Contacts of the helix formed by residues 168 - 181 (chain A) in PDB entry 5Y7G
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 168 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 4.8 14.0 - - + -
63A LEU* 6.5 0.2 - - + -
98A GLY 5.7 0.2 - - - -
99A TRP* 3.2 52.4 + - + +
166A LEU* 3.5 7.4 - - + +
167A ARG* 1.3 79.8 - - - +
169A MET* 1.3 63.7 + - - +
170A ALA* 3.0 5.7 + - - -
171A LEU* 3.1 24.6 + - + +
172A CYS* 3.7 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET 5.1 0.2 - - - +
67A VAL* 4.0 35.9 - - + +
69A ARG 5.7 1.1 - - - +
70A LYS 5.6 2.5 - - - +
71A GLY 4.7 15.7 - - - +
72A THR* 5.1 9.2 - - - -
166A LEU* 3.7 39.1 - - + +
167A ARG 3.5 2.4 - - - -
168A CYS* 1.3 76.1 - - - +
170A ALA* 1.3 62.4 + - - +
172A CYS* 3.0 10.3 + - - +
173A ASP* 3.0 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG 5.2 1.3 + - - +
168A CYS 3.0 2.1 + - - +
169A MET* 1.3 79.4 - - - +
171A LEU* 1.3 63.7 + - - +
173A ASP* 3.4 6.2 + - - +
174A ARG* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLN* 4.7 3.1 - - + +
45A GLU* 3.3 41.3 - - + +
48A PHE* 3.5 42.2 - - + -
168A CYS* 3.1 18.1 + - + +
170A ALA* 1.3 77.7 - - - +
172A CYS* 1.3 59.3 + - - +
174A ARG* 3.0 23.4 + - + +
175A LEU* 2.9 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.7 17.3 - - - -
48A PHE* 4.8 16.8 - - - -
63A LEU* 5.4 2.7 - - - -
67A VAL* 3.8 43.5 - - + -
166A LEU* 6.2 0.9 - - - -
168A CYS* 3.7 8.7 + - - -
169A MET* 3.0 16.3 + - - +
171A LEU* 1.3 78.8 - - - +
173A ASP* 1.3 60.0 + - - +
175A LEU* 3.2 9.5 + - - +
176A ARG* 2.8 29.6 + - - +
187A TRP* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 5.8 1.4 - - - +
169A MET* 3.0 36.0 + - - +
170A ALA* 4.0 5.6 - - - +
172A CYS* 1.3 75.9 - - - +
174A ARG* 1.3 61.0 + - - +
176A ARG* 3.7 31.6 + - - +
177A LEU* 2.9 30.5 + - - +
183A LEU* 3.9 13.9 - - + +
222A LEU* 5.0 5.1 - - + +
225A PHE* 5.4 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 4.0 20.4 + - - -
170A ALA* 3.0 17.4 + - - +
171A LEU* 3.0 20.4 + - - +
173A ASP* 1.3 78.0 - - - +
175A LEU* 1.3 56.6 + - - +
177A LEU* 3.3 2.3 + - - +
178A MET* 3.0 47.1 + - + +
215A ARG* 3.5 23.6 - - - +
218A VAL* 3.9 15.2 - - + +
219A ASP* 2.4 34.6 + - - +
222A LEU* 4.3 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 5.3 5.8 - - + -
29A VAL* 5.6 0.7 - - + -
30A LEU* 4.1 26.0 - - + -
33A ILE* 3.4 31.2 - - + +
41A LEU* 4.5 9.4 - - + -
45A GLU* 5.5 2.9 - - + -
48A PHE* 4.4 22.4 - - + -
49A ILE* 4.9 6.7 - - + -
171A LEU* 2.9 34.2 + - + +
172A CYS* 3.7 9.0 - - - +
173A ASP 3.2 0.2 - - - -
174A ARG* 1.3 73.0 - - - +
176A ARG* 1.3 67.0 + - - +
178A MET* 2.9 23.8 + - + -
179A TYR* 2.9 20.6 + - - +
187A TRP* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A CYS 2.8 20.5 + - - +
173A ASP* 3.7 24.9 + - - +
175A LEU* 1.3 72.2 - - - +
177A LEU* 1.3 57.3 + - - +
179A TYR* 3.9 0.9 - - - +
180A PHE* 3.0 37.0 + - + +
182A ASN 4.5 1.1 + - - +
183A LEU* 2.7 54.8 + - - +
184A TRP 4.3 0.2 - - - -
185A GLN 2.7 34.7 + - - -
186A ASP* 4.4 16.5 + - - +
187A TRP* 3.5 48.9 - - + +
225A PHE* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP 2.9 19.3 + - - +
174A ARG* 3.7 3.6 - - - +
176A ARG* 1.3 77.6 - - - +
178A MET* 1.3 57.2 + - - +
180A PHE* 5.2 0.2 - - - -
181A GLY* 2.7 30.2 + - - +
182A ASN* 4.0 15.7 - - - +
183A LEU* 3.9 17.9 - - + +
212A PHE* 3.2 26.4 - - + -
218A VAL* 4.2 7.0 - - + +
221A TYR* 3.6 35.7 - - + -
222A LEU* 3.4 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.6 4.3 - - + -
37A TYR* 3.1 53.5 + - + -
40A LEU* 4.1 24.7 - - - +
41A LEU* 4.6 12.1 - - + -
45A GLU* 5.4 1.3 - - - +
174A ARG* 3.0 43.6 + - + +
175A LEU* 2.9 29.6 + - + +
177A LEU* 1.3 79.0 - - - +
179A TYR* 1.3 60.8 + - - +
181A GLY* 4.0 2.9 + - - -
211A GLY* 4.9 0.7 + - - -
212A PHE* 4.0 8.5 - - + -
215A ARG* 5.5 1.6 - - - -
218A VAL* 3.4 26.9 - - + -
411A PHE* 5.7 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.6 30.7 - - + -
32A TRP* 3.6 40.7 + + + -
33A ILE* 3.9 19.1 - - + -
37A TYR* 4.6 4.8 - - - -
175A LEU 2.9 13.5 + - - +
176A ARG* 4.3 1.1 - - - +
178A MET* 1.3 79.6 - - - +
180A PHE* 1.3 95.8 + + - +
187A TRP* 4.2 3.4 - + - -
190A PHE* 3.3 15.7 - + - -
411A PHE* 4.6 5.9 - - - +
412A HIS* 3.8 28.1 - - + +
413A PRO* 3.8 6.2 - - + +
414A PHE* 2.9 29.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG* 3.0 24.2 + - + +
179A TYR* 1.3 106.8 - + - +
181A GLY* 1.3 61.5 + - - +
182A ASN* 3.3 15.6 + - - +
185A GLN* 3.4 54.8 - - + +
186A ASP 3.0 31.2 - - - -
187A TRP* 4.3 9.0 - + - -
189A GLU* 3.6 19.7 - - + -
190A PHE* 4.9 2.0 - + - -
411A PHE* 3.7 5.3 - - - -
412A HIS* 3.2 28.6 + + - -
414A PHE* 4.1 14.6 - + + -
415A HIS* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 2.7 29.9 + - - +
178A MET 4.0 1.5 + - - -
179A TYR 3.5 1.4 - - - -
180A PHE* 1.3 71.5 - - - +
182A ASN* 1.3 70.6 + - - +
212A PHE* 3.7 14.1 - - - -
253A TRP* 3.2 21.0 - - - -
411A PHE* 4.2 14.8 - - - -
----------------------------------------------------------
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