + -
226B PHE* 5.2 1.1 - - - +
230B LEU* 4.1 1.4 - - + +
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 4.8 0.2 - - - -
153B SER* 2.5 34.0 + - - -
154B PHE* 5.0 0.4 - - - -
158B ASP* 2.6 35.0 + - - -
159B CYS* 1.3 69.2 - - - +
161B LYS* 1.3 66.3 + - - +
164B PHE* 2.9 54.0 + - - -
230B LEU* 4.1 16.6 - - - -
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Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LYS* 4.1 16.0 - - - +
145B TYR* 3.8 26.1 + - - +
146B GLU* 6.2 0.2 - - - +
148B MET 3.7 23.4 + - - -
149B ASP* 3.7 22.2 + - - +
150B VAL* 3.9 18.8 - - + +
153B SER* 5.4 0.9 - - - +
159B CYS* 3.3 1.3 - - - +
160B SER* 1.3 81.9 + - - +
162B GLY* 1.3 61.8 + - - +
165B LEU* 3.0 44.8 + - + +
501B GOL 4.2 23.8 + - - +
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TYR* 3.7 14.7 + - - -
159B CYS* 3.4 5.6 + - - +
160B SER 3.2 0.4 - - - -
161B LYS* 1.3 77.3 - - - +
163B PHE* 1.3 65.6 + - - +
166B VAL* 3.1 29.7 + - - +
220B HIS* 3.6 25.9 + - - -
221B VAL* 3.5 5.8 - - - -
501B GOL 5.1 2.0 + - - -
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 5.9 1.3 - + - -
129B CYS* 5.8 1.1 - - - -
130B VAL* 5.1 4.5 - - + -
159B CYS 3.0 17.1 + - - +
160B SER 4.2 0.4 - - - +
162B GLY* 1.3 75.3 - - - +
164B PHE* 1.3 88.2 + + - +
166B VAL* 4.1 1.8 - - - +
167B SER* 3.0 42.5 + - - -
217B ILE* 5.0 5.1 - - + +
221B VAL* 3.4 14.3 - - + +
226B PHE* 3.9 13.0 - + - -
230B LEU* 3.6 23.3 - - + -
234B LEU* 4.1 15.5 - - + -
263B SER 5.9 0.7 - - - -
264B ALA* 4.1 26.0 - - + -
503B HEM 3.5 45.3 - + + -
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B CYS* 3.1 54.1 - - + +
130B VAL* 3.6 19.6 - - + +
133B ASN* 3.4 16.8 - - - +
150B VAL* 3.8 15.0 - - + -
152B PHE 4.1 6.1 - - - -
154B PHE* 4.8 9.0 - + - -
160B SER* 2.9 42.2 + - - +
163B PHE* 1.3 99.7 - + - +
165B LEU* 1.3 59.4 + - - +
167B SER* 3.4 2.4 + - - -
168B LEU* 2.8 28.6 + - - +
230B LEU* 4.5 6.1 - - + -
234B LEU* 4.5 15.0 - - + -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TRP* 4.2 4.9 - - + -
145B TYR* 3.7 22.9 - - + +
148B MET* 3.8 41.5 - - + +
149B ASP* 3.9 12.6 - - - +
150B VAL* 3.9 17.3 - - + -
161B LYS* 3.0 42.3 + - + +
164B PHE* 1.3 79.2 - - - +
166B VAL* 1.3 58.0 + - - +
168B LEU* 3.2 24.7 + - + +
169B LEU* 2.7 34.3 + - + +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TYR* 4.5 6.5 - - + -
162B GLY 3.1 18.6 + - - +
163B PHE 4.3 1.3 - - - +
165B LEU* 1.3 73.5 - - - +
167B SER* 1.3 66.7 + - - +
169B LEU* 3.2 7.5 + - + +
170B VAL* 3.0 27.2 + - + +
213B VAL* 4.3 14.8 - - + +
214B PHE* 4.4 5.6 - - + +
216B GLN* 4.0 25.6 - - + +
217B ILE* 3.8 35.7 - - + +
220B HIS* 4.2 17.0 - - + -
503B HEM 5.7 1.1 - - + -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 3.6 21.4 + - - -
130B VAL* 4.0 12.6 - - - -
163B PHE* 3.0 35.1 + - - -
164B PHE 3.6 3.6 - - - -
166B VAL* 1.3 77.1 - - - +
168B LEU* 1.3 61.9 + - - +
170B VAL* 3.3 5.1 + - - +
171B GLU* 3.1 23.9 + - - +
