Contacts of the helix formed by residues 147 - 161 (chain A) in PDB entry 2R5S
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 ARG 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MES 4.2 15.4 - - - +
118A LEU* 4.2 12.6 - - - +
143A GLU 3.4 6.1 + - - +
144A LEU* 3.1 44.2 + - + +
146A SER* 1.3 77.6 - - - +
148A GLY* 1.3 67.8 + - - +
149A ASP* 2.6 39.6 + - - +
150A VAL* 3.0 13.6 + - + -
151A LYS* 3.1 10.4 + - - +
178A TYR* 4.4 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER 3.3 4.9 + - - -
147A ARG* 1.3 77.1 - - - +
149A ASP* 1.3 59.5 + - - +
151A LYS* 3.7 12.4 - - - +
152A LEU* 3.2 28.4 + - - +
174A ILE* 4.7 1.0 - - - +
175A PRO* 4.9 5.4 - - - -
178A TYR* 3.6 38.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MES 3.6 24.0 - - - +
147A ARG* 2.6 53.1 + - - +
148A GLY* 1.3 74.8 - - - +
150A VAL* 1.4 70.3 + - - +
152A LEU* 3.4 13.5 + - + +
153A ALA* 3.2 21.1 + - - +
178A TYR* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MES 3.8 21.5 - - - +
118A LEU* 4.0 18.4 - - + -
137A ILE* 3.8 36.1 - - + -
140A LEU* 3.9 8.5 - - + -
144A LEU* 3.5 32.1 - - + +
145A GLN* 4.1 7.2 - - - +
147A ARG* 3.0 6.3 + - + +
149A ASP* 1.4 82.9 + - - +
151A LYS* 1.3 58.0 + - - +
153A ALA* 3.1 6.1 - - - +
154A LYS* 2.8 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN 3.9 10.7 + - - +
146A SER* 3.8 30.9 + - - +
147A ARG 3.1 12.2 + - - +
148A GLY* 3.7 13.9 - - - +
150A VAL* 1.3 72.7 - - - +
152A LEU* 1.3 65.8 + - - +
154A LYS* 3.2 3.7 + - + -
155A ALA* 2.9 21.0 + - - +
170A LEU* 3.4 27.1 - - + +
173A THR* 3.1 47.6 + - - +
174A ILE* 3.8 16.8 - - + -
175A PRO* 5.0 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLY 3.2 23.3 + - - +
149A ASP* 3.6 13.0 - - + +
150A VAL 3.3 0.4 - - - -
151A LYS* 1.3 76.9 - - - +
153A ALA* 1.3 65.5 + - - +
155A ALA* 2.9 8.4 + - - +
156A ASP* 2.9 23.4 + - - +
171A LEU* 4.8 0.9 - - + -
174A ILE* 3.3 38.1 - - + -
178A TYR* 3.8 25.1 - - + +
180A ASP* 4.2 12.6 - - - +
182A SER* 4.2 14.6 - - - +
183A TYR* 4.1 19.3 - - + +
186A LEU* 4.0 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MES 3.7 24.5 - - - +
121A VAL* 4.6 6.5 - - + -
125A LEU* 4.2 20.8 - - + +
137A ILE* 5.1 2.7 - - + -
149A ASP 3.2 6.7 + - - +
150A VAL* 3.1 13.5 - - + +
152A LEU* 1.3 77.1 - - - +
154A LYS* 1.3 56.4 + - - +
156A ASP* 3.3 8.0 + - - +
157A CYS* 3.0 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.8 23.3 - - + -
137A ILE* 4.1 28.5 - - + -
138A GLN* 6.0 5.0 - - - +
145A GLN* 4.5 16.3 - - + +
150A VAL 2.8 18.9 + - - +
151A LYS* 3.7 7.0 - - + +
153A ALA* 1.3 72.7 - - - +
155A ALA* 1.3 57.2 + - - +
157A CYS* 2.9 10.0 + - - +
158A LEU* 2.8 43.5 + - + +
170A LEU* 3.6 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS 2.9 13.6 + - - +
152A LEU* 3.2 9.4 - - - +
154A LYS* 1.3 75.9 - - - +
156A ASP* 1.3 62.5 + - - +
158A LEU* 3.2 8.5 + - - +
159A LEU* 3.2 23.9 + - - +
167A ALA* 4.1 5.4 - - + +
170A LEU* 3.6 13.1 - - + +
171A LEU* 3.7 36.3 - - + -
186A LEU* 4.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.4 13.5 - - + +
130A HIS* 4.7 6.5 - - - -
152A LEU 2.9 12.0 + - - +
153A ALA* 3.5 12.1 - - - +
155A ALA* 1.3 75.2 - - - +
157A CYS* 1.3 63.0 + - - +
159A LEU* 3.5 4.1 + - - +
160A GLU* 3.1 40.4 + - - +
186A LEU* 4.1 27.1 - - + +
189A LYS* 5.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 6.0 0.7 - - - -
125A LEU* 3.3 33.7 - - - -
130A HIS* 3.7 30.1 - - - +
133A ALA* 3.8 10.8 - - - -
134A LEU* 3.5 25.4 - - + -
137A ILE* 5.9 2.0 - - - -
153A ALA* 3.0 13.4 + - - -
154A LYS* 2.9 11.2 + - - +
156A ASP* 1.3 75.2 - - - +
158A LEU* 1.3 62.1 + - - +
160A GLU* 3.3 1.0 + - - +
161A THR* 2.7 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.9 17.7 - - + -
154A LYS* 2.8 36.3 + - + +
155A ALA* 3.2 5.6 + - - +
157A CYS* 1.3 75.3 - - - +
159A LEU* 1.3 58.9 + - - +
161A THR* 2.8 17.6 + - - -
162A LYS 2.8 15.4 + - - -
163A GLN* 2.9 47.8 + - + +
166A LEU* 3.8 39.0 - - + +
167A ALA* 3.8 7.9 - - + +
170A LEU* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA 3.2 11.3 + - - +
156A ASP* 3.8 5.4 - - - +
158A LEU* 1.3 82.7 - - - +
160A GLU* 1.3 69.8 + - - +
161A THR 3.0 0.2 - - - -
162A LYS* 3.2 15.0 + - - +
164A PHE* 3.7 21.3 - - + -
167A ALA* 3.4 25.8 - - + -
171A LEU* 5.1 4.3 - - + -
186A LEU* 4.5 18.2 - - + +
189A LYS* 3.6 38.8 - - + -
190A LEU* 3.7 28.5 - - + -
193A HIS* 4.5 9.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A HIS* 3.3 50.4 + - + -
156A ASP* 3.1 33.2 + - - +
157A CYS 3.9 0.4 - - - +
159A LEU* 1.3 84.4 - - - +
161A THR* 1.3 60.2 + - - +
162A LYS* 3.3 8.7 + - - +
189A LYS* 4.0 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A HIS* 3.8 20.6 - - + -
131A ALA* 4.4 15.7 - - + +
134A LEU* 4.2 5.7 - - + +
157A CYS 2.7 22.3 + - - +
158A LEU 2.8 10.2 + - - -
160A GLU* 1.3 79.6 - - - +
162A LYS* 1.3 71.1 + - - +
163A GLN* 3.1 28.4 + - - +
265A LEU* 4.8 15.7 - - - +
269A ASN* 4.1 10.0 + - - -
----------------------------------------------------------
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