Contacts of the helix formed by residues 149 - 165 (chain A) in PDB entry 3D0O
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 THR 149 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER 3.2 0.4 + - - -
148A GLY* 1.3 71.9 - - - -
150A ILE* 1.3 57.6 + - - +
151A LEU 3.2 2.9 - - - -
152A ASP* 3.2 22.9 - - - +
153A SER* 2.8 34.0 + - - -
175A ILE* 2.8 39.2 + - + +
176A ILE* 4.2 1.5 - - - -
177A GLY 3.6 24.5 - - - +
178A GLU 4.3 8.5 - - - +
179A HIS* 4.3 2.7 - - - -
256A THR* 3.4 19.0 + - - -
257A VAL* 4.5 0.4 - - - +
273A GLY* 4.1 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER* 3.0 35.0 + - - +
148A GLY 3.3 1.5 - - - +
149A THR* 1.3 77.9 - - - +
151A LEU* 1.3 67.4 + - + +
153A SER* 4.2 2.6 - - - -
154A ALA* 3.5 17.5 + - - +
236A VAL* 5.6 1.3 - - - +
239A GLY* 3.7 34.8 - - - +
240A LEU 4.9 0.2 - - - +
242A ARG* 4.6 7.2 - - + -
243A ILE* 4.0 23.8 - - + -
255A LEU* 4.1 28.9 - - + -
256A THR* 2.9 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLY 4.7 1.0 + - - +
149A THR* 4.3 0.2 - - - +
150A ILE* 1.3 84.7 - - + +
152A ASP* 1.3 67.2 + - - +
153A SER 3.2 1.8 - - - -
154A ALA* 3.1 12.4 + - + +
155A ARG* 2.8 68.5 + - + +
179A HIS* 5.2 9.2 - - + -
232A THR* 5.2 0.4 - - - +
235A GLY* 3.7 28.5 - - - +
236A VAL* 3.5 37.0 - - + +
239A GLY* 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A THR* 3.1 24.1 + - - +
151A LEU* 1.3 75.5 - - - +
153A SER* 1.3 63.4 + - - +
155A ARG* 3.2 19.6 + - - +
156A PHE 2.9 19.6 + - - -
175A ILE* 3.5 30.9 - - + +
179A HIS* 2.5 38.0 + - - -
183A GLU* 2.9 28.3 - - - +
218A THR* 3.5 7.1 - - + +
219A ARG 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A THR 2.8 13.3 + - - -
150A ILE* 4.2 3.1 - - - -
152A ASP* 1.3 73.4 - - - +
154A ALA* 1.3 56.8 + - - +
156A PHE* 3.3 4.0 + - - +
157A ARG* 2.9 38.1 + - - +
173A ALA 4.2 11.6 - - - +
174A GLN* 3.7 2.2 - - - -
175A ILE* 2.9 32.0 + - - +
256A THR* 2.7 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE 3.5 12.4 + - - +
151A LEU* 3.1 19.5 + - + +
153A SER* 1.3 77.6 - - - +
155A ARG* 1.3 52.3 + - - +
157A ARG* 3.3 16.9 + - - +
158A LEU* 2.7 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 2.8 55.2 + - + +
152A ASP* 3.4 23.4 + - - +
154A ALA* 1.3 75.0 - - - +
156A PHE* 1.3 58.4 + - - +
158A LEU* 3.3 11.3 + - + +
159A LEU* 2.9 36.8 + - + +
179A HIS* 4.6 8.3 - - - -
218A THR* 4.0 21.5 + - + -
219A ARG 5.8 1.0 + - - -
221A ALA* 3.3 30.6 - - + +
222A ALA* 4.0 23.6 - - - +
225A ILE* 4.1 10.7 - - - +
232A THR* 3.6 20.2 + - - +
235A GLY* 5.8 0.6 - - - -
236A VAL* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASP 2.9 12.4 + - - +
153A SER 3.5 7.4 - - - +
155A ARG* 1.3 76.5 - - - +
157A ARG* 1.3 56.3 + - - +
159A LEU* 3.3 2.6 + - - +
160A LEU* 2.9 45.8 + - + +
173A ALA* 3.7 25.4 - - + -
174A GLN 3.6 28.9 - - - -
175A ILE* 3.7 15.0 - - + -
185A PRO* 3.7 22.7 - - + -