503B HEM 3.3 29.5 - - - +
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Residues in contact with LEU 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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24B ALA* 3.6 31.0 - - + -
130B VAL* 3.8 19.0 - - + +
131B LEU* 4.7 0.4 - - - -
134B TRP* 3.4 45.1 - - + +
148B MET* 3.5 22.9 - - + -
164B PHE 2.8 17.7 + - - +
165B LEU* 3.4 10.8 - - + +
166B VAL 3.1 0.2 - - - -
167B SER* 1.3 77.6 - - - +
169B LEU* 1.3 58.0 + - - +
171B GLU* 2.9 9.9 + - + +
172B ILE* 2.9 35.3 + - + +
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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
----------------------------------------------------------
143B LEU 3.6 24.9 - - - +
144B THR* 4.4 1.1 - - - -
145B TYR* 4.0 35.4 - - + +
148B MET* 4.0 20.0 - - + -
165B LEU* 2.7 24.5 + - + +
166B VAL* 3.2 6.2 + - - +
168B LEU* 1.3 72.4 - - - +
170B VAL* 1.3 57.9 + - - +
172B ILE* 3.7 17.6 - - + +
173B ALA* 2.9 27.2 + - - +
213B VAL* 3.7 17.0 - - + +
216B GLN* 4.2 19.7 - - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B VAL* 3.0 18.9 + - + +
167B SER* 3.5 8.5 - - - +
168B LEU 3.1 0.2 - - - -
169B LEU* 1.3 74.5 - - - +
171B GLU* 1.3 59.2 + - - +
173B ALA* 3.1 5.5 + - - +
174B ALA* 2.8 28.5 + - + +
210B ALA* 4.4 16.2 - - + +
213B VAL* 4.0 10.5 - - + -
214B PHE* 4.0 41.1 - - + +
269B VAL* 5.8 5.6 - - + -
270B PHE* 6.1 2.9 - - + -
342B LEU* 5.6 3.6 - - + -
503B HEM 3.6 24.5 - - + -
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Residues in contact with GLU 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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21B VAL 3.9 10.5 - - - +
22B GLY* 4.8 1.9 - - - -
23B PHE* 3.7 21.8 + - - +
24B ALA* 4.7 3.6 - - + -
126B TYR* 3.1 25.5 + - - +
131B LEU* 3.9 17.9 - - + -
167B SER 3.1 16.3 + - - +
168B LEU* 2.9 9.8 + - - +
170B VAL* 1.3 75.3 - - - +
172B ILE* 1.3 61.4 + - - +
174B ALA* 3.2 7.5 + - - +
175B ALA* 3.1 20.4 + - - +
178B ILE* 5.1 0.9 - - - +
267B SER* 2.5 27.7 + - - -
268B SER 4.6 0.8 + - - -
269B VAL* 3.2 21.4 - - - +
503B HEM 4.4 3.5 - - + +
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Residues in contact with ILE 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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20B GLU 3.9 12.1 - - - +
21B VAL* 3.6 35.9 - - + +
134B TRP* 5.6 0.7 - - + -
143B LEU* 3.9 33.2 - - + +
148B MET* 4.3 10.5 - - + -
168B LEU* 2.9 35.0 + - + +
169B LEU* 3.7 17.7 - - + +
171B GLU* 1.3 73.2 - - - +
173B ALA* 1.3 66.6 + - - +
175B ALA* 3.2 17.2 + - - +
176B SER* 4.0 2.8 + - - -
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Residues in contact with ALA 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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169B LEU 2.9 15.9 + - - +
170B VAL* 3.5 8.3 - - - +
172B ILE* 1.3 77.5 - - - +
174B ALA* 1.3 59.2 + - - +
175B ALA 3.2 0.3 + - - -
