Contacts of the helix formed by residues 159 - 179 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY* 3.3 7.7 - - - -
158A ASP* 1.3 79.9 + - - +
160A SER* 1.3 63.4 + - - +
161A LYS* 3.3 3.1 - - - +
162A GLY 3.4 4.1 + - - +
163A PHE* 3.1 24.3 + - - +
220A HIS 4.2 11.7 - - - +
221A VAL* 4.3 15.3 - - + -
222A ASN* 3.6 27.1 - - - +
225A ALA* 3.9 18.6 - - + -
226A PHE 5.2 1.1 - - - +
230A LEU* 4.1 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 4.7 0.2 - - - -
153A SER* 2.6 31.7 + - - -
154A PHE* 5.0 0.7 - - - -
158A ASP* 2.5 36.7 + - - -
159A CYS* 1.3 69.1 - - - +
161A LYS* 1.3 60.1 + - - +
164A PHE* 2.9 59.0 + - - +
230A LEU* 4.0 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LYS* 4.3 13.3 - - - +
145A TYR* 3.7 27.3 + - - +
148A MET 3.9 15.0 + - - -
149A ASP* 3.7 24.1 + - - +
150A VAL* 3.9 20.3 - - + +
153A SER* 4.6 1.1 + - - +
159A CYS* 3.3 1.0 - - - +
160A SER* 1.3 81.1 + - - +
162A GLY* 1.3 57.7 + - - +
165A LEU* 2.9 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 3.9 7.0 + - - -
159A CYS* 3.4 5.6 + - - +
160A SER 3.2 0.4 - - - -
161A LYS* 1.3 80.0 - - - +
163A PHE* 1.3 62.2 + - - +
166A VAL* 3.0 30.4 + - - +
220A HIS* 3.5 34.4 + - - -
221A VAL* 3.5 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 5.8 1.1 - + - -
129A CYS* 5.9 1.1 - - - -
130A VAL* 5.1 4.9 - - + -
159A CYS 3.1 16.8 + - - +
160A SER 4.2 0.4 - - - +
162A GLY* 1.3 75.1 - - - +
164A PHE* 1.3 86.3 + + - +
166A VAL* 4.1 1.5 - - - +
167A SER* 2.9 42.3 + - - -
217A ILE* 4.7 4.9 - - + -
221A VAL* 3.4 14.5 - - + +
226A PHE* 4.2 11.4 - + + -
230A LEU* 3.7 22.0 - - + -
234A LEU* 4.0 19.3 - - + -
263A SER 5.9 0.7 - - - -
264A ALA* 4.0 26.2 - - + -
502A HEM 3.5 44.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A CYS* 6.6 0.2 - - - -
129A CYS* 3.1 55.2 - - + +
130A VAL* 3.4 18.6 - - + +
133A ASN* 3.4 17.5 - - - +
150A VAL* 3.8 15.0 - - + -
152A PHE 4.2 6.3 - - - -
154A PHE* 4.7 8.7 - + - -
160A SER* 2.9 41.3 + - - +
163A PHE* 1.3 99.9 - + - +
165A LEU* 1.3 58.1 + - - +
167A SER* 3.5 2.4 - - - -
168A LEU* 2.8 29.5 + - - +
230A LEU* 4.6 5.2 - - + -
234A LEU* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 4.3 2.7 - - + -
145A TYR* 3.9 23.6 - - + +
148A MET* 3.9 42.4 - - + +
149A ASP* 4.0 9.9 - - - +
150A VAL* 4.0 16.6 - - + -
161A LYS* 2.9 43.7 + - + +
164A PHE* 1.3 78.4 - - - +
166A VAL* 1.3 58.7 + - - +
168A LEU* 3.4 24.8 - - + +
169A LEU* 2.7 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 4.5 7.0 - - + -
162A GLY 3.0 23.2 + - - +
163A PHE 4.3 0.9 - - - +
165A LEU* 1.3 73.5 - - - +
167A SER* 1.3 67.8 + - - +
169A LEU* 3.1 7.2 + - + +
170A VAL* 3.0 26.8 + - + +
213A VAL* 4.2 15.0 - - + +
214A PHE* 4.5 6.1 - - + +
216A GLN* 4.1 25.4 - - + +
217A ILE* 3.8 35.7 - - + +
220A HIS* 4.1 16.8 - - + -
502A HEM 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 3.6 23.2 + - - -
130A VAL* 4.0 9.9 - - - -
163A PHE* 2.9 35.9 + - - -
164A PHE 3.5 3.6 - - - -
166A VAL* 1.3 77.5 - - - +
168A LEU* 1.3 62.2 + - - +
170A VAL* 3.3 4.7 + - - +
171A GLU* 3.1 24.1 + - - +
217A ILE* 6.0 0.3 - - - +
502A HEM 3.2 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.7 29.4 - - + -
130A VAL* 3.8 18.3 - - + +
131A LEU* 4.8 1.6 - - - -
134A TRP* 3.4 45.1 - - + +
148A MET* 3.6 23.1 - - + -
164A PHE 2.8 20.9 + - - +
165A LEU* 3.4 11.7 - - + +
167A SER* 1.3 74.2 - - - +
169A LEU* 1.3 58.2 + - - +
171A GLU* 3.0 9.5 + - + +
172A ILE* 2.9 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU 3.8 23.1 - - - +
144A THR* 4.6 0.7 - - - -
145A TYR* 4.0 30.7 - - + +
148A MET* 3.9 21.8 - - + -
165A LEU* 2.7 26.6 + - + +
166A VAL* 3.1 7.4 + - - +
168A LEU* 1.3 72.3 - - - +
170A VAL* 1.3 57.3 + - - +
172A ILE* 3.4 16.9 + - + +
173A ALA* 2.9 26.3 + - - +