186A VAL 4.4 3.4 - - - -
187A TRP* 3.7 40.2 - + - -
190A ALA* 4.4 5.8 - - + -
214A ILE* 3.9 16.2 - - + -
215A PHE* 5.2 3.4 - - - -
218A THR* 3.5 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A SER* 2.9 25.2 + - - +
154A ALA* 3.6 13.0 - - - +
156A PHE* 1.3 74.4 - - - +
158A LEU* 1.3 53.5 + - - +
160A LEU* 3.4 1.8 + - - +
161A SER* 2.7 37.0 + - - -
168A PRO* 3.0 30.7 + - + +
169A ARG* 3.5 24.7 + - - +
171A VAL* 2.9 38.5 + - + +
172A ASP* 4.9 0.6 - - - +
173A ALA* 3.5 32.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
154A ALA 2.7 21.5 + - - +
155A ARG* 3.3 11.9 + - + +
157A ARG* 1.3 72.8 - - - +
159A LEU* 1.3 74.9 + - + +
161A SER* 2.6 26.3 + - - +
162A GLU* 3.1 35.8 + - - +
168A PRO* 5.1 9.3 - - + +
----------------------------------------------------------
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 ARG* 2.9 19.2 + - + +
156A PHE 3.8 2.9 - - - +
158A LEU* 1.3 84.3 - - + +
160A LEU* 1.3 59.6 + - - +
162A GLU* 3.2 22.4 + - - +
163A ALA* 2.9 28.1 + - - +
214A ILE* 3.7 30.7 - - + +
217A GLN* 3.7 32.8 - - + +
218A THR* 3.4 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 2.9 39.8 + - + +
157A ARG 3.8 3.6 - - - +
159A LEU* 1.3 77.4 - - - +
161A SER* 1.3 55.5 + - - +
163A ALA* 3.2 2.6 + - - +
164A PHE* 2.9 46.4 + - + +
171A VAL* 3.9 15.9 - - + +
173A ALA* 3.6 29.6 - - + -
187A TRP* 3.8 27.6 - - + -
190A ALA* 4.5 2.9 - - + -
197A LEU* 4.1 20.4 - - + -
201A LEU* 4.4 0.2 - - + -
214A ILE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG 2.7 20.0 + - - -
158A LEU* 2.6 22.9 + - - +
160A LEU* 1.3 73.2 - - - +
162A GLU* 1.3 56.0 + - - +
165A ASP* 2.8 27.5 + - - -
166A VAL* 3.1 32.5 + - - +
168A PRO* 3.8 26.3 - - - +
171A VAL* 3.9 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 3.1 34.1 + - + +
159A LEU* 3.5 21.6 - - - +
161A SER* 1.3 83.4 + - - +
163A ALA* 1.3 65.6 + - - +
164A PHE 3.4 0.5 + - - -
165A ASP* 3.5 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU 2.9 15.5 + - - +
160A LEU* 3.2 4.0 + - - +
162A GLU* 1.3 75.9 - - - +
164A PHE* 1.3 67.8 - - + +
165A ASP* 5.5 0.2 - - - +
201A LEU* 4.6 1.1 - - + -
204A ARG* 2.9 37.5 + - - +
210A GLN* 5.7 0.9 - - - +
214A ILE* 4.2 22.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
160A LEU* 2.9 23.3 + - + +
161A SER 3.7 0.2 - - - -
163A ALA* 1.3 80.2 - - + +
165A ASP* 1.3 72.6 + - - +
166A VAL* 3.5 5.0 + - + +
192A ILE* 3.6 25.6 - - + -
195A GLN* 6.3 0.2 - - + -
197A LEU* 3.7 48.0 - - + -
200A LEU* 3.9 24.9 - - + -
201A LEU* 3.7 39.3 - - + -
204A ARG* 3.7 17.3 - - - +
284B ARG* 4.5 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A SER 2.8 12.7 + - - -
162A GLU* 3.5 9.6 + - - +
164A PHE* 1.3 79.5 - - - +
166A VAL* 1.3 56.1 + - - +
252B ASP* 4.4 6.4 - - - +
284B ARG* 2.9 48.5 + - - +
----------------------------------------------------------
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