176B SER* 2.9 26.7 + - - -
177B ALA 4.2 0.7 + - - -
206B CYS 4.4 6.2 - - - +
209B LYS* 4.7 7.2 - - + +
210B ALA* 3.7 30.3 - - + +
213B VAL* 4.1 13.9 - - + -
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Residues in contact with ALA 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 VAL* 2.8 13.3 + - + +
171B GLU 3.2 8.3 + - - +
173B ALA* 1.3 77.5 - - - +
175B ALA* 1.3 62.8 + - - +
177B ALA* 2.9 10.7 + - - +
178B ILE* 2.9 28.3 + - + +
206B CYS 5.6 0.4 - - - -
207B LEU* 5.1 6.5 - - + -
210B ALA* 4.4 7.5 - - + +
269B VAL* 3.8 36.6 - - + -
273B PHE* 4.5 4.2 - - + -
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Residues in contact with ALA 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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18B ASP 4.4 0.9 - - - +
19B GLU 4.0 7.6 - - - +
20B GLU 3.4 15.3 - - - +
21B VAL 3.6 2.2 - - - -
22B GLY* 3.3 33.4 - - - +
171B GLU 3.1 7.1 + - - +
172B ILE 3.3 13.7 - - - +
173B ALA 3.1 0.6 - - - -
174B ALA* 1.3 77.8 - - - +
176B SER* 1.3 60.8 + - - +
178B ILE* 3.1 12.6 + - - +
179B LYS* 3.0 26.5 + - - +
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU 5.2 0.9 - - - -
172B ILE 4.0 2.5 + - - -
173B ALA* 2.9 18.0 + - - -
175B ALA* 1.3 78.0 - - - +
177B ALA* 1.3 60.5 + - - +
179B LYS* 3.6 27.9 - - - +
180B VAL* 3.6 18.2 - - - +
202B GLU* 5.0 0.9 - - - +
206B CYS* 3.5 26.6 - - - +
209B LYS* 6.1 1.2 - - - +
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Residues in contact with ALA 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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174B ALA* 2.9 9.0 + - - +
176B SER* 1.3 81.2 + - - +
178B ILE* 1.3 64.4 + - - +
179B LYS 3.2 0.7 - - - -
180B VAL* 3.1 18.8 + - - +
181B ILE* 3.8 4.3 + - - +
203B ILE* 3.6 28.5 - - + +
206B CYS* 3.7 21.7 - - + +
207B LEU* 4.4 9.2 - - + -
273B PHE* 3.7 20.4 - - + -
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 4.0 4.9 + - - +
17B ILE* 3.8 33.2 - - + -
22B GLY* 4.6 6.7 - - - -
23B PHE* 3.6 32.5 - - + +
171B GLU 5.1 0.4 - - - +
174B ALA* 2.9 34.5 + - + +
175B ALA* 3.1 11.8 + - - +
177B ALA* 1.3 77.0 - - - +
179B LYS* 1.3 60.7 + - - +
180B VAL 3.0 2.0 + - - -
181B ILE* 3.1 32.7 + - + +
182B PRO* 3.8 3.1 - - - +
269B VAL* 4.8 0.4 - - + -
272B CYS* 4.5 4.7 - - - -
273B PHE* 3.8 18.4 - - + -
306B PHE* 4.6 7.0 - - + -
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 4.9 4.0 - - - +
12B SER* 5.0 6.1 - - - +
17B ILE* 6.4 0.4 - - - -
19B GLU* 3.7 52.7 + - + +
175B ALA 3.0 11.3 + - - +
176B SER* 3.6 32.4 - - - +
178B ILE* 1.3 77.2 - - - +
180B VAL* 1.3 66.3 + - + +
181B ILE 3.4 0.7 - - - -
182B PRO* 3.6 12.1 - - - +
183B THR* 4.6 3.8 + - - -
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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
------------------------------------------------------------
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