213A VAL* 3.6 16.6 - - + +
216A GLN* 3.9 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 3.0 17.1 + - + +
167A SER* 3.5 8.5 - - - +
168A LEU 3.1 0.2 - - - -
169A LEU* 1.3 75.2 - - - +
171A GLU* 1.3 59.3 + - - +
173A ALA* 3.1 5.2 + - - +
174A ALA* 2.9 29.5 + - + +
210A ALA* 4.6 14.9 - - + +
213A VAL* 3.8 17.9 - - + +
214A PHE* 4.0 33.4 - - + +
269A VAL* 5.7 5.6 - - + -
270A PHE* 6.2 2.2 - - + -
342A LEU* 5.7 3.6 - - + -
502A HEM 3.4 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL 3.8 8.9 - - - +
22A GLY* 4.8 1.6 - - - -
23A PHE* 3.6 22.4 + - - +
24A ALA* 4.7 9.2 - - + -
126A TYR* 3.1 24.6 + - - +
131A LEU* 3.9 20.0 - - + -
167A SER 3.1 15.4 + - - +
168A LEU* 3.0 10.0 + - - +
170A VAL* 1.3 74.6 - - - +
172A ILE* 1.3 62.4 + - - +
174A ALA* 3.3 7.2 + - - +
175A ALA* 3.1 17.5 + - - +
178A ILE* 5.2 0.7 - - - +
267A SER* 2.6 28.1 + - - -
268A SER 4.6 0.8 + - - -
269A VAL* 3.3 18.6 - - - +
502A HEM 4.5 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 3.9 13.2 - - - +
21A VAL* 4.1 25.4 - - + +
134A TRP* 5.8 1.3 - - + -
143A LEU* 4.1 29.4 - - + +
148A MET* 4.1 18.4 - - + -
168A LEU* 2.9 39.2 + - + +
169A LEU* 3.6 20.6 - - + +
170A VAL 3.2 0.2 - - - -
171A GLU* 1.3 71.9 - - - +
173A ALA* 1.3 66.4 + - - +
175A ALA* 3.2 17.4 + - - +
176A SER* 3.9 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU 2.9 15.9 + - - +
170A VAL* 3.5 7.9 - - - +
172A ILE* 1.3 77.7 - - - +
174A ALA* 1.3 61.7 + - - +
176A SER* 3.2 21.0 + - - -
177A ALA 4.1 1.2 + - - -
206A CYS* 4.5 7.8 - - - +
209A LYS* 4.7 2.5 - - + +
210A ALA* 3.7 28.7 - - - +
213A VAL* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 2.9 16.5 + - + +
171A GLU 3.7 5.4 - - - +
173A ALA* 1.3 75.0 - - - +
175A ALA* 1.3 66.3 + - - +
177A ALA* 2.8 19.7 + - - +
178A ILE* 2.9 20.0 + - + +
206A CYS 5.6 0.4 - - - -
207A LEU* 5.2 4.0 - - + -
210A ALA* 4.4 9.6 - - + +
269A VAL* 3.9 36.3 - - + -
273A PHE* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP 4.3 1.1 - - - +
19A GLU 4.0 7.3 - - - +
20A GLU 3.4 15.5 - - - +
21A VAL 3.6 2.0 - - - -
22A GLY* 3.4 32.8 - - - +
171A GLU 3.1 7.0 + - - +
172A ILE 3.3 13.7 - - - +
173A ALA 3.2 0.4 - - - -
174A ALA* 1.3 76.2 - - - +
176A SER* 1.3 56.7 + - - +
178A ILE* 3.7 13.4 - - - +
179A LYS* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 5.3 0.2 - - - -
172A ILE 3.9 3.0 + - - -
173A ALA* 3.2 14.0 + - - -
174A ALA 3.0 0.8 - - - -
175A ALA* 1.3 78.7 - - - +
177A ALA* 1.3 58.4 + - - +
179A LYS* 3.6 35.7 + - - +
180A VAL* 3.7 9.2 - - - +
202A GLU* 4.9 2.6 + - - +
206A CYS* 3.7 25.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 2.8 9.6 + - - +
176A SER* 1.3 77.2 - - - +
178A ILE* 1.3 66.4 + - - +
179A LYS 3.2 1.6 - - - -
180A VAL* 3.0 18.8 + - - +
181A ILE* 3.8 4.0 + - - +
203A ILE* 3.7 26.6 - - - +
206A CYS* 3.8 21.3 - - + +
207A LEU* 4.3 9.0 - - + -
273A PHE* 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER 6.1 0.4 - - - +
17A ILE* 3.8 26.9 - - + -
18A ASP 6.1 0.2 - - - +
22A GLY* 4.6 7.4 - - - -
23A PHE* 3.5 35.9 - - + +
171A GLU 5.2 1.1 - - - +
174A ALA* 2.9 32.9 + - + +
175A ALA* 3.2 12.1 + - - +
177A ALA* 1.3 75.5 - - - +
179A LYS* 1.3 57.5 + - - +
181A ILE* 2.9 39.3 + - + +
182A PRO* 3.8 3.1 - - - +
269A VAL* 4.8 1.6 - - + -
272A CYS* 4.5 3.6 - - - -
273A PHE* 4.0 15.7 - - + -
306A PHE* 4.6 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 6.3 0.4 - - - -
19A GLU* 3.8 52.4 + - + +
175A ALA 3.0 10.7 + - - +
176A SER* 3.6 36.3 + - - +
178A ILE* 1.3 76.8 - - - +
180A VAL* 1.3 64.3 + - + +
181A ILE 3.4 0.4 - - - -
182A PRO* 3.7 12.6 - - - +
183A THR* 4.6 4.2 + - - -
202A GLU* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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